title: Replicate3

city: Cambridge

first: Sanja

last: Vickovic

state: Massachusetts

address: 415 Main Street

institute: Broad Institute

data_processing:
ST Pipeline v1.5.1
Celery v2.0
ST Aligner v0.1.0
The codes BX and BY are included in the read name and describe X and Y positions on the spatial arrays. The fastq read can be single-end mapped to the reference genome and the UR (UMI) and UY (UMI quality scores) used to filter reads based on the unique molecular identifiers. BX and BY in the fastq header correspond to x and y in the counts file and spot_x and spot_y in the annotation file.
Genome_build: mm10
Supplementary_files_format_and_content: Tissue annotation data where each barcode is assigned with an annotation region tag  (*annot.tsv)
Supplementary_files_format_and_content: Tab-delimited file where each barcode is assigned with a transcript count (*ut.tsv)
Supplementary_files_format_and_content: H&E stained histology image (*HE.tif)

molecule: polyA RNA

source_name: Main olfactory bulb

extract_protocol:
Spatial Transcriptomics. Github:  https://github.com/klarman-cell-observatory/hdst
RNA-Seq libraries were constructed for sequencing using standard Illumina protocols

value: 12 weeks

value: Main olfactory bulb

tag: plane

value: Coronal


title: 190305_snm3Cseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A4_AD010

status: Public on Sep 09 2019

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Library strategy: single-nucleus methyl-3C sequencing (sn-m3C)
Raw reads were trimmed first 25bp and last 3bp of both read1 and read2 to remove random primer sequence and adaptase low complexity tails. For the alignment, Bismark is used. C to T converted and G to A converted reference genomes are prepared for hg19 using bismark_genome_preparation. Each read end is mapped separately using Bismark with Bowtie1 with read1 as complementary (always G to A converted) and read2 (always C to T converted) as original strand. After first alignment, unmapped reads are retained and splitted into 3 pieces by 40bp, 32bp, and 40bp after removing 5bp of both ends results in having 6 reads (read1 and read2). Six reads derived from unmapped reads are mapped separately using Bismark Bowtie1. All aligned reads are merged into BAM using picard that is query name sorted. The fragments with all the mapped reads aligned to the same positions are considered as duplicates and removed and DNA methylation tracks are generated. For each fragment, the outermost aligned reads are chosen for the chromatin conformation map generation.
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited text files of methylcytosine calls; columns in allc files are: column 1 - chromosome; column 2 - position; column 3 - strand; column 4 - class; column 5 - mC reads; column 6 - total reads; column 7 - methylated (Boolean value indicating the result of statistical test for methylated cytosines)
tab delimited text files of contact.txt files; columns in contact.txt files are: column 1 - Sample_ID; column 2- chromosome_1; column 3 - Position_1; column 4 - Chromosome_2 ; column5 - Position_2; column6 - Strand_1; column 7 - Strand_2

molecule: genomic DNA

organism: Homo sapiens

source_name: Human frontal cortex

growth_protocol: Postmortem human brain biospecimens were obtained from brain donors of NIH NeuroBioBank and University of Maryland Brain and Tissue Bank.

extract_protocol: in situ Hi-C was performed as previously described using the NlaIII restriction enzyme. in situ 3C experiments were performed based on the previously described in situ Hi-C protocol with minor modifications. Briefly, prior to fixation, adherent cells were trypsinized, counted, and collected by centrifugation, and suspension cells were counted and collected by centrifugation. Cells were resuspended in culture media at a concentration of 1x106 cells per mL of media and fixed in 1% formaldehyde for 10 minutes at room temperature with shaking. For standard species mixture experiments, equal numbers of mouse and human cells were combined into a single tube prior to fixation. For the 1:10 dilution species mixture experiment, cells were resuspended at a concentration of 1x105 cells per mL of media prior to fixation. For the species mixture experiments where samples were mixed after fixation, each cell type was fixed independently as described above and combined at later stages in the protocol. in situ Hi-C samples were digested with the MboI restriction enzyme and processed as described previously. For in situ 3C experiments, samples were digested with DpnII enzyme overnight at 37ºC with gentle mixing. The following day, the sample was incubated at 62ºC for 10 minutes to inactivate the restriction enzyme. The typical biotin fill in step in the Hi-C protocol is omitted. The sample is then ligated for 4 hours at room temperature with T4 DNA ligase in the same manner as in in situ Hi-C experiments. The sample is then stained with Hoechst (0.1µg/µL) for the final 30 minutes of the ligation step. The sample is then passed through a 40 µM nylon cell strainer (Corning 431750) into a FACS tube prior to sorting. As a quality control step, 10% of the sample is taken for conventional library preparation and sequenced using shallow sequencing on a MiSeq. Libraries for bulk and single-cell methylomes were generated using snmC-seq2. A detailed step-by-step bench protocol for snmC-seq2 is provided as Supplement Methods in Luo et al. (2018) 23. Bulk methylome libraries were prepared manually using individual tubes. Single-cell methylome libraries were prepared using a Tecan Evo 100 robotic platform as described in Luo et al. (2018) 23. Sequencing libraries were sequenced using Illumina MiSeq and HiSeq 4000 instruments in PE150 mode.

tag: tissue

value: frontal cortex

tag: age

tag: Sex

value: Male

tag: donor


title: 181218_snm3Cseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A12_AD010


title: 190305_snm3Cseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A5_AD001


title: 190305_snm3Cseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A4_AD008


title: 181218_snm3Cseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A12_AD008


title: Genomic DNA from glioma sample; IDHwt_GIII_33

type: genomic

city: Clermont-Ferrand

first: franck

last: court

address: 28 Place Henri Dunant

country: France

institute: GReD CNRS

hyb_protocol: Hybridisation on the arrays was performed by Integragen, SA following the Illumina Infinium HD methylation protocol.

scan_protocol: Standard protocol defined by Illumina for HM450K

data_processing: GenomeStudio V2011.1

label: Cy5 and Cy3

source_name: DNA from Glioma sample

label_protocol: Bisulfite conversion was performed by Integragen, SA.

growth_protocol: Immediately after surgery, glioma samples were snap-frozen and stored in liquid nitrogen. non-tumoral control brain samples were cadaveric specimens removed by autopsy 4-16 h following accidental death (Brain and Tissue Bank of Maryland).

extract_protocol: DNA was isolated from frozen tissues using the QIAamp DNA Mini Kit (Qiagen), according to the manufacturer’s recommendations

treatment_protocol: Controls and glioma samples were homogenized by cryogenic grinding.

tag: gliomas classification

value: grade:Grade IIII

value: IDH statut:IDHwt

tag: gender

value: Female

tag: disease

value: glioma sample


title: E14.5 Adamts19-/- mouse heart r7

city: Montreal

first: Florian

last: Wuennemann

address: 5000 Rue Bélanger

country: Canada

institute: Montreal Heart Institute

description: Biological replicate 7. R1 files contain cell barcodes, R2 files contain cDNA sequences.

library_source: transcriptomic

data_processing:
Base calls and demultiplexing was performed using bcl2fastq (v2.17).
Raw fastq files were processed with the Drop-seq tools pipeline (v.1.12) as described in Macosko et al 2015. (PMID 26000488).
The number of cells for each sample was determined by calculating the inflection point from the cumulative read distribution.
A digital expression matrix was created by counting the number of unique UMIs per gene for each cell. In the joined UMI matrix, columns are cells and rows are genes.
The raw UMI matrix for each sample was imported into R and cells with less than 250 detected genes were filtered out.
Sample level UMI matrices were merged in R using Seurat (v.2.1) and cells with more than 3500 detected genes and more than 15000 detected UMI were filtered to exclude potential doublets. Cells with more than 10% mitochondrial genes expressed and genes that were not expressed with at least 1 UMI in 5 cells were filtered out to produce a final set of high quality single cells.
The joined UMI matrix provided contains raw UMI counts for all filtered cells used for clustering.
Genome_build: mm10
Supplementary_files_format_and_content: GSE109247_E14.5_joined_UMI_counts_DGE.txt.gz: Compressed, flat text file with raw UMI counts for cells from all 15 samples (7 wild-type, 8 Adamts19 knockout) used for clustering in the manuscript. Cells were filtered as descripted in data processing to remove potential doublets and low quality cells.

organism: Mus musculus

source_name: Heart

extract_protocol:
Single cells were co-encapsulated with barcoded microbeads to produce single cell transcriptomes attached to microparticles (STAMPS) accodring to Drop-seq protocol. STAMPS were counted and PCR amplified for 13 cycles. Amplified cDNA was measured using Bioanalyzer and used for library preparation.
A modified Nextera-XT protocol as described in Macosko et al. 2015 was used to construct libraries. Illumina i7 primer were used in combination with a custom i5 primer

tag: strain/background

value: Heart

tag: sample type

value: Adamts19 homozygous knockout

tag: genotype

tag: litter

value: Litter 7

tag: illumina flowcell


title: 190305_snm3Cseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A4_AD007


title: 181218_snm3Cseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A12_AD006


title: Genomic DNA from glioma sample; IDHwt_GIII_31


title: E14.5 Adamts19-/- mouse heart r6

description: Biological replicate 6. R1 files contain cell barcodes, R2 files contain cDNA sequences.


title: 190305_snm3Cseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A4_AD004


title: 190305_snm3Cseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A6_AD012


title: E14.5 Adamts19-/- mouse heart r5

description: Biological replicate 5. R1 files contain cell barcodes, R2 files contain cDNA sequences.


title: 181218_snm3Cseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A12_AD001


title: 181218_snm3Cseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A12_AD004


title: Genomic DNA from glioma sample; IDHwt_GIII_30


title: Genomic DNA from glioma sample; IDHwt_GIII_26


title: Replicate1

tag: strain


title: 190305_snm3Cseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A4_AD002


title: 190305_snm3Cseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A3_AD012


title: E14.5 Adamts19-/- mouse heart r8

description: Biological replicate 8. R1 files contain cell barcodes, R2 files contain cDNA sequences.


title: E14.5 Adamts19-/- mouse heart r3

description: Biological replicate 3. R1 files contain cell barcodes, R2 files contain cDNA sequences.

value: Litter 6


title: 181218_snm3Cseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A11_AD012


title: Genomic DNA from glioma sample; IDHwt_GIII_19


title: 190305_snm3Cseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A3_AD010


title: 181218_snm3Cseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A11_AD010


title: E14.5 Adamts19-/- mouse heart r2

description: Biological replicate 2. R1 files contain cell barcodes, R2 files contain cDNA sequences.


title: 190305_snm3Cseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A3_AD008


title: Genomic DNA from glioma sample; IDHwt_GIII_34


title: Genomic DNA from glioma sample; IDHwt_GIII_29


title: Genomic DNA from glioma sample; IDHwt_GIII_35


title: Genomic DNA from glioma sample; IDHwt_GIII_17


title: Replicate2


title: Genomic DNA from glioma sample; IDHwt_GIII_23


title: E14.5 Adamts19-/- mouse heart r1

description: Biological replicate 1. R1 files contain cell barcodes, R2 files contain cDNA sequences.

value: Litter 5


title: E14.5 Adamts19+/+ mouse heart r7

value: wild-type

value: WT

value: Litter 4


title: 181218_snm3Cseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A11_AD006


title: 190305_snm3Cseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A3_AD007


title: 181218_snm3Cseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A12_AD002


title: 181218_snm3Cseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A11_AD004


title: E14.5 Adamts19-/- mouse heart r4

description: Biological replicate 4. R1 files contain cell barcodes, R2 files contain cDNA sequences.


title: 181218_snm3Cseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A12_AD007


title: Genomic DNA from glioma sample; IDHwt_GIII_15


title: 190305_snm3Cseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A3_AD004


title: Genomic DNA from glioma sample; IDHwt_GIII_20


title: E14.5 Adamts19+/+ mouse heart r6


title: E14.5 Adamts19+/+ mouse heart r5

value: Litter 3


title: 181218_snm3Cseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A11_AD002


title: Genomic DNA from glioma sample; IDHwt_GIII_12


title: Genomic DNA from glioma sample; IDHwt_GIII_11


title: E14.5 Adamts19+/+ mouse heart r4

description:
Heart_E14.5_r4_170814
Illumina Flowcell: HGGV2BGX2
Replicate 3. R1 files contain cell barcodes, R2 files contain cDNA sequences.

data_processing:
Base calls and demultiplexing was performed using bcl2fastq (v2.17).
Raw fastq files were processed with the Drop-seq tools pipeline (v.1.12) as described in Macosko et al 2015. (PMID 26000488).
The number of cells for each sample was determined by calculating the inflection point from the cumulative read distribution.
A digital expression matrix was created by counting the number of unique UMIs per gene for each cell. In the joined UMI matrix, columns are cells and rows are genes.
The raw UMI matrix for each sample was imported into R and cells with less than 50 detected genes and genes detected in less than 10 cells were filtered out.
Sample level UMI matrices were merged in R using Seurat (v.2.1) and cells with more than 3000 detected genes and more than 10000 detected UMI were filtered to exclude potential doublets. Cells with more than 10% mitochondrial genes expressed were filtered out to produce a final set of high quality single cells.
The joined UMI matrix provided contains raw UMI counts for all filtered cells used for clustering.
Genome_build: mm10
Supplementary_files_format_and_content: E14.5_raw_UMI_counts_DGE.tsv: Flat text file with raw UMI counts for cells from all four replicates used for clustering in the manuscript. Cells were filtered as descripted in data processing to remove potential doublets and low quality cells.

extract_protocol:
Single cells were co-encapsulated with barcoded microbeads to produce single cell transcriptomes attached to microparticles (STAMPS) according to Drop-seq protocol (Macosko et al. 2015). STAMPS were counted and PCR amplified for 13 cycles. Amplified cDNA was measured using Bioanalyzer and used for library preparation.
A modified Nextera-XT protocol as described in Macosko et al. 2015 was used to construct libraries. Illumina i7 primer were used in combination with a custom i5 primer

tag: genotype/variation

value: Wild-type

value: Litter 2


title: 190305_snm3Cseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A2_AD012

value: frontal cortex


title: 181218_snm3Cseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A10_AD012

value: Male


title: Genomic DNA from glioma sample; IDHwt_GIII_27

value: grade:Grade IIII


title: E14.5 Adamts19+/+ mouse heart r3

description:
Heart_E14.5_r3_170814
Illumina Flowcell: HGGV2BGX2
Replicate 3. R1 files contain cell barcodes, R2 files contain cDNA sequences.


title: 181218_snm3Cseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A10_AD008


title: 190305_snm3Cseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A2_AD006


title: E14.5 Adamts19+/+ mouse heart r2

description:
Heart_E14.5_r2_170622
Illumina Flowcell: HLLVHBGXY
Replicate 2. R1 files contain cell barcodes, R2 files contain cDNA sequences.

value: Litter 1


title: 181218_snm3Cseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A10_AD007


title: 190305_snm3Cseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A4_AD006


title: 181218_snm3Cseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A10_AD010


title: 190305_snm3Cseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A2_AD008


title: Genomic DNA from glioma sample; IDHwt_GIII_9

value: IDH statut:IDHwt


title: E14.5 Adamts19+/+ mouse heart r1

description:
Heart_E14.5_r1_170622
Illumina Flowcell: HLLVHBGXY
Replicate 1. R1 files contain cell barcodes, R2 files contain cDNA sequences.


title: 190305_snm3Cseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A3_AD002


title: 190305_snm3Cseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A2_AD004


title: 190305_snm3Cseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A2_AD001


title: 22RV1 Negative Control_Replicate 3 [HITS-CLIP]

city: Bedford Park

first: Luke

last: Selth

state: SA

address: Flinders Drive

department: College of Medicine and Public Health

country: Australia

institute: Flinders University

description:
processed data file:
HITS-CLIP_22Rv1_scr.bigwig
HITS-CLIP_Annotated peaks.xlsx

data_processing:
RNA libraries generated by HITS-CLIP were sequenced on the Illumina Nextseq 500 platform using the single end protocol with a read length of 85. Raw reads were adapter trimmed and filtered for short sequences using cutadapt v1.8.1 (Martin, 2011) setting minimum-length option to 18, error-rate 0.2, and overlap 5. The resulting FASTQ files (averaging 41.6 million reads per sample) were analysed and quality checked using the FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc) program.
Filtered reads were mapped against the human reference genome (hg19) using the Tophat2 alignment algorithm (version 2.0.9 with default parameters) (Kim et al 2013)
Unique molecular identifiers (UMIs) were used to de-duplicate reads that mapped to the same start site, possessed identical CIGAR strings and UMI barcodes sequences ≤1 edit distance apart
Enriched regions of the genome were identified from Samtools quality-filtered alignments (Li et al 2009) (-q 5) with the MACS2 peak caller (version 2.1.1) (Zhang et al 2008) (setting; --nomodel, --shift -15, --extsize 50, -B,  --slocal 0, --llocal 0, --fe-cutoff 10, -q 0.05).
Peak calling was performed using pooled alignment files and carried out separately for each strand. The resulting peak files from each strand were merged.
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig files of combined alignments for all replicates of miR-194 or negative control; Peak annotation

molecule: total RNA

source_name: 22RV1 Negative Control

growth_protocol: 22RV1 cells were grown in RPMI1640 with 10% FBS

extract_protocol:
After 24 h, transfected 22RV1 cells were rinsed once with ice-cold PBS and UV irradiated with 600 mJ/cm2, 254 nm, in ice-cold PBS using a UV Stratalinker-1800 (Agilent). Cells were collected by scraping, and cell pellets stored at -80°C as one pellet per 100mm plate. One pellet per CLIP IP was lysed in 500 μl of 1 X PXL (1 X PBS, 0.1% SDS, 0.5% deoxycholate, 0.5% Igepal) + EDTA-free Complete protease inhibitor cocktail (PIC; Roche) for 15 min on ice, followed by trituration through a 21G needle and syringe 5 times. DNA was digested with 20 μl RQ1 DNAse (Promega) at 37°C for 10 min on a Thermomixer (750 rpm, Eppendorf). RNA was partially digested with RNase 1 (ThermoFisher) by adding 5 μl of 1:40 diluted RNase 1 in 1 X PBS at 37°C for 5 min on a Thermomixer (750 rpm), then returned to ice. Lysates were centrifuged at 21,000 g for 20 min at 4°C and supernatant transferred to a fresh tube.AGO-RNA complexes were immunoprecipitated using mouse IgA2 monoclonal anti-Ago2 antibody 4F9(Ikeda et al 2006); hybridoma sourced from University of Florida ICBR) with a mouse IgA antibody (GeneTex S107) used as a control. Antibodies (8 μg) were conjugated to 20 μl protein L Dynabeads (ThermoFisher, 88849) in PBS-Tw (1 X PBS, 0.05% Tween-20) for 45 min and washed three times with 1 X PXL (1 X PBS, 0.1% SDS, 0.5% sodium deoxycholate, 0.5% Igepal) before resuspending the beads with 450 μl of prepared lysate and rotating for 2 hr at 4°C. Bound AGO-RNA complexes were washed twice each consecutively with ice cold 1 X PXL, 5 X PXL (5 X PBS, 0.1% SDS, 0.5% sodium deoxycholate, 0.5% Igepal), and 1 X PNK (50 mM Tris-Cl pH 7.5, 10 mM MgCl2, and 0.5% Igepal). Beads were first treated with T4 PNK (NEB, M0201L; 20 U in 80 μl reaction volume) in the absence of ATP (37°C, 850 rpm for 20 min) to dephosphorylate 3’ RNA ends followed by washes with 1 X PNK, 5 X PXL, and two washes with 1 X PNK at 4°C. The 3’ preadenylated linker (NEBNext 3’SR adaptor for Illumina; /5rApp/AGA TCG GAA GAG CAC ACG TCT /3AmMO/) was ligated to the RNA fragments on bead using T4 RNA ligase 2 truncated KQ (NEB M0373; 100 U in a 40 μl reaction volume, 12% PEG8000, 1x RNA ligase buffer, 0.125 μM adaptor) in the absence of ATP at 16°C, overnight with periodic mixing. Beads were washed consecutively with ice cold 1 X PXL, 5 X PXL, and twice with 1 X PNK. Bound RNAs were then labelled with P32 γ-ATP using T4 PNK, 20 min at 37°C, and washed as above. AGO-RNA complexes were eluted with 40 μl 1 X Bolt LDS sample buffer (ThermoFisher) + 1% β-mercaptoethanol at 70°C for 10 min on a Thermomixer (1200 rpm). Samples were separated through Bolt 8% Bis-tris Plus gels (ThermoFisher) using BOLT MOPS SDS running buffer at 200 V for 75 min. Complexes were then transferred to nitrocellulose (Schleicher&Schuell, BA-85) by wet transfer using 1 X BOLT transfer buffer with 10% methanol. Filters were placed on a phosphor screen and exposed using a Typhoon imager (GE). 115-160 kDa regions (corresponding to RNA tags > 30 nt) were excised from the nitrocellulose. RNA was extracted by proteinase K digestion (2 mg/mL proteinase K, 100 mM Tris-HCl pH 7.5, 50 mM NaCl, 10 mM EDTA, 0.2% SDS) at 50°C for 60 min on a Thermomixer (1200 rpm) followed by extraction with acid phenol (ThermoFisher, AM9712) and precipitation with 1:1 isopropanol:ethanol. RNA was pelleted by centrifugation then separated on a 15% denaturing polyacrylamide gel (1:19 acrylamide, 1 X TBE, 7 M urea). The wet gel was wrapped in plastic wrap and exposed to a phosphor screen and imaged using a Typhoon. Gel slices were cut corresponding to the expected size of the cross-linked RNA eluted by the “crush and soak” method as previously described (Jensen and Darnell 2008).
Reverse transcription, 5’ linker ligation and amplification were performed essentially as previously described (Van Nostrand et al 2016) using SR-RT primer for reverse transcription (IDT, AGACGTGTGCTCTTCCGATCT) with SuperScript IV, and a custom synthesised 5’ linker (IDT, 5’SRdeg /5Phos/NN NNN NNN NNG ATC GTC GGA CTG TAG AAC TCT GAA C/3SpC3/). Products were amplified for 20 cycles using a common forward primer (NEBNext SR primer for Illumina) and barcoded reverse primers for each sample (NEBNext Index primers for Illumina). PCR products were purified using Qiagen Qiaquick PCR purification kit, separated on an 8% acrylamide (29:1) TBE non- denaturing gel, stained with SYBR Gold nucleic acid gel stain (ThermoFisher) and imaged on a ChemiDoc (BioRad). Products corresponding to an insert size of ~30 – 70 nt were excised from the gel and extracted by the “crush and soak” method as previously described (Jensen and Darnell 2006). Library quality and quantity was assessed by Bioanalyzer (Agilent) and qPCR, pooled and sequenced on an Illumina NextSeq 500 (1 x 75bp).

treatment_protocol: 22RV1 cells were transfected with 20nM miR-194 mimic or negative control in suspension

tag: cell line

tag: cell type

value: Prostate cancer cell line

tag: passages

tag: antibody

value: IgA2 monoclonal anti-Ago2 antibody 4F9


title: 190305_snm3Cseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A1_AD010

tag: tissue

tag: age


title: Genomic DNA from glioma sample; IDHwt_GIII_18

value: glioma sample


title: 181218_snm3Cseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A10_AD001

tag: Sex

tag: donor


title: PP020

city: New York

first: Hanna

middle: Mendes

last: Levitin

state: NY

address: Department of Systems Biology 3960 Broadway, Lasker 203A

department: Department of Systems Biology

institute: Columbia University Medical Center

data_processing:
We corrected the raw sequencing data for index swapping, a phenomenon that occurs during solid-phase clonal amplification on the Illumina HiSeq 4000 platform and results in cross-talk between sample index sequences. We corrected index swapping using the algorithm proposed by Griffiths et al. First, we aligned the reads associated with each sample index to GRCh38 (GENCODE v.24) using STAR v.2.5.0 after trimming read 2 to remove 3’ poly(A) tails (> 7 A’s) and discarding fragments with fewer than 24 remaining nucleotides. For each read with a unique, strand-specific alignment to exonic sequence, we constructed an address comprised of the cell-identifying barcode, unique molecular identifier (UMI) barcode, and gene identifier. Next, we counted the number of reads associated with each address in each sample. Because of index swapping, we found that some addresses occurred in multiple samples at much higher frequencies than one would expect by chance. For the vast majority of addresses, there was a single sample containing most of the associated reads. If >80% of reads for a given address were associated with a single sample (e.g. a single index sequence), we kept all of the reads corresponding to that address in that sample and removed all of the reads associated with that address from all other samples42.  We also identified addresses for which no sample contained >80% of the corresponding reads and removed all of these reads from all samples.
After correction for index swapping, we collapsed amplification duplicates using the UMIs and corrected errors in both the cell-identifying and UMI barcodes to generate a preliminary matrix of molecular counts for each cell.
We filtered the cell-identifying barcodes to avoid dead cells and other artifacts. We removed all cell-identifying barcodes where >10% of molecules aligned to genes expressed from the mitochondrial genome or for which the ratio of molecules aligning to whole gene bodies (including introns) to molecules aligning exclusively to exons was >1.5. Finally, we also removed cell-identifying barcodes for which the average number of reads per molecule or average number of molecules per gene deviated by >2.5 standard deviations from the mean for a given sample.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text files that contain the gene expression counts of each individual cell.

source_name: Resting cells from blood of Donor B after negative selection to enrich CD3+ cells

extract_protocol:
Tissues acquired from donors were maintained in cold saline during transport to the laboratory, typically within 2-4 hours of procurement. We flushed the left lobe of the lungs with cold complete medium (RPMI 1640, 10% FBS, 100 U/ml penicillin, 100 ug/ml streptomycin, 2 mM L-glutamine) and isolated lymph nodes from the hilum, near the intersections of major bronchi and pulmonary veins and arteries, removing all fat. To obtain mononuclear cell suspensions, hilar lymph nodes and the left lateral basal segment of the lung were mechanically processed using a gentleMACS tissue dissociator (Miltenyi Biotec), enzymatically digested (complete medium with 1 mg/ml collagenase D, 1 mg/ml trypsin inhibitor and 0.1 mg/ml DNase for 1 hour at 37°C in a mechanical shaker) and centrifuged on a density gradient using 30% Percoll Plus (GE Healthcare). We aspirated bone marrow from near the anterior superior iliac crest. For bone marrow and peripheral blood, we isolated mononuclear cells by density gradient centrifugation using Lymphocyte Separation Medium (Corning). Next, we enriched single cell suspensions from all tissues and blood for untouched CD3+ T cells using magnetic negative selection (MojoSort Human CD3+ T cell Isolation Kit; BioLegend). To eliminate any dead cells prior to stimulation, we used a dead cell removal kit (Miltenyi Biotec). We cultured 0.5 – 1 x 106 CD3+ enriched cells from each donor tissue for 16 hours at 37°C in complete medium, with or without TCR stimulation using Human CD3/CD28 T Cell Activator (STEMCELL Technologies). After stimulation, we removed dead cells as above before preparing cells for single-cell RNA-seq.
We loaded single-cell suspensions into a Chromium Single Cell Chip (10x Genomics) according to the manufacturer’s instructions for co-encapsulation with barcoded Gel Beads at a target capture rate of ~5,000 individual cells per sample. We barcoded the captured mRNA during cDNA synthesis and converted the barcoded cDNA into pooled single-cell RNA-seq libraries for Illumina sequencing using the Chromium Single Cell 3’ Solution (10x Genomics) according to the manufacturer’s instructions. We processed all of the samples for a given donor simultaneously with the Chromium Controller (10x Genomics) and prepared the resulting libraries in parallel in a single batch.  We pooled all of the libraries for a given donor, each of which was barcoded with a unique Illumina sample index, for sequencing in a single Illumina flow cell.

value: Blood donor B

value: Blood

tag: stimulation


title: 22RV1 Negative Control_Replicate 1 [HITS-CLIP]


title: 22RV1 Negative Control_Replicate 2 [HITS-CLIP]


title: 190305_snm3Cseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A1_AD008


title: Genomic DNA from glioma sample; IDHwt_GIII_8

tag: gliomas classification

tag: gender

value: Female

tag: disease


title: 22RV1 miR-194_Replicate 3 [HITS-CLIP]

description:
processed data file:
HITS-CLIP_22Rv1_miR194.bigwig
HITS-CLIP_Annotated peaks.xlsx


title: 181218_snm3Cseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A10_AD004


title: 190305_snm3Cseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A1_AD006


title: 22RV1 miR-194_Replicate 2 [HITS-CLIP]


title: 190305_snm3Cseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A12_AD012


title: Genomic DNA from glioma sample; IDHwt_GIII_4


title: PP017

source_name: AntiCD3/AntiCD28-activated cells from blood of Donor A after negative selection to enrich CD3+ cells

value: Blood donor A

value: CD3/CD28 T Cell Activator (STEMCELL Technologies)


title: 22RV1 Negative Control_Replicate 4

data_processing:
Raw reads were adapter trimmed and filtered for short sequences using cutadapt v1.8.1 (Martin 2011), setting minimum-length option to 18, error-rate 0.2, quality cut-off 28, overlap 5 and trim N's on. The resulting FASTQ files (averaging 60.2 million read pairs per sample) were analysed and quality checked using the FastQC program (http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Reads were mapped against the human reference genome (hg19) using the STAR spliced alignment algorithm (Dobin et al 2013) (version 2.5.3a with default parameters and --chimSegmentMin 20, --quantMode GeneCounts).
Differential expression analysis was evaluated from TMM normalised gene counts using R (version 3.2.3) and edgeR (Robinson et al 2010) (version 3.3)
Genome_build: hg19
Supplementary_files_format_and_content: Processed data presented as raw gene counts

extract_protocol:
At 36 hours post-transfection, cells were collected in Qiazol (Qiagen) and total RNA was extracted using a miRNeasy Mini Kit (Qiagen)
RNA sequencing libraries were constructed with the mRNAseq Library prep kit.

tag: treatment

value: Transfected with 20nM negative control


title: PP018

source_name: Resting cells from blood of Donor A after negative selection to enrich CD3+ cells


title: 22RV1 miR-194_Replicate 1 [HITS-CLIP]


title: 190305_snm3Cseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A12_AD008


title: 190305_snm3Cseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A12_AD010


title: Genomic DNA from glioma sample; IDHwt_GIII_5


title: 22RV1 Negative Control_Replicate 3


title: PP014

source_name: AntiCD3/AntiCD28-activated cells from lymph node of Donor 2 after negative selection to enrich CD3+ cells

value: Tissue donor 2

value: Lymph node


title: Genomic DNA from glioma sample; IDHwt_GIII_2


title: 22RV1 Negative Control_Replicate 2


title: 190305_snm3Cseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A12_AD006


title: 190305_snm3Cseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A12_AD007


title: 22RV1 Negative Control_Replicate 1


title: 190305_snm3Cseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A2_AD002


title: 190305_snm3Cseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A12_AD004


title: Genomic DNA from glioma sample; IDHwt_GIII_7


title: PP012

source_name: AntiCD3/AntiCD28-activated cells from bone marrow of Donor 2 after negative selection to enrich CD3+ cells

value: Bone marrow


title: Genomic DNA from glioma sample; IDHwt_GBM_34


title: PP011

source_name: Resting cells from bone marrow of Donor 2 after negative selection to enrich CD3+ cells


title: Genomic DNA from glioma sample; IDHwt_GBM_35


title: PP010

source_name: AntiCD3/AntiCD28-activated cells from lung of Donor 2 after negative selection to enrich CD3+ cells

value: Lung


title: Genomic DNA from glioma sample; IDHwt_GBM_29

value: Male


title: 190305_snm3Cseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A12_AD002

value: frontal cortex


title: PP009

source_name: Resting cells from lung of Donor 2 after negative selection to enrich CD3+ cells


title: 190305_snm3Cseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A11_AD012


title: PP019

source_name: AntiCD3/AntiCD28-activated cells from blood of Donor B after negative selection to enrich CD3+ cells


title: 22RV1 miR-194_Replicate 2

value: Transfected with 20nM miR-194 mimic


title: 22RV1 miR-194_Replicate 3


title: 22RV1 miR-194_Replicate 4


title: Genomic DNA from glioma sample; IDHwt_GBM_32

value: IDH statut:IDHwt


title: PP006

source_name: AntiCD3/AntiCD28-activated cells from lymph node of Donor 1 after negative selection to enrich CD3+ cells

value: Tissue donor 1


title: 190305_snm3Cseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A11_AD008


title: Genomic DNA from glioma sample; IDHwt_GBM_30


title: Genomic DNA from glioma sample; IDHwt_GIII_3

value: grade:Grade IIII


title: PP013

source_name: Resting cells from lymph node of Donor 2 after negative selection to enrich CD3+ cells


title: Genomic DNA from glioma sample; IDHwt_GBM_27

value: glioma sample


title: 22RV1 miR-194_Replicate 1

value: Prostate cancer cell line


title: Genomic DNA from glioma sample; IDHwt_GBM_31


title: Genomic DNA from glioma sample; IDHwt_GIII_10


title: Genomic DNA from glioma sample; IDHwt_GIII_16


title: PP005

source_name: Resting cells from lymph node of Donor 1 after negative selection to enrich CD3+ cells


title: 190305_snm3Cseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A11_AD004


title: Liver Spheroid [S5]

city: Oxford

first: Enrique

middle: M

last: Toledo

address: Innovation Building, Old Road Campus, Roosevelt Drive

department: R&D

country: United Kingdom

institute: Novo Nordisk

data_processing:
CellRanger version 2.2 pipeline was used for demultiplexing, basecalling, gene counts. Default option were used.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix as csv text file with header of cell barcodes and rows as genes. Cells metadata in metadata_cells.csv file

source_name: Liver

growth_protocol: Human primary hepatocytes from a mixture of 10 donors grown in a 3D spheroid, were purchased from InSphero AG (Switzerland) and maintained in the culture medial provided by the company.

extract_protocol: Single cell libraries were prepare with a 10X Genomics 3’ kit

value: Mixture of primary human liver spheroid of 10 donors. Enriched in hepatocytes.

tag: index

value: Samples multiplexed by i7 barcodes of index SI-GA-E12


title: 181218_snm3Cseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A10_AD006

source_name: Human frontal cortex


title: PP004

source_name: AntiCD3/AntiCD28-activated cells from bone marrow of Donor 1 after negative selection to enrich CD3+ cells


title: 190305_snm3Cseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A11_AD002


title: Liver Spheroid [S1]

value: Samples multiplexed by i7 barcodes of index SI-GA-A12


title: 190305_snm3Cseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A11_AD001


title: 1D x/Entr

city: Incheon Metropolitan City

first: Yong Seung

last: Lee

address: SimGokro 100gil 25

department: College of Medicine

country: South Korea

institute: Catholic Kwandong University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer v.0.0.14), then mapped to hg19 whole genome using tophat2 v.2.0.9
Read count were calculated using edgeR.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: dermal fibroblast cells

growth_protocol: x/Entr cells were cultured with ultrasound treated hES culture medium include DMEM/F12, 20% serum replacement, 1 mM glutamine, 0.1% NEAA, 0.1% penicillin/streptomycin, 0.1 mM β-ME, and 4 ng/mL FGF-2.  HDF cells were cultured with DMEM including 10% FBS, and 1% penicillin/streptomycin at 37 oC in an atmosphere of 5% CO2.

extract_protocol:
RNA was isolated using Trizol reagent. The construction of library was performed using SENSE 3’ mRNA-Seq Library Prep Kit from 1 ug of total RNA.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit standard protocols.

treatment_protocol: The HDF cells were directly exposed to ultrasound stimulus (20 KHz, 1.0 W/cm2) for 5 sec. And then, 2 x 105 cells of ultrasound treated cells were cultured with ultrasound-treated media (20 KHz, 5.0 W/cm2, for 10min) on the 35mm petri dish.

value: skin

tag: passage


title: PP003

source_name: Resting cells from bone marrow of Donor 1 after negative selection to enrich CD3+ cells


title: PP002

source_name: AntiCD3/AntiCD28-activated cells from lung of Donor 1 after negative selection to enrich CD3+ cells

value: CD3/CD28 T Cell Activator (STEMCELL Technologies)


title: 190305_snm3Cseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A10_AD012


title: Genomic DNA from glioma sample; IDHwt_GBM_25

source_name: DNA from Glioma sample


title: Genomic DNA from glioma sample; IDHwt_GBM_22

value: Female


title: PP001

source_name: Resting cells from lung of Donor 1 after negative selection to enrich CD3+ cells


title: 190305_snm3Cseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A10_AD010


title: HDF_control

description: This sample is identical to GSM2308274.


title: Genomic DNA from glioma sample; IDHwt_GBM_24


title: TDP-43 Rescue rep. 3

city: New Haven

first: Shawn

middle: Michael

last: Ferguson

state: CT

address: 295 Congress Ave

department: Cell Biology

institute: Yale School of Medicine

data_processing:
The reads were trimmed for quality using custom scripts.  The trimmed reads were aligned to the reference mouse genome (hg19 UCSC) using TopHat2.
cufflinks and cuffdiff was used to estimate transcript abundances, and to determine differentially expresed genes.  The cuffdiff output was processed further with R and cummeRbund for visualizations and downstream analyses.
Genome_build: hg19 (UCSC)
Supplementary_files_format_and_content: FPKM table.

source_name: HeLaM cell line

growth_protocol: HeLaM cells grown in Dulbecco’s modified Eagle’s medium (DMEM), 10% fetal bovine serum (FBS), and 1% penicillin/streptomycin supplement (all from Thermo Fisher Scientific).

extract_protocol:
Total RNA was extracted from each sample using the RNeasy kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: HeLa M

tag: genotype

value: Rescued TDP-43 KO


title: TDP-43 Rescue rep. 2


title: 190305_snm3Cseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A10_AD007


title: Genomic DNA from glioma sample; IDHwt_GBM_20


title: Genomic DNA from glioma sample; IDHwt_GBM_33


title: TDP-43 Rescue rep. 1


title: Genomic DNA from glioma sample; IDHwt_GBM_21


title: 190305_snm3Cseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A10_AD001


title: 190305_snm3Cseq_hs_21yr_BA10_UMB5577_1_UMB5577_2_A10_AD008


title: TDP-43 KO rep. 3

value: TDP-43 KO


title: 181218_snm3Cseq_hs_21yr_BA10_UMB5577_3_UMB5577_3_H9_AD012

value: Male


title: Genomic DNA from glioma sample; IDHwt_GBM_18


title: Genomic DNA from glioma sample; IDHwt_GBM_19


title: CS11_CH_10x

city: Beijing

first: Jian

last: He

address: DongDaJie #8

country: China

institute: the Fifth Medical Center of the PLA General Hospital

data_processing:
10X Genomics CellRanger version 2.1 were used to the basecalling.
Sequencing data from 10X genomics was processed with CellRanger software package (version 2.1.0) with default mapping arguments. For modified STRT-seq data, raw reads were first split for each cell by specific barcode sequence attached in Read 2. The TSO sequence and polyA tail sequence were trimmed for the corresponding Read 1 after UMI information was aligned to it. Reads with adapter contaminants or low-quality bases (N > 10%) were discarded. Subsequently, we aligned the stripped Read 1 sequences to hg19 human transcriptome (UCSC) using Hisat2 (version 2.10). Uniquely mapped reads were counted by HTSeq package83 and grouped by the cell-specific barcodes. Duplicated transcripts were removed based on the UMI information for each gene. Finally, for each individual cell, the copy number of transcripts of a given gene was the number of the distinct UMIs of that gene.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include UMI values for each cell

source_name: human embryonic cells

extract_protocol: A modified STRT-seq protocol was applied for single-cell RNA-seq. Briefly, sorted single cells in good condition were picked into lysis by mouth pipetting, and the scRNA-seq libraries were constructed based on STRT-seq with some modifications. cDNAs were synthesized using sample-specific 25-nt oligo-dT primer containing 8-nt barcode (TCAGACGTGTGCTCTTCCGATCT-XXXXXXXX-DDDDDDDD-T25, X representing sample-specific barcode while D standing for unique molecular identifiers (UMI).  After reverse transcription and second-strand cDNA synthesis, the cDNAs were amplified by 16 cycles of PCR using ISPCR primer and 3’ Anchor primer. Samples were pooled and purified using Agencourt AMPure XP beads . 4 cycles of PCR were performed to introduce index sequence  and subsequently, 400 ng cDNAs were fragmented to around 300 bp by Covaris S2. After being incubated with Dynabeads MyOneTM Streptavidin C1 beads (Thermo Fisher, 65002) for 1 hour at room temperature, cDNA Libraries were generated using KAPA Hyper Prep Kit (Kapa Biosystems, kk8505). After adaptor ligation, the libraries were amplified by 8 cycles of PCR using QP2 primer and short universal primer. The libraries were sequenced on Illumina Hiseq X Ten platform in 150 bp pair-ended manner

value: Caudal Half

tag: development stage


title: TDP-43 KO rep. 2

tag: cell line


title: 181218_snm3Cseq_hs_21yr_BA10_UMB5577_3_UMB5577_3_H9_AD010

value: frontal cortex


title: TDP-43 KO rep. 1


title: T42

city: Paris

first: Monot

last: Marc

address: 25, rue du docteur roux

department: Genomes and Genetics

institute: Institut Pasteur

data_processing:
Illumina Casava1.7 software used for basecalling.
Only sequence with a minimum length of 30 were considered.
Sequences were mapped to their de novo Peptoclostridium difficile whole genome sequences using bowtie v1.0.1 with parameter -k 2000
MAP2COV was used for counting genes with parameters -t RNA -b NO -v MEAN
Genome_build: Peptoclostridium difficile E1 (CAMD01) ; T20(CAMC01) ; T5 (CAMB01) ; E12 (CAMZ01) ; T14 (CANC01) ; E14 (CAMS01) ; T6 (CAMR01) ; E23 (CAMY01) ; T10 (CANB01) ; E15 (CAMM01) ; T11 (CAML01) ; E25 (CAMJ01) ; T15 (CAMK01) ; E16 (CAMH01) ; T61 (CAND01) ; E24 (CAMP01) ; T42 (CAMQ01)
Supplementary_files_format_and_content: Genes-count: Gene ID ; count
Supplementary_files_format_and_content: Couple-comparison: Organization (Class, Operon) ; Gene ID ; RNASeq (Coverage, Ratio) ; Gene Information (Orthologuous, Name, Product)

organism: Clostridioides difficile

source_name: Wild type strain T24

growth_protocol: Strains were grown aerobically in TY 6h at 37°C

extract_protocol:
Total RNA was extracted using phenol, Trizol reagent and chloroform/isoamylalcohol.
RNA libraries were prepared for sequencing using standard Illumina protocols (Truseq non stranded RNA seq kit)

tag: strain

tag: strain type

value: Control

value: wild type


title: CS10_body_10x

value: Body


title: E24

source_name: Wild type strain E24

value: Severe


title: Ime4 KO Yeast PolyA RNA Direct RNA Sequencing rep3

city: Barcelona

first: Eva Maria

last: Novoa

address: Dr. Aiguader 88

country: Spain

institute: Center for Genomic Regulation

description: NDT80 and Ime4 KO

data_processing:
Reads were locally basecalled using Albacore 2.1.7 and the "U" in basecalled reads were replaced with "T"
Reads were then mapped to reference using minimap2 : minimap2 -ax map-ont ref.fasta sample.fastq > sample.sam
use htseq-count to count reads mapped to each gene
Supplementary_files_format_and_content: *expression.txt files contain per-gene counts in a tab seperated format
Supplementary_files_format_and_content: gene symbols; number of reads mapped to gene in column1

organism: Saccharomyces cerevisiae SK1

source_name: Yeast

growth_protocol: Sk1 strains used in this study were SAy841 comprising a deletion of NDT80, and SAy966, in which both NDT80 and IME4 were deleted; These strains are characterized in Agarwala et al 2012. To induce synchronous meiotic entry, cells were grown for 24 hr in 1% yeast extract, 2% peptone, 4% dextrose at 30°C, diluted in BYTA (1% yeast extract, 2% tryptone, 1% potassium acetate, 50 mM potassium phthalate) to OD600 = 0.2 and grown for another 16 h at 30°C, 200 rpm. Cells were then washed twice with water and re-suspended in SPO (0.3% potassium acetate) at OD600 = 2.0 and incubated at 30°C at 190 rpm. Cells were isolated from SPO following 5 hours and collected by 2 min centrifugation at 3000g. Pellets were snap frozen and stored at -80ºC for RNA extraction.

extract_protocol:
Yeast total RNA samples were prepared using a modified protocol of nucleospin® 50 RNA kit (Machery-Nagel, cat 740955.50). Specifically, cells lysis was done in a 1.5ml tube by adding 450µl of lysis buffer containing 1M sorbitol (SIGMA-ALDRICH), 100mM EDTA and 0.45µl lyticase (10U/µl). The sample was incubated in 30°C for 30 minutes to break the cell wall, centrifuged for 10' at 3000 rpm, and supernatant was removed. From this stage, extraction proceeded as in the protocol of nucleospin® 50 RNA kit, only substituting β-mercaptoethanol with DTT. Enrichment of polyadenylated RNA from total RNA was performed using Oligo(dT) dynabeads mRNA-DIRECT kit (Thermo Scientific, 61012) for small mRNA amounts.
RNA libraries were prepared by following the standart ONT direct RNA sequencing (SQK-RNA001) protocol. Model: GridION R9.4.1 Flowcell FLO-MIN106 MiKNOW 1.15.1

tag: tag

tag: genotype/variation

value: NDT80 and Ime4 KO


title: CS12_CH

tag: tissue


title: Wild Type Yeast PolyA RNA Direct RNA Sequencing rep3

description: NDT80 KO (WT)

value: NDT80 KO (WT)


title: E25

source_name: Wild type strain E25


title: Genomic DNA from glioma sample; IDHwt_GBM_16

value: IDH statut:IDHwt

value: glioma sample


title: E16

source_name: Wild type strain E16


title: Genomic DNA from glioma sample; IDHwt_GBM_15


title: Stranded RNA-seq from glioma sample; IDHmut_GIII_24

data_processing:
RNA-seq were mapped to the human genome (hg19) using tophat2 (version 2.1.0) with a transcript annotation file from Gencode (Release 19)
The reads count per gene were obtained with the HTseq-count script on properly paired reads and Genecode V19 transcript annotation file
Differential expression analysis between groups was based on reads count using DESeq2 and edgeR R packages
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include count values for each Sample …

source_name: total RNA from glioma sample

extract_protocol:
RNA were isolated from frozen  tissue samples  using the RNeasy Mini Kit (Qiagen, Hamburg, GmbH),
RNA-seq were performed on total RNA following ribosomal RNAs depletion (Ribo-zero removal kit, illumina). RNA processing, rRNA depletion, library preparation and running on illumina Hiseq 2500 were performed by Integragen, SA (Evry, France), according to the manufacturer's protocol.

value: grade:Grade III

value: idh statut:IDHmut


title: Wild Type Yeast PolyA RNA Direct RNA Sequencing rep2

description: NDT80 KO (WT)


title: Stranded RNA-seq from glioma sample; IDHmut_GII_5

value: grade:Grade II


title: Stranded RNA-seq from glioma sample; IDHmut_GII_4


title: Stranded RNA-seq from glioma sample; IDHmut_GII_2

value: Female


title: Ime4 KO Yeast PolyA RNA Direct RNA Sequencing rep1

description: NDT80 and Ime4 KO


title: Genomic DNA from glioma sample; IDHwt_GBM_11


title: Genomic DNA from glioma sample; IDHwt_GBM_12


title: Genomic DNA from glioma sample; IDHwt_GBM_6


title: Stranded RNA-seq from glioma sample; IDHwt_GIII_12

value: idh statut:IDHwt


title: Stranded RNA-seq from glioma sample; IDHwt_GIII_11


title: Wild Type Yeast PolyA RNA Direct RNA Sequencing rep1

description: NDT80 KO (WT)


title: Stranded RNA-seq from glioma sample; IDHwt_GIII_17


title: T10

source_name: Wild type strain T10


title: Genomic DNA from glioma sample; IDHwt_GBM_4


title: Stranded RNA-seq from glioma sample; IDHwt_GIII_4


title: T61

source_name: Wild type strain T61


title: Genomic DNA from glioma sample; IDHwt_GBM_9


title: E23

source_name: Wild type strain E23

value: Prevalent


title: Genomic DNA from glioma sample; IDHwt_GBM_7


title: Genomic DNA from glioma sample; IDHwt_GBM_17


title: E16.5_3

type: RNA

city: Lille

first: Jérôme

last: Eeckhoute

address: Bâtiment J&K, Faculté de Médecine de Lille-Pôle Recherche, Boulevard du Professeur Leclerc

institute: CNRS

description: Transcriptomic MPH

hyb_protocol: Affymetrix GeneChip Hybridization Oven 640 for 16h at 45°C and 60 rpm on MoGene-2_1-st Chip. GeneChips were washed and stained in the Affymetrix Fluidics.

scan_protocol: Affymetrix GeneChip Scanner 7G and Affymetrix GeneChip Command Console software (AGCC).

data_processing: Raw transcriptomic data from Affymetrix microarrays were normalized using the Partek Genomics Suite (v7.0) using background correction by Robust Multi-array Average (RMA), quantile normalization and summarization via median-polish. RMA values from different probes matching to the same gene were averaged.

label: Biotin

source_name: C57Bl6J embryo

label_protocol: RNA were processed using Affymetrix GeneChip® WT PLUS Reagent Kit.

growth_protocol: Mice were housed in a temperature-controlled room (22–24°C) with a relative humidity of 36%–80%, and 12-hour light/12-hour dark cycles. Animal studies were performed in compliance with European Community specifications regarding the use of laboratory animals and approved by the Nord-Pas de Calais Ethical Committee for animal use. Embryos were dated taking Embryonic day (E) 0.5 as the day after the vaginal plug.

extract_protocol: RNA was extracted using RNeasy Microkit (Qiagen). cDNA was obtained with a reverse transcription Kit (High-capacity cDNA reverse transcription Kit, Life Technologies). Total RNA was checked for quantity and quality using the Agilent 2100 Bioanalyzer (Agilent Biotechnologies).

treatment_protocol: Mice and embryos did not receive any treatment.

tag: strain/background

value: WT

tag: developmental stage

value: Brown adipose tissue (BAT)


title: Stranded RNA-seq from glioma sample; IDHwt_GBM_34

value: Male


title: T6

source_name: Wild type strain T6

value: Control


title: Ime4 KO Yeast PolyA RNA Direct RNA Sequencing rep2

description: NDT80 and Ime4 KO


title: E16.5_2

description: Transcriptomic MPH


title: E16.5_1

description: Transcriptomic MPH


title: Stranded RNA-seq from glioma sample; IDHwt_GBM_27


title: Genomic DNA from glioma sample; IDHwt_GBM_1


title: T15

source_name: Wild type strain T15

value: wild type


title: hAECs + placental basal medium day0_2

city: Tsukuba

first: Farhana

last: Ferdousi

state: Ibaraki

address: Tennodai 1-1-1

country: Japan

institute: University of Tsukuba

hyb_protocol: Following fragmentation, 250 ng of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array (HG-219). GeneChips were washed and stained in the Gene Atlas Fluidics Station 400

scan_protocol: GeneChips were scanned using the GeneAtlas Imaging Station

data_processing:
The raw data were normalized using Expression Console Software provided by the Affymetrix following robust multichip average (RMA) algorithm (http://www.affymetrix.com). Subsequent analysis of the gene expression data was carried out in the freely available Transcriptome Analysis Console (TAC) version 4 (Thermofisher inc.). Further analysis was conducted using an online data mining tool DAVID (Database for Annotation, Visualization and Integrated Discovery, ver. 6.8). We used 'Functional Annotation' tool of DAVID to identify the most relevant biological terms, including gene ontology (GO) terms, biological pathways, tissue expression, and disease associations (Huang da et al., 2009). We also performed gene set enrichment analysis (GSEA) for the DEGs between day 7 treated hAECs and D0 hAECs and for DEGs between day 7 treated hAECs and D7 hAECs to test whether a priori-defined groups of genes associated with neural differentiation were significantly related to the DEGs between verbenalin-treated and control cells on day 0 and day 7
Expression console signal intensity. For calculating average value, standard deviation, fold change, and Anova p-value of signal intensity of replicates, we used freely available Transcriptome Analysis Console software (CHP files ).

label: biotin

source_name: Untreated control hAECs on day0, biological rep2

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 9.4 ug total RNA

growth_protocol: AECs were isolated from delivered term placenta and were maintained in Placenta Epithelial Cell Basal Medium (PromoCell, Cat. # C-26140) in 2D culture plate. Finally, 3D spheroids were formed by seeding 1×106 AECs in Placenta Basal Epithelial Cell Medium into each well of the 24-well plate.

extract_protocol: For RNA extraction, Isogen (Nippon Gene Co. Ltd., Toyama, Japan) was added and the cell suspensions were centrifuged for 5 minutes at 500 g and the pellet was stored at -80oC until use.

treatment_protocol: After the initial 24 hour culture, the medium was changed with 20 μM of verbenalin every 48 hours for three times (7days) for the treatment samples. Control samples were maintained in Placental medium that was also changed every 48 hours. Finally, we collected the treatment and control samples from one-week culture. Day 0 control samples were collected after the initial treatment.

tag: cell type

value: amnion epithelial cells

value: untreated control hAECs on day 0


title: E14

source_name: Wild type strain E14


title: Stranded RNA-seq from glioma sample; IDHwt_GBM_7

tag: gliomas classification


title: E15.5_3

description: Transcriptomic MPH


title: T14

source_name: Wild type strain T14


title: Genomic DNA from healthy donor 3; frontal cortex

source_name: DNA from  frontal cortex

value: grade:not applicable

value: IDH statut:not applicable

tag: gender

value: healthy control


title: Genomic DNA from healthy donor 4; frontal cortex

tag: disease


title: hAECs + placental basal medium day0_1

source_name: Untreated control hAECs on day0, biological rep1

tag: treatment


title: Genomic DNA from glioma sample; IDHwt_GBM_8

source_name: DNA from Glioma sample

value: IDH statut:IDHwt

value: glioma sample


title: T11

source_name: Wild type strain T11


title: E15.5_2

description: Transcriptomic MPH


title: Stranded RNA-seq from glioma sample; IDHwt_GBM_4


title: E12

source_name: Wild type strain E12


title: Genomic DNA from healthy donor 5; corpus callosum

source_name: DNA from corpus callosum


title: Stranded RNA-seq from healthy donor 4; frontal cortex

source_name: total RNA from frontal cortex

value: idh statut:not applicable


title: T5

source_name: Wild type strain T5


title: Genomic DNA from healthy donor 3; corpus callosum


title: E15

source_name: Wild type strain E15

value: Severe


title: hAECs + placental basal medium day7_3

source_name: Untreated control hAECs on day7, biological rep3

value: untreated control hAECs on 7th day


title: Genomic DNA from glioma sample; IDHwt_GBM_14


title: hAECs + placental basal medium day7_2

source_name: Untreated control hAECs on day7, biological rep2


title: E15.5_1

description: Transcriptomic MPH

source_name: C57Bl6J embryo


title: Stranded RNA-seq from healthy donor 4; corpus callosum

source_name: total RNA from corpus callosum


title: hAECs + placental basal medium day7_1

source_name: Untreated control hAECs on day7, biological rep1


title: E14.5_3

description: Transcriptomic MPH


title: Genomic DNA from healthy donor 2; corpus callosum


title: hAECs+ Verbenalin 3

source_name: hAECs treated with verbenalin for 7 days, biological rep3

value: verbenalin treated hAECs on 7th day


title: Stranded RNA-seq from healthy donor 1; corpus callosum


title: E1

source_name: Wild type strain E1

value: Prevalent


title: Genomic DNA from healthy donor 5; frontal cortex


title: hAECs+ Verbenalin 2

source_name: hAECs treated with verbenalin for 7 days, biological rep2


title: Genomic DNA from healthy donor 4; corpus callosum


title: Matched control for AMB + LF rep 3

status: Public on Sep 08 2019

city: Sydney

first: Chi Nam Ignatius

last: Pang

state: NSW

address: School of Biotechnology and Biomolecular Sciences, UNSW Australia

department: The NSW Systems Biology Initiative

institute: The University of New South Wales

description:
7B
raw_read_counts.tab
edgeR_normalized_read_counts.tab
logFC_and_FDR_values.tab

data_processing:
Quality Control: Sequencing reads for all samples were assessed for quality using FastQC (version 0.10.1; www.bioinformatics.babraham.ac.uk/projects/fastqc). All samples had an average Phred score of 30 or greater.
Mapping: Reads reads were mapped against the C. neoformans H99 genome using HISAT2 (version 2.1.0; Kim, Langmead, & Salzberg, 2015. Nature Methods, 12(4), 357 360) with following settings:  hisat2 -p 4 --known-splicesite-infile splicesites.txt -x $INDEX_DIR -1 ${job_name}_R1.fastq.gz -2 ${job_name}_R2.fastq.gz -S ${job_name}.sam . The splicesites.txt file contained a list of splice sites and was generated using the command "python hisat2_extract_splice_sites.py genes.gtf > splicesites.txt". hisat2_extract_splice_sites.py was a script included in the HISAT2 package and genes.gtf is a gene annotation file.
Counting: The number of unique reads were calculated using the featureCount function of Subread (version 1.6.4; Liao, Smyth & Shi. 2014 Bioinformatics, 30(7):923 930.) and the C. neoformans var. grubii H99 CNA3 gene annotation GTF file (RefSeq accession: GCF_000149245.1) . The following featureCounts settings were used:  featureCounts -s 0 -T 12 -p -a $GTF_FILE -t CDS -g gene_id -o ${job_name}_featurecounts.txt ${job_name}.sorted.bam .
Differentially expressed genes: Genes with low raw read counts were removed and only genes at least one counts per million (cpm) for at least six samples were kept for analysis. Differential expression of genes was analysed using in R (version 3.5.3) and the edgeR library (version 3.24.3) (Robinson, McCarthy, & Smyth, 2010 Bioinformatics, 26(1), 139 140). Multiple dimension scaling was used to examine the similarity in read counts between the samples and to assess reproducibility of the replicates. The sample 5A was identified as an outlier and were discarded from further analyses. The samples were normalized with respect to the library size and tag-wise biological coefficient of variation. Signifcantly differentially expressed genes was idenified using the quasi-likelihood methods (e.g. glmQLFit and glmQLFTest). A Benjamini-Hochberg adjusted p-value of 0.05 was used as the cutoff for identifying differentially expressed genes. To identify the genes that are differentially expressed upon synergistic amphotericin B (AMB) and lactoferrin (LF) treatment, C. neofrmans cultures were treated with i) AMB only; ii) a growth control for (i) with no AMB treatment; iii) a synergistic combination of AMB + LF; and iv) a growth control for (iii) with no AMB-LF treatment. For the analysis of treatments (i) to (iv), biological triplicate RNA-Seq samples were analyzed for the four treatments, with 12 samples in total. The AMB treatment was compared with the matched control, abbreviated as  AMB only  treatment. The AMB + LF treatment was compared with its matched control, abbreviated as  AMB+LF  treatment.
Genome_build: Cryptococcus neoformans var. grubii H99 (basidiomycetes) reference assembly. RefSeq accession: GCF_000149245.1
Supplementary_files_format_and_content: The 'raw_read_counts.tab' file is tab-delimited and contains the raw read counts of the mapped reads for all samples.
Supplementary_files_format_and_content: The 'edgeR_normalized_read_counts.tab' file is tab-delimited and contains the read counts in log counts per millin (logCPM) after normalization with edgeR tool. The values for Sample 5A is not included as the sample is considered to be an outlier from the multiple dimension scaling analysis of the samples.
Supplementary_files_format_and_content: The 'logFC_and_FDR_values.tab' file is tab-delimited and contains the log fold-change values and FDR values for the AMB only, and AMB + LF treatments.

organism: Cryptococcus neoformans H99

source_name: Matched control for AMB + LF

growth_protocol: C. neoformans strain H99 was cultured in yeast nitrogen broth (YNB; 0.171% (w/v) yeast nitrogen base without amino acids and ammomium sulphate (BD), 0.5% (w/v) ammonium sulfate, 2% (w/v) D-glucose, 0.192 % (w/v) synthetic dropout media without uracil (Sigma-Aldrich, USA), 0.0076% (w/v) uracil (Sigma-Aldrich, USA)) at 37 °C in a shaking incubator at 180 rpm. Stock concentrations of amphotericin B (AMB; Sigma-Aldrich, USA) at 1,600 µg/mL and lactoferrin (LF; MP Biomedical, USA) at 5,120 µg/mL were made in sterile MilliQ water.

extract_protocol:
For transcriptomic analysis, RNA was extracted from the following treatment conditions: i) AMB only, ii) growth control of (i), iii) AMB+LF and iv) growth control for (iii). Growth controls were extracted at the same time as its corresponding treatment and LF only treatment was excluded from transcriptomic analysis. RNA extraction was performed from freeze dried cells via bead beating and the Qiagen RNeasy mini kit as detailed in Pang et. al. (Scientific Reports, 2017. 7: 40232). RNA was sequenced at the Ramaciotti Centre for Genomics using the Illumina HiSeq 2000 to generate 100 bp paired-end reads.
For the AMB only treatment, the AMB+LF treatment and their corresponding matching controls, the TruSeq RNA Library prep kit v2 (Illumina) with a poly-A pulldown was used according to the manufacturer’s instructions, with 2 μg of total RNA for each of the three biological triplicate samples as input. The libraries were enriched using 15 cycles of PCR and the insert size ranged from 80 to 330 base pair (bp). The libraries were randomized and sequenced in two separate lanes using HiSeq 2000 with the TruSeq v3 SBS reagents to generate 100 bp paired-end reads. The data was demultiplexed using Casava 1.8.2.

treatment_protocol: To understand the synergy of AMB+LF treatment in H99, time-kill curves of AMB only, LF only and AMB+LF treatment were performed to determine ID20 (inhibition of cell growth by 20%) for RNA extraction and comparative transcriptomic analyses (as performed in (6)). The synergistic fractional inhibitory concentrations of AMB+LF (determined by (5)) were used for kill curve assays at 0.06 µg/mL AMB and 2 µg/mL LF. The ID20 for AMB only and AMB+LF treatments were determined to be at 1 hr and 50 min post treatment, respectively, where LF treatment did not affect growth.

value: control for amphotericin B (0.06 ug/mL) + lactoferrin (2 ug/mL)

tag: growth time

value: 50 minutes at ID20

tag: illumina lane


title: Matched control for AMB + LF rep 2

description:
3D
raw_read_counts.tab
edgeR_normalized_read_counts.tab
logFC_and_FDR_values.tab


title: Matched control for AMB + LF rep 1

description:
6F
raw_read_counts.tab
edgeR_normalized_read_counts.tab
logFC_and_FDR_values.tab


title: T20

source_name: Wild type strain T20

tag: genotype


title: AMB + LF rep 2

description:
5A
raw_read_counts.tab
logFC_and_FDR_values.tab

source_name: AMB + LF

value: amphotericin B (0.06 ug/mL) + lactoferrin (2 ug/mL)


title: Stranded RNA-seq from glioma sample; IDHmut_GIII_22

source_name: total RNA from glioma sample

value: grade:Grade III

value: idh statut:IDHmut

value: Female


title: AMB + LF rep 1

description:
8H
raw_read_counts.tab
edgeR_normalized_read_counts.tab
logFC_and_FDR_values.tab


title: AMB + LF rep 3

description:
2G
raw_read_counts.tab
edgeR_normalized_read_counts.tab
logFC_and_FDR_values.tab


title: Matched control for AMB only rep 2

description:
5L
raw_read_counts.tab
edgeR_normalized_read_counts.tab
logFC_and_FDR_values.tab

source_name: Matched control for AMB only

value: control for amphotericin B (0.06 ug/mL)

value: 60 minutes at ID20


title: Matched control for AMB only rep 1

description:
8G
raw_read_counts.tab
edgeR_normalized_read_counts.tab
logFC_and_FDR_values.tab


title: E14.5_1

description: Transcriptomic MPH

value: WT

value: Brown adipose tissue (BAT)


title: hAECs+ Verbenalin 1

source_name: hAECs treated with verbenalin for 7 days, biological rep1

value: amnion epithelial cells


title: 35_SAP11mbsp_MQexposed

first: Archana

last: Singh

state: England

address: Downing Street

department: Plant Science

institute: Cambridge University

data_processing:
Raw fastq files were converted to fasta format.
Adapter sequences and reads less than 20 nt were trimmed using Trim Galore
Trimmed reads were aligned to the human genome (v.38) using HISAT2
Count matrix for genes was created using Kallisto
Differential expression analysis was done using the DESeq2 package available in R
Genome_build: Arabidopsis thaliana

organism: Zea mays

source_name: Zea mays leaf tissue

growth_protocol: Arabidopsis plants were grown  under  controlled  environmental  conditions  with  a  14h,  22  C°/  10h,  20°C  dark  /  light  period.   Zea mays plants were grown  under  controlled  environmental  conditions with 16h,  26°C/  8h,  20°C  light/dark  period.

extract_protocol:
Total RNA was extracted from ground leaf tissue using RNeasy plant mini kit
libraries were generated with the llumina Truseq strand-specific mRNA library preparation withhout size selection.

treatment_protocol: Seven week A.thaliana old plants were exposed to M. quadrilineatus for three days. Three week Z.mays old platns were exposed to  D. maidis for three days.

tag: line

value: SAP11mbsp overexpressed

value: exposed to M. quadrilineatus

value: leaf


title: 36_SAP11mbsp_MQexposed


title: AMB only rep 2

description:
1C
raw_read_counts.tab
edgeR_normalized_read_counts.tab
logFC_and_FDR_values.tab

source_name: AMB only

value: amphotericin B (0.06 ug/mL)


title: AMB only rep 1

description:
5F
raw_read_counts.tab
edgeR_normalized_read_counts.tab
logFC_and_FDR_values.tab


title: AMB only rep 3

description:
4A
raw_read_counts.tab
edgeR_normalized_read_counts.tab
logFC_and_FDR_values.tab


title: 34_SAP11mbsp_MQexposed


title: 33_SAP11mbsp_MQexposed


title: E14.5_2

description: Transcriptomic MPH


title: Genomic DNA from healthy donor 1; corpus callosum

data_processing: GenomeStudio V2011.1

source_name: DNA from corpus callosum

extract_protocol: DNA was isolated from frozen tissues using the QIAamp DNA Mini Kit (Qiagen), according to the manufacturer’s recommendations

value: grade:not applicable

value: IDH statut:not applicable

value: Male

value: healthy control


title: 32_SAP11aywb_MQexposed

value: SAP11aywb overexpressed


title: 31_SAP11aywb_MQexposed


title: Matched control for AMB only rep 3

description:
2K
raw_read_counts.tab
edgeR_normalized_read_counts.tab
logFC_and_FDR_values.tab


title: 1123+sgZNF596

city: Shanghai

first: Haizhong

last: Feng

state: Shanghai

address: Pujian Road 160

department: Ren Ji Hospital

institute: Shanghai Jiao Tong University

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 mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Fragments Per Kilobase of transcript per Million fragments mapped (FPKM) were calculated using a protocol from Trapnell et al., Nat Biotechnol, 2010. In short, A fragment corresponds to a single cDNA molecule, which can be represented by a pair of reads from each end. Exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library. FPKM is conceptually analogous to the reads per kilobase per million reads sequenced (RPKM) measure, but it explicitly accommodates sequencing data with one, two, or – if needed for future sequencing platforms – higher numbers of reads from single source molecules.
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

extract_protocol:
Trizol extraction of total RNA
from purified polyA RNA

value: glioma stem-like cell (GSC)

tag: tissue source

value: brain

value: ZNF596 sgRNA


title: 1123/shL115 with Dox treatment


title: 1123+L115-WT

value: Ectopic expression of LINC00115


title: 1123+sgC

value: control sgRNA


title: 1123/shL115 without Dox treatment


title: 28_HiIIA_MQexposed

value: HillA overexpressed


title: 29_SAP11aywb_MQexposed


title: 528+TGF-beta-2

value: 20ug/ml TGF-beta for 8 h


title: 528+TGF-beta-1


title: 27_HiIIA_MQexposed


title: 528+vehicle-2

value: vehicle; ddH2O


title: 528+vehicle-1


title: 25_HiIIA_MQexposed


title: 24_SAP11mbsp_DMexposed

value: SAP11mbsp overexpressed

value: exposed to D. maidis


title: 1123+TGF-beta-2


title: 23_SAP11mbsp_DMexposed

value: leaf


title: 21_SAP11mbsp_DMexposed


title: 1123+empty vector

value: expression of empty vector


title: 19_SAP11aywb_DMexposed


title: 22_SAP11mbsp_DMexposed


title: 1123+vehicle-1


title: 1123+vehicle-2


title: 18_SAP11aywb_DMexposed


title: neuruloid_day7_56CAG

first: Tiago

last: Rito

state: NEW YORK

address: 1230 York Avenue

institute: Rockefeller University

description: 10X Genomics

data_processing:
The Cell Ranger (v2.0.2) software pipeline was used to create FASTQ files which were aligned to the hg19 genome using default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: Filtered gene expression matrices of genes versus detected barcodes (cells) with counts of unique molecular identifiers (UMI) were generated and subsequently used for downstream analyses. UMI count matrices for RUES2 and 56CAG were loaded into R (v3.5.1) and analysed using Seurat (v2.3.4). The raw matrices were filtered to have a minimum of 200 detected genes per cell and a gene was only kept if expressed (non-zero) in at least 3 cells. Matrices were exported as csv.

source_name: neuruloid (3ng/mL BMP4) 500um colony diameters

growth_protocol: All hESC lines were grown in HUESM medium that was conditioned with mouse embryonic fibroblasts and supplemented with 20 ng/ml bFGF (MEF-CM) (Deglincerti et al., 2016). Cells were tested for mycoplasma at 2-month intervals. Cells were grown on tissue culture dishes coated with Geltrex (Life Technologies) solution.

extract_protocol:
Two micropatterned glass cover slips with 500μm of diameter neuruloids (BMP4 3ng/ml) were grown in parallel using RUES2 hESCs and the isogenic 56CAG HD line. At day 7, approximately half of each cover slip with neuruloids was scraped off and treated with Accutase (Stemcell technologies) for 10min at 37°C. The remaining neuruloids on the cover slip were fixed for immunofluorescence analysis as quality control. After dissociation the cells were washed three times in PBS+/+ (gibco) with 0.04% BSA and strained through a Flowmi tip strainer (40 μm, cat.no. 136800040). Cell count and viability were determined on a Countess II Automated Cell Counter using trypan blue.
The two samples were separately loaded for capture with the Chromium System using the Single Cell 3' v2 reagents (10× Genomics). Following cell capture and lysis, cDNA was synthesized and amplified according to the manufacturer’s instructions (10× Genomics). The resulting libraries were sequenced on the Illumina NextSeq500 platform with 150-cycle high output.

treatment_protocol: Micropatterned glass cover slips (CYTOOCHIPS™ Arena A, Arena 500 A, Arena EMB A) were first coated with 100 μg/ml of recombinant Laminin-521 (BioLamina, LN521-03) diluted in PBS+/+ (gibco) for 3 h at 37 °C. To do that, place micropatterns face-up on to a Parafilm that seated in 10 cm dish then put 800 μl laminin solution on to the micropattern. After 3 h at 37 °C, transfer the coated micropattern to 35 mm dish with 5 ml of PBS+/+. Laminin was then removed with six serial dilutions in PBS+/+ (dilution 1:4) before two complete washes in PBS+/+. Then the coated micropattern was kept in PBS+/+ at 37 °C. Cells were seeded as follows. Cells growing in MEF-CM on culture dish were washed once with PBS-/- (gibco), then treated with Accutase (Stem Cell Technologies) for 5 min. Cells were then triturated with a pipet to ensure single cell suspension and Accutase was diluted out with 4x HUESM medium supplemented with 20 ng/ml bFGF and Rock inhibitor Y27632 (10 μM, Abcam ab120129). Cells were then further diluted with the same medium and 5 x 105 (or as indicated) cells in 3.0 ml of medium were placed over the micropattern in a 35 mm tissue culture dish, then incubated at 37 °C. After 3 h, the micropattern in a dish was washed once with PBS+/+. For SB+LDN condition: PBS+/+ was replaced with 3N medium (Shi et al., 2012) with 10 μM SB431542 (Stemgent 04-0010-10) and 0.2 μM LDN 193189 (Stemgent 04-0019). At Day 3 and 5, the medium was replaced with the same fresh medium and incubated at 37 °C till day 7. For SB+BMP4 condition (Neuruloid), PBS was replaced with HUESM with 10 μM SB431542 and 0.2 μM LDN 193189. At Day 3, the medium was replaced with HUESM with 10μM SB431542 and BMP4 (50ng/ml or indicated each experiment). At Day 5, the medium was replaced with the same fresh medium then incubated till day 7.

value: hESC-derived neuruloid

tag: cell line

value: HD line 56CAG (isogenic RUES2)

tag: culture time


title: neuruloid_day7_RUES2

description: 10X Genomics


title: 17_SAP11aywb_DMexposed


title: D8_SAP11aywb_NONexposed

organism: Arabidopsis thaliana

source_name: A.thaliana leaf tissue

value: SAP11 overexpressed

value: non treated

tag: tag

value: Leaf tissue


title: D7_SAP11aywb_NONexposed


title: col0_exposed_H1

value: Wild type Col-0

value: exposed to M. quadrilineatus


title: 14_HiIIA_DMexposed


title: 15_HiIIA_DMexposed


title: col0_exposed_H3


title: col0_exposed_H4


title: 10_SAP11mbsp_NONexposed


title: D6_SAP11aywb_NONexposed


title: 13_HiIIA_DMexposed


title: D5_SAP11aywb_NONexposed


title: 9_SAP11mbsp_NONexposed


title: 16_HiIIA_DMexposed


title: SAP11mbsp_exposed_E4


title: 12_SAP11mbsp_NONexposed


title: 8_SAP11aywb_NONexposed

value: SAP11aywb overexpressed


title: 7_SAP11aywb_NONexposed


title: 6_SAP11aywb_NONexposed


title: SAP11mbsp_exposed_E3


title: 5_SAP11aywb_NONexposed


title: 4_HiIIA_NONexposed


title: SAP11mbsp_exposed_E2


title: 3_HiIIA_NONexposed


title: H6_col0_NONexposed


title: SAP11mbsp_exposed_E1


title: 2_HiIIA_NONexposed


title: H5_col0_NONexposed


title: 1_HiIIA_NONexposed


title: SAP11aywb_exposed_D4


title: E8_SAP11mbsp_NONexposed


title: E7_SAP11mbsp_NONexposed


title: E6_SAP11mbsp_NONexposed


title: RNA Seq-KO T cells

first: Xiang

last: Sun

address: 320 Yue Yang Road

institute: Institute of Biochemistry and Cell Biology, SIBS, CAS

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing poly-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.4 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.4. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
HTSeq v0.9.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Prior to differential gene expression analysis, for each sequenced library, the read counts were adjusted by edgeR program package through one scaling normalized factor. Differential expression analysis of two conditions was performed using the DEGSeq R package (1.20.0). The P values were adjusted using the Benjamini & Hochberg method. Corrected P-value of 0.005 and log2(Fold change) of 1 were set as the threshold for significantly differential expression.
Genome_build: Mus_musculus.Ensembl release 91
Supplementary_files_format_and_content: Tab-delimited text files include raw and  normalized reads count for each RNA-seq sample

source_name: CD4+ T cells

growth_protocol: Naïve CD4+ T cells were stimulated for 3 days in 48-well flat-bottomed plates with plate-bound anti-CD3 and anti-CD28 (1 µg/mL each; BD Bioscience), β-mercaptoethanol (Shanghai Genebase Gene-Tech, 50 µM), and 10% fetal bovine serum in RPMI 1640 medium unless otherwise indicated.

extract_protocol:
Total RNA was extracted using TRIZOL reagent (Invitrogen),  A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase（RNase H-）. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

tag: strain

value: lymph nodes

value: CD4+ T cells

tag: age

value: 7 weeks


title: SAP11aywb_exposed_D3


title: RNA Seq-WT T cells

tag: tissue

value: wild type


title: H8_col0_NONexposed


title: SAP11aywb_exposed_D2


title: RNA Seq-WT T cells-3

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.4 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.4. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
HTSeq v0.9.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Prior to differential gene expression analysis, for each sequenced library, the read counts were adjusted by edgeR program package through one scaling normalized factor. Differential expression analysis of two conditions was performed using the DEGSeq R package (1.20.0). The P values were adjusted using the Benjamini & Hochberg method. Corrected P-value of 0.005 and log2(Fold change) of 1 were set as the threshold for significantly differential expression.
Genome_build: Mus_musculus.Ensembl release 91
Supplementary_files_format_and_content: Tab-delimited text files include normalized raw reads count for each RNA-seq sample

source_name: lymph nodes


title: RNA Seq-KO T cells-2


title: SAP11aywb_exposed_D1


title: RNA Seq-KO T cells-3


title: RNA Seq-WT T cells-2


title: E5_SAP11mbsp_NONexposed


title: H7_col0_NONexposed


title: WGBS-KO T cells

data_processing:
Quality control:    First of all, we use FastQC (fastqc_v0.11.5) to perform basic statistics on the quality of the raw reads. Then, those reads sequences produced by the Illumina pipleline in FASTQ format were pre-processed through Trimmomatic (Trimmomatic-0.36) software use the parameter (SLIDINGWINDOW: 4:15 ; LEADING:3, TRAILING:3 ; ILLUMINACLIP: adapter.fa: 2: 30: 10 ;MINLEN:36)
Reads mapping to the reference genome:    Bismark software (version 0.16.3; Krueger F, 2011) was used to perform alignments of bisulfite-treated reads to a reference genome (-X 700 --dovetail).  The results of methylation extractor (bismark_methylation_extractor, --no_overlap) were transformed into bigWig format for visualization using IGV browser. The sodium bisulfite non-coversion rate was calculated as the percentage of cytosine sequenced at cytosine reference positions in the lambda genome.
Estimating methylation level:    In order to calculate the methylation level of the sequence, we divided the sequence into multiple bins, with bin size is 10kb. The sum of methylated and unmethylated read counts in each window were calculated. Methylation level (ML) for each window or C site shows the fraction of methylated Cs.
Differentially methylated analysis:    Differentially methylated regions (DMRs) were identified using the DSS software (Hao Feng HaoWu, 2014；Hao Wu，2015；Yongseok Park Hao Wu,2016 ) , The core of DSS is a new dispersion shrinkage method for estimating the dispersion parameter from Gamma-Poisson or Beta-Binomial distributions.  According to the distribution of DMRs through the genome, we defined the genes related to DMRs as genes whose gene body region (from TSS to TES) or promoter region (upstream 2kb from the TSS) have a overlap with the DMRs.
GO and KEGG enrichment analysis of DMR-related genes:    Gene Ontology (GO) enrichment analysis of genes related to DMRs was implemented by the GOseq R package (Young MD, 2010), in which gene length bias was corrected. GO terms with corrected P-value less than 0.05 were considered significantly enriched by DMR-related genes.  KEGG (Kanehisa M, 2008) is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high- through put experimental technologies (http://www.genome.jp/kegg/). We used KOBAS software (Mao X, 2005) to test the statistical enrichment of DMR-related genes in KEGG pathways.
Genome_build: Mus_musculus.Ensembl release 91
Supplementary_files_format_and_content: On sample record: Tab-delimited text files include identification of methylated cytosine sites for each bisulfite-seq sample
Supplementary_files_format_and_content: On series record: Tab-delimited text files include identification of DMRs for each bisulfite-seq sample

growth_protocol: Naïve CD4+ T cells were stimulated for 60h in 48-well flat-bottomed plates with plate-bound anti-CD3 and anti-CD28 (1 µg/mL each; BD Bioscience), β-mercaptoethanol (Shanghai Genebase Gene-Tech, 50 µM), and 10% fetal bovine serum in RPMI 1640 medium unless otherwise indicated.

extract_protocol:
Genomic DNA was extracted with phenol/chloroform method. Genomic DNA degradation and contamination was monitored on agarose. DNA purity was checked using the NanoPhotometer® spectrophotometer. DNA concentration was measured using Qubit® DNA Assay Kit in  Qubit® 2.0 Flurometer  gels.
A total amount of 5.2 microgram genomic DNA spiked with 26 ng lambda DNA were fragmented by sonication to 200-300bp with Covaris S220, followed by end repair and adenylation. Cytosine-methylated barcodes were ligated to sonicated DNA as per manufacturer’s instructions. Then these DNA fragments were treated twice with bisulfite using EZ DNA Methylation-GoldTM Kit (Zymo Research), before the resulting single-strand DNA fragments were PCR amplificated using KAPA HiFi HotStart Uracil + ReadyMix (2X).  Library concentration was quantified by Qubit® 2.0 Flurometer (Life Technologies, CA, USA) and quantitative PCR, and the insert size was assayed on Agilent Bioanalyzer 2100 system.

value: 8 weeks


title: WGBS-WT T cells


title: LNCaP_Robins AR5

status: Public on Sep 07 2019

city: Ann Arbor

first: Steven

last: Kregel

state: MI

address: 1500 E. Medical Center Drive, Room 5320 RCC

department: MCTP

institute: University of Michigan

description: LNCaP ChIP 48 hour CSS 12h 1nM R1881 0.1uM Doxorubicin AR PG-21

data_processing:
Alignment using STAR version 2.4.1 (splicing disabled)
Peak calling using MAC2 (default parameters)
BigWig created using bedtools and kent utils
Coverage was normalized to total sequencing depth
GRCh38
BigWig (coverage)

source_name: LNCaP

extract_protocol:
The ChIP assays were performed using HighCell ChIP kit with IPure 2.0 kit elution (Diagenode) according to manufacturer's protocol. The antibodies used for ChIP assay are AR_PG-21 (Millipore Cat. # 06-680); TBP (Abcam Cat. #ab63766), and Normal Rabbit IgG Control (Diagenode). LNCaP cells were grown in charcoal-stripped serum containing media for 48 hrs followed by 12 hrs of vehicle or 1 nM R1881 and dox treatment (0.1 µM for ‘low,’ 0.4 µM for ‘medium,’ and 0.7 µM for ‘high’) for all ChIP-qPCR and ChIP-seq conditions.  ChIP-seq sample preparation for sequencing was performed according to the manufacturer's instructions (Illumina).
The ChIP-seq sample preparation for sequencing was performed according to the manufacturer’s instructions (Illumina). ChIP-enriched DNA samples (1-10 ng) were converted to blunt-ended fragments using T4 DNA polymerase, E.coli DNA polymerase I large fragment (Klenow polymerase) and T4 polynuleotide kinase (New England BioLabs, NEB). A single A-base was added to fragment ends by Klenow fragment (3’ to 5’ exo minus; NEB) followed by ligation of Illumina adaptors (Quick ligase, NEB). The adaptor-modified DNA fragments were enriched by PCR using the Illumina Barcode primers and Phusion DNA polymerase (NEB). PCR products were size selected using 3% NuSieve agarose gels (Lonza) followed by gel extraction using QIAEX II reagents (QIAGEN). Libraries were quantified with the Bioanalyzer 2100 (Agilent) and sequenced on the Illumina HiSeq 2000 Sequencer (100 nucleotide read length).
RNA-seq using cDNA based on manufacturer's instructions (Illumina)

value: Prostate Adenocarcinoma

tag: passage

value: passage 30-50

tag: doxorubicin treatment

value: Low


title: LNCaP_Robins TBP1

description: LNCaP ChIP 48 hour CSS TBP (abcam)

tag: cell type


title: LNCaP_Robins AR3

description: LNCaP ChIP 48 hour CSS 0.7uM Doxorubicin AR PG-21

value: High


title: LNCaP_Robins AR6

description: LNCaP ChIP 48 hour CSS 12h 1nM R1881 0.4uM Doxorubicin AR PG-21

value: Medium


title: LNCaP_Robins TBP3

description: LNCaP ChIP 48 hour CSS 0.7uM Doxorubicin TBP (abcam)


title: LNCaP_Robins TBP7

description: LNCaP ChIP 48 hour CSS 12h 1nM R1881  0.7uM Doxorubicin  TBP (abcam)


title: LNCaP_Robins AR7

description: LNCaP ChIP 48 hour CSS 12h 1nM R1881  0.7uM Doxorubicin AR PG-21


title: LNCaP_Robins TBP6

description: LNCaP ChIP 48 hour CSS 12h 1nM R1881 0.4uM Doxorubicin TBP (abcam)


title: LNCaP_Robins TBP2

description: LNCaP ChIP 48 hour CSS 0.1uM Doxorubicin TBP (abcam)


title: LNCaP_Robins AR1

description: LNCaP ChIP 48 hour CSS AR PG-21


title: LNCaP_Robins AR2

description: LNCaP ChIP 48 hour CSS 0.1uM Doxorubicin AR PG-21


title: LNCaP_Robins TBP5

description: LNCaP ChIP 48 hour CSS 12h 1nM R1881 0.1uM Doxorubicin TBP (abcam)


title: LNCaP_Robins TBP4

description: LNCaP ChIP 48 hour CSS 12h 1nM R1881 TBP (abcam)


title: LNCaP R1881 0.7 Dox-3

description:
Poly-A selected RNA
LNCaP Charcoal Stripped Serum Starved 48h- 1nM R1881 and 0.7uM Doxorubin treated 12 hours replicate-3

data_processing:
Align to GRCh38 using version STAR 2.4.1
Count reads using featureCounts (default settings, strand specific mode)
FPKM - upper quartile normalized using edgeR
GRCh38
counts


title: LNCaP R1881 0.7 Dox-2

description:
Poly-A selected RNA
LNCaP Charcoal Stripped Serum Starved 48h- 1nM R1881 and 0.7uM Doxorubin treated 12 hours replicate-2


title: LNCaP_Robins AR4

description: LNCaP ChIP 48 hour CSS 12h 1nM R1881 AR PG-21


title: NR8383_Control for MW5

first: Katsuhide

last: Fujita

address: 16-1 Onogawa

department: Research Institute of Science for Safety and Sustainability

institute: National Institute of Advanced Industrial Science and Technology

description:
Gene expression after 24hr in rat alveolar macrophages as cotrol for MW5
Each raw data file represents an independent biological replicate.

hyb_protocol: Each labeled cRNA probe was used separately for hybridization to a 4×44 K Whole Rat Genome Microarray (G4131F; Agilent Technologies) at 65 °C for 17 h.

scan_protocol: Hybridized microarray slides were washed according to the manufacturer’s instructions and scanned with a DNA Microarray Scanner (Agilent) at 5 μm resolution.

data_processing: The scanned images were analyzed numerically using Agilent Feature Extraction Software, version 12.0.3.1.  The supplementary files CN900*txt include the log2 average normalized signal intensity.

organism: Rattus norvegicus

source_name: Rat alveolar macrophages, 24hr, Control (BSA) for MW5, replicate 4

label_protocol: Cyanine-3-labeled cRNA was prepared from RNA using a Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer’s instructions, followed by RNeasy column purification (Qiagen). Dye incorporation and cRNA yield were checked with the NanoDrop 2000 spectrophotometer.

growth_protocol: Rat alveolar macrophage cells (NR8383) obtained the American Type Culture Collection were cultured at 37 °C in 75-cm2 cell culture flasks in F-12K with 10 % (v/v) heat-inactivated fetal bovine serum (FBS) in a humidified atmosphere of 95% air and 5% CO2.

extract_protocol: Total RNA was extracted using a RNeasy Mini Kit (Qiagen, Japan) following the manufacturer’s instructions. RNA was quantified using a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific Inc., US), and sample qualities were monitored with an Agilent 2100 Bioanalyzer (Agilent Technologies, US).

treatment_protocol: F-12K + FBS medium was removed by centrifugation. Cell cultures were replaced with six kinds of the MWCNTs working solutions (MW1, MW2, MW3, MW4, MW5 or MW6), respectively. The cultures were seeded into each well of a 6-well plate and grown for 24 hours at 37 ºC in a humidified incubator with 5% CO2. Cell concentrations at this point were approximately 3.0 x 10^5 cells/mL.

value: alveolar macrophages

value: Control for MW5

tag: time


title: NR8383_Control for MW4

description:
Gene expression after 24hr in rat alveolar macrophages as cotrol for MW4
Each raw data file represents an independent biological replicate.

source_name: Rat alveolar macrophages, 24hr, Control (BSA) for MW4, replicate 4

value: Control for MW4


title: NR8383_Control for MW1

description:
Gene expression after 24hr in rat alveolar macrophages as cotrol for MW1
Each raw data file represents an independent biological replicate.

source_name: Rat alveolar macrophages, 24hr, Control (BSA) for MW1, replicate 4

value: Control for MW1


title: NR8383_Control for MW3

description:
Gene expression after 24hr in rat alveolar macrophages as cotrol for MW3
Each raw data file represents an independent biological replicate.

source_name: Rat alveolar macrophages, 24hr, Control (BSA) for MW3, replicate 4

value: Control for MW3


title: NR8383_MW5

description:
Gene expression after 24hr in MW5-exposed rat alveolar macrophages
Each raw data file represents an independent biological replicate.

source_name: Rat alveolar macrophages, 24hr, MW5, replicate 4


title: NR8383_Control for MW6

description:
Gene expression after 24hr in rat alveolar macrophages as cotrol for MW6
Each raw data file represents an independent biological replicate.

source_name: Rat alveolar macrophages, 24hr, Control (BSA) for MW6, replicate 4

value: Control for MW6


title: NR8383_MW1

description:
Gene expression after 24hr in MW1-exposed rat alveolar macrophages
Each raw data file represents an independent biological replicate.

source_name: Rat alveolar macrophages, 24hr, MW1, replicate 4


title: NR8383_MW2

description:
Gene expression after 24hr in MW2-exposed rat alveolar macrophages
Each raw data file represents an independent biological replicate.

source_name: Rat alveolar macrophages, 24hr, MW2, replicate 4


title: NR8383_MW4

description:
Gene expression after 24hr in MW4-exposed rat alveolar macrophages
Each raw data file represents an independent biological replicate.

source_name: Rat alveolar macrophages, 24hr, MW4, replicate 4


title: NR8383_MW3

description:
Gene expression after 24hr in MW3-exposed rat alveolar macrophages
Each raw data file represents an independent biological replicate.

source_name: Rat alveolar macrophages, 24hr, MW3, replicate 4


title: NR8383_Control for MW2

description:
Gene expression after 24hr in rat alveolar macrophages as cotrol for MW2
Each raw data file represents an independent biological replicate.

source_name: Rat alveolar macrophages, 24hr, Control (BSA) for MW2, replicate 4

value: Control for MW2


title: NR8383_MW6

description:
Gene expression after 24hr in MW6-exposed rat alveolar macrophages
Each raw data file represents an independent biological replicate.

source_name: Rat alveolar macrophages, 24hr, MW6, replicate 4


title: LNCaP R1881 0.4 Dox-1

description:
Poly-A selected RNA
LNCaP Charcoal Stripped Serum Starved 48h- 1nM R1881 and 0.4uM Doxorubin treated 12 hours replicate-1


title: LNCaP CSS 0.4 Dox-2

description:
Poly-A selected RNA
LNCaP Charcoal Stripped Serum Starved 48h- 0.4uM Doxorubin treated 12 hours replicate-2


title: LNCaP R1881 0.1 Dox-3

description:
Poly-A selected RNA
LNCaP Charcoal Stripped Serum Starved 48h- 1nM R1881 and 0.1uM Doxorubin treated 12 hours replicate-3


title: LNCaP R1881-2

description:
Poly-A selected RNA
LNCaP Charcoal Stripped Serum Starved 48h- 1nM R1881 treated 12 hours replicate-2


title: LNCaP R1881-3

description:
Poly-A selected RNA
LNCaP Charcoal Stripped Serum Starved 48h- 1nM R1881 treated 12 hours replicate-3


title: LNCaP R1881 0.7 Dox-1

description:
Poly-A selected RNA
LNCaP Charcoal Stripped Serum Starved 48h- 1nM R1881 and 0.7uM Doxorubin treated 12 hours replicate-1


title: LNCaP R1881 0.1 Dox-2

description:
Poly-A selected RNA
LNCaP Charcoal Stripped Serum Starved 48h- 1nM R1881 and 0.1uM Doxorubin treated 12 hours replicate-2


title: LNCaP R1881 0.4 Dox-3

description:
Poly-A selected RNA
LNCaP Charcoal Stripped Serum Starved 48h- 1nM R1881 and 0.4uM Doxorubin treated 12 hours replicate-3


title: LNCaP CSS 0.7 Dox-1

description:
Poly-A selected RNA
LNCaP Charcoal Stripped Serum Starved 48h- 0.7uM Doxorubin treated 12 hours  replicate-1


title: LNCaP CSS 0.7 Dox-3

description:
Poly-A selected RNA
LNCaP Charcoal Stripped Serum Starved 48h- 0.7uM Doxorubin treated 12 hours  replicate-3


title: LNCaP R1881 0.4 Dox-2

description:
Poly-A selected RNA
LNCaP Charcoal Stripped Serum Starved 48h- 1nM R1881 and 0.4uM Doxorubin treated 12 hours replicate-2


title: LNCaP CSS 0.7 Dox-2

description:
Poly-A selected RNA
LNCaP Charcoal Stripped Serum Starved 48h- 0.7uM Doxorubin treated 12 hours  replicate-2


title: LNCaP CSS 0.1 Dox-3

description:
Poly-A selected RNA
LNCaP Charcoal Stripped Serum Starved 48h- 0.1uM Doxorubin treated 12 hours replicate-3


title: LNCaP R1881-1

description:
Poly-A selected RNA
LNCaP Charcoal Stripped Serum Starved 48h- 1nM R1881 treated 12 hours replicate-1


title: LNCaP CSS 0.4 Dox-1

description:
Poly-A selected RNA
LNCaP Charcoal Stripped Serum Starved 48h- 0.4uM Doxorubin treated 12 hours replicate-1


title: LNCaP CSS 0.1 Dox-2

description:
Poly-A selected RNA
LNCaP Charcoal Stripped Serum Starved 48h- 0.1uM Doxorubin treated 12 hours replicate-2


title: LNCaP CSS 0.1 Dox-1

description:
Poly-A selected RNA
LNCaP Charcoal Stripped Serum Starved 48h- 0.1uM Doxorubin treated 12 hours replicate-1


title: LNCaP CSS-3

description:
Poly-A selected RNA
LNCaP Charcoal Stripped Serum Starved 48h replicate 3


title: LNCaP CSS-2

description:
Poly-A selected RNA
LNCaP Charcoal Stripped Serum Starved 48h replicate 2


title: LNCaP CSS 0.4 Dox-3

description:
Poly-A selected RNA
LNCaP Charcoal Stripped Serum Starved 48h- 0.4uM Doxorubin treated 12 hours replicate-3