title: R2_Hth_Exd_Dfd_wt_Lib21_HthF_HthR_SELEX_seq

description: To extract reads for Hth libraries in either orientation (F or R) use SELEX package R with the following flank design: Hth-F: TGACAG-21xN-CCCGGG Hth-R: CTGTCA-21xN-CCCGGG or match pattern to grep from fastq

data_processing:
Library strategy: SELEX-seq
SELEX-seq 16-bp libraries: Fastq files were reverse-complemented and both forward and reverse-complement read merged into one (fastx_reverse_complement -Q33 -z ; FASTX toolkit 0.0.12;Hannon lab). Next, fixed primer sites were trimmed using the following options: fastx_trimmer -Q33 -f 12 -l 41 –z (FASTX toolkit 0.0.12;Hannon lab). Kmer counting and relative affinity estimates were computed using the R package bioconductor.org/packages/SELEX. SELEX-seq 21-bp and 30bp libraries: Sequencing primer sequences were removed as part of the Illumina demultiplexing. For the 21-bp libraries both Hth-F and Hth-R Homothorax orientations are present in the same fastq and can be isolated by using the R package bioconductor.org/packages/SELEX and matching left an right barcode to either CTGTCA-21xN-CCCGGG (Hth-R) or TGACAG-21xN-CCCGGG (Hth-F).
ChIP-Seq: Deposited fastq files contain the merged and demultiplexed files from the four separate NextSeq 500 sequening lanes.
Files were aligned using bowtie-2 to the D. melanogaster genome version dm6.
Aligned sam files were next converted into bam files, sorted and cleared from duplicate reads using the samtools functions view, sort and rmdup. The sorted bam files containing unique reads were indexed (Samtools: index) and converted into bigwig files using the bamCoverage function from the Deeptools suite with parameters -bs 1 -e 125.
Peaks were called using the MACS2 function callpeak with input samples as control and parameters -g dm -q 0.01 --nomodel --extsize 125
ATAC-seq: like ChIP-seq but without removing duplicates.
Genome_build: dm6
Supplementary_files_format_and_content: processed data files contain bigwig coverage tracks for all IP and input samples at 1 bp resolution with reads extended by 125bp. The wild-type Exd-V5 peak file used in the study is provided as a bed file containing the peak summit genome coordinates. No processed data are available for SELEX-seq or RNA-seq.

growth_protocol: ChIP-seq & ATAC-seq: D. melanogaster larvae were grown at 25 degree Celsius on molasses food for 5-6 days.

extract_protocol:
SELEX-seq: All samples were assembled at RT for 30 mins. Procedures followed as described previously (Slattery, Cell, 2011; Kribelbauer, Cell Rep, 2017). ChIP-seq: Inverted larvae were cross-linked at room temperature (RT) for 10 min in 10 ml 1% formaldehyde solution buffered with 50mM HEPES (pH=8.0). Samples were quenched with 1 ml 2.5M Glycine and washed for 5 minutes in quench-solution (125 mM glycine, in 1X PBS and 0.01% Triton X-100). Inverted and cross-linked larvae were washed twice with Buffer A (10mM HEPES, pH=8.0; 10mM EDTA, pH=8.0, 0.5mM EGTA, pH=8.0; 0.025 % Triton-X) and twice with Buffer B (10mM HEPES, pH=8.0; 200mM NaCl, 1mM EDTA, pH=8.0; 0.5mM EGTA, 0.01 % Triton X-100). Wing discs were detached on ice in Buffer B and transferred into a final volume of 1 ml Buffer C (10mM HEPES, pH=8.0 ;1mM EDTA, pH=8.0; 0.5mM EGTA, pH=8.0). Chromatin was sheared into fragments by using a probe sonicator at 15 % amplitude (total time: 12 min with 15 seconds on and 40 second off intervals) and flash-frozen in liquid nitrogen for storage at -80℃ until further processing. Sheared chromatin was diluted in 5X RIPA dilution buffer (1x RIPA: 140mM NaCl; 10mM HEPES, pH=8.0; 1mM EDTA, pH=8.0; 1 % Glycerol; 1% Triton X-100; 0.1% DOC) and blocked with 10μg of the respective IgG-coated magnetic beads (Dynabeads, ThermoFisher) for 1h at 4℃. Beads were removed with a magnetic stand and supernatant was transferred into a new tube. 10 % of the sample was set aside to serve as an input control. Specific antibody and 1 % of Bovine Serum Albumine (BSA) was added to the remaining chromatin and incubated over night at 4℃. 30 μg of IgG-coated and pre-blocked (with 1 % BSA) Dynabeads were added to each chromatin antibody solution and incubated for another 2 hours. Antibody-bound TF-chromatin complexes were isolated by magnetic separation (5 min on a magnetic stand) and beads were washed twice with 1x RIPA, once with high salt RIPA (500mM NaCl), once with LiCl-Buffer and once with TE (10 mM Tris-Base, pH=8.0; 1mM EDTA, pH=8.0). Beads with chromatin and the input sample were redissolved in 0.5 ml Elution-Buffer (TE with 0.5 % Sodium Dodecyl Sulfate (SDS) and 50mM NaCl) and incubated for 30 min at 37℃ with RNase, followed by 2 hours at 55℃ with proteinase K (ThermoFisher). Remaining DNA-protein complexes were decrosslinked by incubating for 16 hours at 65℃. DNA was separated from the Dynabeads by magnetic separation and purified by phenol:chloroform extraction and DNA precipitation using 1x volume of isopropanol in 100mM ammonium acetate and 1 μl glycogen. Precipitated DNA was redissolved in 30 μl TE. ATAC-seq: Wing imaginal discs of third instar larvae were dissected from a lab stock of yw genotype in Phosphate-Buffered-Saline. Discs were washed in nuclear extraction buffer (NEB, 10nM HEPES pH. 7.5, 2.5mM MgCL2, 10mM KCl) and placed in a 1mL dounce homogenizer (Wheaton) on ice. Discs were treated with 15 strokes of the loose pestle, followed by a 10 minute incubation on ice, then 20 strokes of the tight pestle. Nuclei were counted using a hemocytometer, and 50,000 nuclei were transferred to a fresh Eppendorf containing 1mL of NEB buffer +0.1% tween-20. Following a brief mixing the nuclei were immediately pelleted for 10 min at a speed of 1000xg. The pellet was re-suspended in ATAC transposition buffer as in (Buenrostro et al., 2015) and tagmentation was carried out as previously described (Buenrostro et al., 2015). Amplified libraries were purified, and size-selected using  ampureXP (Beckman) beads for  a double-sided selection.
Extrated SELEX-seq libraries were amplified using Illumina compatible amplification primers (Illumina small RNAseq or NEBNext Mulitplex Oligos). ChIP-seq and ATAC-seq libraries were constructed using the NEBNext Ultra DNA Library Prep Kit for Illumina with NEBNext Mulitplex Oligos (one separate index per sample) following standard instructions. Libraries were sequenced either at the NY Genome Center (HiSeq-2000) or at Columbia University (NextSeq 500, 75 bp kit).

value: Hth-FL; Exd; Dfd


title: T-27

status: Public on Jan 27 2020

type: SRA

city: Uppsala

first: Fredrik

middle: Johansson

last: Swartling

address: Dag Hammarskjölds väg 20

department: Immunology, Genetics and Pathology

country: Sweden

institute: Uppsala University

library_source: transcriptomic

data_processing:
Base calling was performed using standard parameters in build-in software provided with the Ion Torrent Proton sequencer (Torrent suite ver.5.2.2).
Sequenced reads were mapped to hg19_AmpliSeq_Transcriptome_ERCC_v1 using standard parameters and build-in software provided with the Ion Torrent Proton sequencer  (Torrent suite ver.5.2.2).
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file include gene symbol and raw counts.

molecule: total RNA

organism: Homo sapiens

source_name: tumor biopsy

extract_protocol:
RNA from fresh-frozen tumor biospy, alternatively from 10^6 cells, was extracted according to QUIAGEN RNEasy extraction protocol
Library was prepared according to Thermo Fisher Scientific protocol for AmpliSeq next generation sequencing application

tag: sample type

value: TUMOR hbNES (MYCN-WT)


title: CTRL-3

type: genomic

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina MethylationEPIC_v-1-0 DNA analysis BeadChip using standard Illumina protocol

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

data_processing: Illumina Genome Studio software; main result of the methylation assays is shown as a beta-value ranging from zero to one indicating 0 to 100% methylation for each interrogated locus

label: Cy3, Cy5

molecule: genomic DNA

label_protocol: Standard Illumina protocol

extract_protocol: DNA from fresh-frozen tumor biospy, alternatively from 10^6 cells, was extracted according to QUIAGEN DNEasy Blood and Tissue extraction protocol

value: brain tumor biopsy


title: 4970_2_gNT_UT_R2

city: Amsterdam

first: Sander

last: Palit

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute

data_processing:
Deseq2 was used for RNA-seq data normalization.
The differential expression was based on the ratio of normalized read counts (FPKM, after library size correction).
An absolute fold-change threshold of 2 was used. Genes with a coverage <50 in both conditions were excluded from the analyses to prevent spurious results.
Genome_build: hg38
Supplementary_files_format_and_content: readcountfiles: tab-separated gene counts and gene annotation for all samples

source_name: LNCaP_sgNT UT

growth_protocol: LNCaP cells harboring CRISPR constructs were cultured in RPMI (+10% FBS, +1% pen/strep) at 37C in 5% CO2.

extract_protocol:
RNA extraction using Trizol
Stranded RNA libraries were prepared for sequencing according to Illumina instructions

treatment_protocol: Cells were plated (500 000 cells / 10cm dish) in RPMI (+10% FBS, +1% pen/strep) at 37C in 5% CO2. Next day, enzalutamide (10 uM) or vehicle was added, and cells were cultured for 5 days (medium was refreshed daily) before harvesting using Trizol.

tag: cell line

value: LNCaP

tag: cell type

value: prostate cancer cell line

tag: genotype/variation

value: control (sgNT)

tag: treatment

value: vehicle for 5 days


title: 2LCO HpaII (Ly1)

city: Bronx

first: Amit

last: Verma

state: NY

address: 1300 Morris Park Ave

department: Medicine

country: USA

institute: Albert Einstein College of Medicine

library_source: genomic

data_processing:
Library strategy: HELPGT
Images generated by the Illumina sequencer were analyzed by Illumina pipeline software (versions 1.3-1.4). Initial data processing was performed using the default read length of 36 bp, after which we isolated the sequences in which we found adapter-tags on the 3’-end, replaced the tag sequence with a poly(N) sequence of the same length), and re-ran the Illumina ELAND pipeline again on these sequences with the sequence length set at 27 bp (the 2-28 bp subsequence).
The data within the ELAND_extended.txt files were used for counting the number of aligned sequences adjacent to each CCGG (HpaII/MspI) site annotated in the hg19 freeze of the human genome at the UCSC genome browser. We permitted up to two mismatches in each sequence, and allowed a sequence to align to up to a maximum of 10 locations within the genome. For non-unique alignments, a sequence was assigned a partial count for each aligment location amounting to 1/n, where n represents the total number of aligned positions.
Genome_build: hg19
Supplementary_files_format_and_content: Hcount format; col1:  unique identifier for CCGG site;  col2: chromosome; col3: base position; col4: #reads mapped to this location on the forward strand; col5: #reads mapped to reverse strand; col6: #total reads mapped

extract_protocol: Genomic DNA from cell lines were isolated by Puregene Core Kit A (Qiagen) Two custom adapters were created for HELP-tagging, referred to as AE and AS. As well as an Illumina adapter sequence, adapter AE contains an EcoP15I recognition site and a T7 promoter sequence. Adapter AS contains an Illumina sequencing primer sequence. Five micrograms of genomic DNA were digested with HpaII and MspI in separate 200 μl reactions and purified by phenol/chloroform extraction followed by ethanol precipitation. The digested genomic DNA was ligated to adapter AE using an NEB Quick Ligation Kit (25 μl of 2x Quick ligase buffer, 3 μg of HpaII-digested DNA or 1 μg of MspI-digested DNA, 0.1 μl of Adapter AE (1 μM), 3 μl of Quick Ligase in a final volume of 50 μl). After AE ligation, the products were purified using AMpure (Agencort), then digested with EcoP15I (NEB). The restriction fragments were end-repaired to inhibit to dimerization of adapters, and tailed with a single dA, at the 3’ end. After the dA tailing reaction, adapter AS was ligated to the dA-tailed fragments using an NEB Quick Ligation Kit (25 μl of 2x Quick ligase buffer, 2.5 μl of Adapter AS (10 μM), 2.5 μl of Quick Ligase in a final volume 50 μl). After ligation, products were purified using the MinElute PCR purification kit (Qiagen) and in vitro-transcribed using MEGAshortscript (Ambion). Following in vitro transcription, products were purified with an RNeasy clean-up kit (Qiagen) before reverse transcription was performed using the SuperScript III kit (Invitrogen). The first strand cDNA produced was used as a template for PCR using the following conditions: 96°C for 2 minutes, then 18 cycles of 96°C for 15 seconds and 72°C for 15 seconds followed by 5 minutes at 72°C for the final extension. After PCR, the library was purified using a QIAQuick PCR clean-up kit (Qiagen).

tag: protocol

value: HpaII

value: control

value: b-cell lymphoma


title: T-15

value: TUMOR NES-1 (MYCN-WT)


title: 4970_1_gNT_UT_R1


title: T-16


title: 1LVC HpaII (Ly1)

value: ascorbic acid


title: 1LCO MspI (Ly1)

value: MspI


title: R1_Hth_Exd_Dfd_wt_Lib21_HthF_HthR_SELEX_seq

city: New York City

first: Harmen

middle: J

last: Bussemaker

state: New York

address: 1212 Amsterdam Avenue, MC 2441

department: Biological Sciences

institute: Columbia University

organism: Drosophila melanogaster


title: 11_S15_L003: RNA-seq HUDEP2 MBD2KO post-differentiation rep2

city: Richmond

first: Gordon

middle: D

last: Ginder

state: VA

address: 401  College St

department: Massey Cancer Center

institute: Virginia Commonwealth University

description: RNA-seq

data_processing:
All samples were sequenced on the Illumina HiSeq 2500 according to Illumina’s sequencing-by-synthesis protocol. Samples were sequenced at ~21 million 125bp paired-end reads. Sequencing adapters was removed using Trimmomatic [1]. Quality control at each processing step was performed using the FastQC tool (quality base calls, CG content distribution, duplicate levels, complexity level) [2].
Paired-end reads were aligned to the latest assembly of the human genome (GRCh38/hg38) using the subread v.1.6.2 aligner [3]. We obtained gene counts for each sample based on the last hg38 version of Ensembl transcriptome (v.87) using the featureCounts v.1.2.6 software [4]. RNA-seq counts were preprocessed and analyzed for differential expression using the edgeR v.3.18.1 [5] R package. P-values for differentialy expressed genes was corrected using a False Discovery Rate (FDR) multiple testing correction method [6].
References: 1. Bolger AM, Lohse M, Usadel B: Trimmomatic: A flexible trimmer for illumina sequence data. Bioinformatics 2014, 30:2114–2010.1093/bioinformatics/btu170.; 2. Andrews S, others: FastQC: A quality control tool for high throughput sequence data. Reference Source 2010,.; 3. Liao Y, Smyth GK, Shi W: The subread aligner: Fast, accurate and scalable read mapping by seed-and-vote. Nucleic Acids Res 2013, 41:e10810.1093/nar/gkt214.; 4. Liao Y, Smyth GK, Shi W: FeatureCounts: An efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 2014, 30:923–3010.1093/bioinformatics/btt656.; 5. Robinson MD, McCarthy DJ, Smyth GK: EdgeR: A bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 2010, 26:139–4010.1093/bioinformatics/btp616.; 6. Benjamini Y, Hochberg Y: Controlling the false discovery rate: A practical and powerful approach to multiple testing. Journal of the royal statistical society. Series B (Methodological) 1995,:289–300.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: Text format, gene counts, generated using featureCounts

source_name: HUDEP2 cell line

growth_protocol: HUDEP-2 cells were maintained and expanded in StemSpan SFEM II supplemented with 50ng/mL SCF, 3IU/mL EPO, 10-6M of DEX, 1ug/mL of DOX, 1% L-Glutamine and 2% penicillin/streptomycin (expansion medium). To induce erythroid differentiation, HUDEP-2 cells were cultured for 5 days in Iscove's Modified Dulbecco's Media (IMDM) supplemented with 3IU/mL EPO, 1ug/mL DOX, 10ug/mL human recombinant insulin, 3IU/mL heparin, 0.5mg/mL of holo-transferrin, 5% human AB serum, 2% penicillin/streptomycin, and 1% L-Glutamine (differentiation medium).

extract_protocol:
Total RNA was extracted from 107 MBD2KO or sgSCR HUDEP-2 cells before and after 3 days of erythroid differentiation using the mirVana miRNA Isolation Kit (Invitrogen) according to the manufacturer’s protocol, followed by DNaseI treatment.
Library preparation was performed by the Brigham Young University DNA Sequencing Center using the TruSeq Stranded Total RNA with Ribo-Zero Globin Kit (Illumina).

treatment_protocol: See characteristics: Culture media

tag: genotype

tag: differentiation stage

value: late basophilic erythroblast

tag: culture media

value: IMDM + Human AB serum, EPO, DOX, Insulin, Heparin, HTF, L-Glu


title: 12_S16_L003: RNA-seq HUDEP2 MBD2KO post-differentiation rep3

description: RNA-seq


title: 528_87_CDDA_Chol_1pc_week_12

city: Biberach a.d. Riss

first: Eric

last: Simon

address: Birkendorfer Str. 65

country: Germany

institute: Boehringer Ingelheim Pharma GmbH & Co KG

data_processing:
Sequenced read quality was checked with FastQC v0.11.2
RNA-Seq reads from all samples were aligned to the genome using the STAR Aligner v2.5.2a11
Duplication rates of the RNA-Seq samples were computed with bamUtil v1.0.11 to mark duplicate reads and the dupRadar v1.4 Bioconductor R package for assessment
The gene expression profiles were quantified using Cufflinks software version 2.2.114 to get the Reads Per Kilobase of transcript per Million mapped reads (RPKM) as well as read counts from the feature counts software package
Genome_build: Rat Genome (Ensembl Version 86)
Supplementary_files_format_and_content: tab-delimited text files contain RPKM values for each sample

molecule: polyA RNA

organism: Rattus norvegicus

source_name: Liver CDDA Cholesterol 1pc week 12

extract_protocol:
see Tolbol, K. S. et al. Disease Progression and Pharmacological Intervention in a Nutrient-Deficient Rat Model of Nonalcoholic Steatohepatitis. Dig Dis Sci, doi:10.1007/s10620-018-5395-7 (2018).
RNA quality and concentration was measured using the Fragment Analyzer from AATI (now Agilent) with the total RNA Standard Sensitivity protocol. The Sequencing library was prepared from 200 ng total RNA with the TruSeq® Stranded mRNA LT-Set B (RS-122-2102, Illumina Inc., San Diego, CA) producing a 275bp fragment including adapters in average size. In the final step before sequencing, seven individual libraries were normalized and pooled together using the adapter indices supplied by the manufacturer. Pooled libraries have been clustered on the cBot Instrument from Illumina using the HiSeq® 3000 GD-410-1001 3000/4000 SR Cluster Kit (Illumina Inc., San Diego, CA).
Sequencing was performed as 85bp single-end reads and 7 bases index read on an Illumina HiSeq3000 instrument at a sequencing depth of approximately 60 million reads per sample using FC-410-1001, HiSeq® 3000/4000 SBS Kit (50 cycles, Illumina Inc., San Diego, CA).

treatment_protocol: Male Wistar rats (RjHan:WI, 6 weeks of age, 200–250 g) were obtained from Janvier Labs (Le Genest-Saint-Isle, France) and housed pairwise in a controlled environment (21 °C ± 2 °C, humidity 50% ± 10%) with a 12-h light/dark cycle fed with choline-deficient l-amino acid-defined (CDAA, kcal %; protein 11%, fat 31%, carbohydrates 58%) diet supplemented with 1% cholesterol (CDAA + 1%chol, E15666-94). CDAA diets was low in methionine (0.17%) compared to the CSAA diet (0.4%). All diets were obtained from ssniff Spezialdiäten GmbH (Soest, Germany)

tag: animalid

tag: diet

value: CDDA Cholesterol 1pc

tag: timepoint

value: week 12

tag: gender

value: male

tag: strain

value: Wistar

tag: tissue

value: liver


title: 1LCO HpaII (Ly1)


title: R0_Hth_Exd_wt_mut_Lib16_SELEX_seq

description: To extract reads from fastq file match each fastq entry to the following library design: TGGGCCTGG-16xN-CCAGG

value: initial pool


title: S10 RPM

city: Vienna

first: Matthias

last: Hackl

state: Austria

address: Leberstrasse 20

country: Austria

institute: TAmiRNA GmbH

data_processing:
Data quality was assessed using fastqc (0.10.1)
Sequential alignments against reference databases was conducted using bowtie 2 (2.2.6)
file converstions were performed using samtools (1.2)
Reference for microRNA annotations was miRBase version 20 (http://www.mirbase.org)
Genome_build: GRCh37
Supplementary_files_format_and_content: Excel sheet containing tags per million total reads (per lane) for microRNAs annotated in miRBase version 20. One row per microRNA (total 382), one column per sample (total 16).

source_name: Glioblastoma FFPE

growth_protocol: not applicable

extract_protocol:
Total RNA was extracted from FFPE samples using the Qiagen miRNeasy kit (Qiagen, Germany). RNA was eluted in 30 µl nuclease-free water, quantified using the RiboGreen RNA assay, and 200 ng total RNA were used for library preparation.
Ligation of 3‘ and 5‘ adapters, reverse transcription and PCR amplification (17 cycles) was performed using the NEBNext small RNA Kit. Libraries were pooled using equimolar amounts of miRNA peaks, followed by gel purification of 16-50 nucleotide (nt) fragments.

tag: survival

value: Long

value: Control


title: 528_88_CDDA_Chol_1pc_week_12


title: T-35

value: TUMOR NES-2 (MYCN-WT)


title: 528_86_CDDA_Chol_1pc_week_12


title: S12 RPM


title: 9_S13_L003: RNA-seq HUDEP2 sgSCR post-differentiation rep3

description: RNA-seq

value: WT


title: 528_85_CDDA_Chol_1pc_week_12


title: S14 RPM


title: T-17


title: S5RPM


title: 528_84_CDDA_Chol_1pc_week_12


title: 8_S12_L003: RNA-seq HUDEP2 sgSCR post-differentiation rep2

description: RNA-seq


title: 528_83_CDDA_Chol_1pc_week_12


title: 7_S11_L003: RNA-seq HUDEP2 sgSCR post-differentiation rep1

description: RNA-seq


title: XN984-4

data_processing:
Base calling was performed using standard parameters in build-in software provided with the Ion Torrent Proton sequencer (Torrent suite ver.5.2.2).
Sequenced reads were mapped to hg19_AmpliSeq_Transcriptome_ERCC_v1 using standard parameters and build-in software provided with the Ion Torrent Proton sequencer  (Torrent suite ver.5.2.2).
RPM were calculated using internal built-in software provided with the Ion Torrent Proton sequencer (Torrent suite ver.5.2.2)
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file include gene symbol and gene expression in RPM for each sample.

source_name: PDX (tumor)

value: patient-derived medulloblastoma xenograft (SHH)


title: XN984-1


title: 6_S10_L003: RNA-seq HUDEP2 MBD2KO pre-differentiation rep3

description: RNA-seq

value: early basophilic erythroblast

value: SFEM + SCF, EPO, DEX, DOX, L-Glu


title: S13 RPM

value: Short


title: XN1572-3

value: patient-derived medulloblastoma xenograft (G3)


title: 528_82_CDDA_Chol_1pc_week_12


title: T-18

value: TUMOR NES-1 (MYCN-WT)


title: 10_S14_L003: RNA-seq HUDEP2 MBD2KO post-differentiation rep1

description: RNA-seq

value: late basophilic erythroblast

value: IMDM + Human AB serum, EPO, DOX, Insulin, Heparin, HTF, L-Glu


title: S4 RPM


title: 528_81_CDDA_Chol_1pc_week_12

value: CDDA Cholesterol 1pc

value: week 12


title: 4_S8_L003: RNA-seq HUDEP2 MBD2KO pre-differentiation rep1

description: RNA-seq


title: 5_S9_L003: RNA-seq HUDEP2 MBD2KO pre-differentiation rep2

description: RNA-seq


title: T-32


title: 3_S7_L003: RNA-seq HUDEP2 sgSCR pre-differentiation rep3

description: RNA-seq


title: S11 RPM

value: DC Immunotherapy


title: MB511-4


title: 2_S6_L003: RNA-seq HUDEP2 sgSCR pre-differentiation rep2

description: RNA-seq


title: 528_71_CSAA_week_12

source_name: Liver CSAA week 12

treatment_protocol: Male Wistar rats (RjHan:WI, 6 weeks of age, 200–250 g) were obtained from Janvier Labs (Le Genest-Saint-Isle, France) and housed pairwise in a controlled environment (21 °C ± 2 °C, humidity 50% ± 10%) with a 12-h light/dark cycle fed with choline-supplemented l-amino acid-defined (CSAA; E15668-04, kcal %; protein 12%, fat 16%, carbohydrates 72%) control diet

value: CSAA

value: male

value: Wistar

value: liver


title: MB511-107


title: S15 RPM

value: Long


title: 528_69_CSAA_week_12


title: 1_S5_L003: RNA-seq HUDEP2 sgSCR pre-differentiation rep1

description: RNA-seq

value: WT


title: MB211-9


title: MB211-7


title: RCMB40-2


title: S3 RPM

value: Control


title: BT084-5

value: patient-derived medulloblastoma xenograft (SHH)


title: S7 RPM


title: Mouse HSC H3K27ac 1 month recovery

city: La Jolla

first: Tatiana

last: Kisseleva

address: 9500 Gilman Dr

department: School of Medicine

institute: UCSD

description: H3K27ac ChIP-seq in 1 month recovery mouse HSCs

data_processing:
For Chip-seq Basecalling, demultiplexing, and adapter trimming was performed using Illumina's bcl2fastq (v2.17.1.14).  For RNA-seq Base-calling was performed using Illumina Real Time Analysis RTA 1.18.64 with default parameters
ChIP-seq reads were aligned to the mouse (mm10) or human (hg38) genomes using bowtie2 (Langmead and Salzberg, 2012), keeping only reads that map to a single unique genomic location for further analysis (MAPQ > 10). ChIP-seq peaks were called using HOMER’s findPeaks program using “-mode histone” (histone marks, Pol II) using default parameters.  For RNA-seq Sequenced reads were mapped to the Mouse Genomes Project GRCm38_68.fa reference genome using STAR v2.5.1a with default parameters
For RNA-seq Read quantification was performed with RSEM v1.3.0 and Ensembl annotation Mus_musculus.GRCm38.68.gtf
Genome_build: Chip-seq hg38, mm10.  RNA-seq GRCm38.68
Supplementary_files_format_and_content: processed data is in supplementary file, which is a comma-separated text file containing a matrix of read counts for each gene accession number and sample

organism: Mus musculus

source_name: primary mouse HSCs

growth_protocol: Primary murine or human HSCs were cultured in Dulbecco’s modified Eagle’s medium (DMEM Life Technologies, 11965-092) supplemented with 10% FBS (Corning, 35-011-CV) and 1% Antibiotic-Antymycotic (Life Technologies #15240-062).

extract_protocol:
For Chip-seq Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody. Alternatively, DNA was phenol/chloroform-extracted from MNase-treated nuclei, and 134-154 bp long fragments were extractred from a 2% agarose gel. For RNA-seq Total RNA was isolated using Purelink RNA Mini Kit (Life Technologies)
For Chip-seq Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation, ChIP DNA was PCR-amplified with Illumina primers for 12-16 cycles and library fragments of 200-300 bp (ChIP) (insert plus adaptor and PCR primer sequences) were isolated from a 2% agarose gel. For MNase-Seq, size-selected mononucleosome-derived DNA fragments were ligated to modified adapters that incorporate both the adapter sequence as well as the primer landing sites for the flow cell-conjugated primers. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer or Genome Analyzer II following the manufacturer's protocols. For RNA-seq Illumina Stranded Total RNA (Illumina 20020597)

treatment_protocol: shRNA-expressing lentiviral plasmids were co-transfected with plasmids pVSV-G and pCMVd8.2 dvpr into 293T cells. Viral containing media were collected 72 h later, filtered (0.22-μm pore size), concentrated by ultracentrifugation, and purified on a sucrose 20% gradient. Viral titers were measured using immunocapture p24-gag ELISA (Sequencing core facility, LJI). For viral transduction, lentiviral vectors at a multiplicity of infection (moi) of 30 + polybrene (10 μg/ml) were added to primary mHSCs (60-70% confluency, 24h after plating) for 36 hours, afterward fresh media containing ± puromycin (5 μg/ml) was added to infected cells for 48 hours. mHSCs were harvested, gene silencing was analyzed by qRT-PCR and RNA-Seq. Multiple shRNA hairpins were tested: ETS1 (n=5), ETS2 (n=10), NF1 (n=4), NF2 (n=5), GATA4 (n=5), GATA6 (n=5), IRF1 (n=7), IRF2 (n=10). A minimum of two target sequences with the least off-target knockdowns was selected for each gene (Suppl. Table 1), compared to non-coding hairpins. Infection with SHC-002 (CTRL1) was used as a control for targeting NF1/2, ETS1/2, GATA4/6 in mHSCs; SHC-202 (CTRL2) was used as a control for targeting IRF1/2 in mHSCs. CTRL1 (-) or CTRL2 (-) corresponds to SHC-002 (or SHC-202)-infected cells without purimycin treatment.

tag: strain background

value: Hepatic stellate cells isolated from mouse liver

tag: disease stage

value: 1 month recovery

tag: chip antibody

value: H3K27ac (Active Motif 39133)


title: S9 RPM

value: Short


title: 528_72_CSAA_week_12


title: 528_68_CSAA_week_12


title: Mouse HSC H3K27ac activated

description: H3K27ac ChIP-seq in activated(CCL4 treated) mouse HSCs

tag: cell type

value: activated (CCl4 treated)


title: A4-20M

source_name: metastasis (cell line)

tag: sample type

value: spinal cord metastasis derived cell line


title: 528_67_CSAA_week_12


title: Mouse HSC H3K27ac 1 week recovery

description: H3K27ac ChIP-seq in 1 week recovery mouse HSCs

value: 1 week recovery


title: S16 RPM

tag: treatment


title: 528_66_CSAA_week_12

value: week 12


title: Mouse HSC H3K27ac quiescent

description: H3K27ac ChIP-seq in quiescent mouse HSCs

value: quiescent


title: 528_70_CSAA_week_12

value: CSAA


title: S6 RPM

value: DC Immunotherapy


title: 528_65_CSAA_week_12

value: male

value: Wistar


title: A6-20-TL

source_name: tumor cell line (cell line)

value: brain tumor derived cell line


title: Mouse HSC input


title: A4-4M


title: Mouse HSC H3K4me2 1 month recovery

description: H3K4me2 ChIP-seq in 1 month recovery mouse HSCs

value: H3K4me2 (Millipore, 07-030)


title: A6-11-TL


title: 528_55_CDDA_Chol_1pc_week_8

source_name: Liver CDDA Cholesterol 1pc week 8

value: CDDA Cholesterol 1pc

value: week 8

value: liver


title: 528_56_CDDA_Chol_1pc_week_8


title: Pooled Male Control

city: New Delhi

first: Ritu

last: Gupta

state: Delhi

address: Dr. B.R.A.IRCH, Ansari Nagar

department: Laboratory Oncology

country: India

institute: All India Institute of Medical Sciences, New Delhi

description: Normal Control

data_processing:
3' adaptor sequences are removed from the data
16 – 35 bp length filtering has been done
For trimming, alignment, consolidated counts, miRDeep* was used
For reads processing for normalization, differential expression, DESeq2 was used
Genome_build: GRCh37 and miRNet (miRBase v21)
Supplementary_files_format_and_content:  Processed data files are provided in excel format as obtained by DESeq 2 and contains the probable miRNA sequences with abundance.

source_name: Peripheral Blood

extract_protocol:
Total RNA was extracted from peripheral blood mononuclear cells of CLL patients and 19+ B cells of healthy controls using the mirVana miRNA isolation kit (Thermofisher Scientific, MA, USA) . RNA quality/quantity and  miRNA quality/quantity was assessed using RNA 6000 Nano kit and small RNA kit respectively (Agilent technologogies, Santa Clara, USA) on Agilent 2100 bioanalyzer.
For sequencing, libraries were generated using the IlluminaâTruSeqÔsmall RNA sample preparation kit (Illumina, San Diego, CA, USA). Briefly,  RNA adapters were ligated to 1 mg of total RNA. The ligated RNA was reverse transcribed to generate cDNA using RT primer, dNTP Mix, DTT, RNase Inhibitor and SuperScript II Reverse Transcriptase. The cDNA libraries were amplified using PCR to selectively enrich RNA fragments with adapter molecules. The resulting PCR products were purified using Ampure XP magnetic beads (Beckman Coulter) and run on a pre-cast agarose gel (Thermofisher Scientific, MA, USA). The gels were then extracted along the 160 bp RNA ladder band and the bottom of the 145 bp from the gel using the Mini Elute Qiagen Gel-Extraction Kit following the manufacturer’s protocol (Qiagen, CA, USA). The quality and concentration of the libraries was assessed using the Qubit (Thermofisher Scientific, MA, USA) and DNA high sensitivity chip (Agilent Technologies, Santa Clara, USA). The libraries were then mixed at equimolar concentration.

tag: age

value: Age matched pooled control

tag: Sex

value: M


title: Mouse HSC H3K4me2 1 week recovery

description: H3K4me2 ChIP-seq in 1 week recovery mouse HSCs

value: Hepatic stellate cells isolated from mouse liver


title: A6-13-TL


title: 4970_10_gTLE3_Enza_R1

source_name: LNCaP_sgTLE3 ENZ

tag: cell line

value: LNCaP

value: prostate cancer cell line

tag: genotype/variation

value: TLE3KO (sgTLE3)

value: 10 uM enzalutamide for 5 days


title: Pooled Female Control

description: Normal Control

value: F


title: 528_54_CDDA_Chol_1pc_week_8

tag: animalid


title: 528_53_CDDA_Chol_1pc_week_8

tag: diet


title: A6-13-T

source_name: tumor biopsy (tumor)

value: brain tumor biopsy


title: S8 RPM

value: Short

value: DC Immunotherapy


title: A6-20-T


title: CL253

description: CLL

tag: rai stage


title: Mouse HSC H3K4me2 quiescent

description: H3K4me2 ChIP-seq in quiescent mouse HSCs

value: quiescent


title: Mouse HSC H3K4me2 activated

description: H3K4me2 ChIP-seq in activated(CCL4 treated) mouse HSCs

value: activated (CCl4 treated)


title: CL183

description: CLL


title: 528_52_CDDA_Chol_1pc_week_8

tag: timepoint

tag: gender

value: male

value: Wistar


title: S2 RPM


title: A6-11-T


title: R1_Hth_ExdShapeMut_Lib16_SELEX_seq

value: Hth-FL; Exd (R2A & R5A)


title: CL191

description: CLL


title: S1 RPM


title: 528_51_CDDA_Chol_1pc_week_8

value: CDDA Cholesterol 1pc

value: week 8

tag: strain

tag: tissue

value: liver


title: A6-10-T


title: R2_Hth_ExdShapeMut_Dfd_Lib21_HthF_HthR_SELEX_seq

value: Hth-FL; Exd (R2A & R5A); Dfd


title: 528_50_CDDA_Chol_1pc_week_8


title: R2_HthShapeMut_Exd_Dfd_Lib21_HthF_HthR_SELEX_seq

value: Hth (K3A & K4A & R5A)-FL; Exd; Dfd


title: A3-33-TL

value: brain tumor derived cell line


title: CL152

description: CLL


title: A3-24-TL


title: 528_49_CDDA_Chol_1pc_week_8


title: R1_Hth_Exd_wt_Lib16_SELEX_seq

value: Hth-FL; Exd


title: A7-15-T

value: TUMOR hbNS (MYCN-T58A)


title: R2_Hth_Exd_Dfd_wt_Lib30_SELEX_seq

description: To extract reads from fastq match each fastq entry to the following library design: TGG-30xN-CCCGGG

value: Hth-FL; Exd; Dfd


title: 528_40_CSAA_week_8

source_name: Liver CSAA week 8

value: CSAA


title: A3-24-T

value: brain tumor biopsy


title: 528_39_CSAA_week_8


title: R0_Hth_Exd_Dfd_wt_Lib30_SELEX_seq

value: initial pool


title: CL167

description: CLL

value: M


title: 528_38_CSAA_week_8


title: CL154

description: CLL


title: CL172

description: CLL


title: R0_Hth_Exd_Dfd_wt_mut_Lib21_HthF_HthR_SELEX_seq


title: 528_37_CSAA_week_8


title: A3-22-T


title: CL105

description: CLL


title: A3-45-TL


title: shRIPK3#2, biological rep 3

city: Durham

first: Jen-Tsan

last: Chi

state: NC

address: 101 Science Dr., 2133 CIEMAS Box 3382 DUMC

department: Center for Genomic and Computational Biology

institute: Duke University

data_processing:
FastQC was used for confirming quality of sequencing reads.
Sequenced reads were mapped to mm9 reference genome using Hisat2 with default parameters
Quntification of read counts of genes were performed using HTSeq
DESeq2 were applied for differential analysis to compare gene expressions between conditions.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include results of differential analysis using DESeq2.

source_name: Her2 driven murine model of MTB/TAN tumor after the recurrence (recurrent tumors).

growth_protocol: Dox-inducible Her2 driven murine model of MTB/TAN cells were grow in DMEM media with 4.5g/L glucose and 4mM glutamine (11995-DMEM, ThermoFisher Scientific) and supplement with 10ng/ml mouse EGF and 5ug/ml bovine insulin and 10% heat-inactivated fetal bovine serum (Hyclone #SH30070.03HI) in humidified incubator, 37°C with 5% CO2

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen, #74104) according to the manufacturer's instructions.
1μg of total RNA was used to generate cDNA library with Illumina TruSeq Stranded mRNA LT Sample Prep Kit – Set A (Illumina, RS-122-2101) according to manufacturer’s instructions.

treatment_protocol: Recurrent cells were infected by lentivius with non-targeting shRNA control or shRIPK3.

value: breast cancer cell

value: MTB/TAN

tag: shRNA


title: CL53

description: CLL

value: F


title: 528_36_CSAA_week_8

value: male

value: Wistar


title: CL213

description: CLL


title: shRIPK3#2, biological rep 2


title: A3-43-TL


title: 528_35_CSAA_week_8

value: week 8


title: A3-33-T


title: H3K4me3_KO2_input

city: Copenhagen

first: Aditya

last: Sankar

email: cnj376@ku.dk, aditya.sankar@embl.de

address: Ole Maaloes Vej 5

department: Biotech Research and Innovation Centre

country: Denmark

institute: University of Copenhagen

data_processing:
Reads were trimmed using Trimmomatic and the settings ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:4:20 HEADCROP:15 CROP:120 MINLEN:40 for H3K4me3 and SLIDINGWINDOW:4:20 HEADCROP:5 CROP:50 MINLEN:30 for H3K9me3 data
ChIP-seq reads were aligned to the mm10 genome assembly using bowtie2 (Langmead B, Salzberg S. Nature Methods. 2012, 9:357-359.) and the settings --local -X 2000 and sorted using samtools (Li et al, Bioinformatics. 2009, 15;25(16):2078-9).
Mapped reads were imported into EaSeq (Lerdrup et al, Nature Structural & Molecular Biology, 2016, 23, 349–357) for subsequent analysis and generation of wig-files.
Genome_build: mm10
Supplementary_files_format_and_content: Gzip compressed wig files generated using EaSeq (http://easeq.net); Scores represent fragments per kilobasepairs per million reads

source_name: MII oocytes

growth_protocol: MII oocytes were isolated from, crosslinked and frozen for Chip according to previously published protocol (PMID: 27626377)

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Qiagene Ultra low input library preperation kit (180492) according to manufacturers instructions and quantified using KAPA library quantification kit from Roche (07960298001)

treatment_protocol: Antibodies

tag: genotype

value: Kdm4a knockout (m-/p-)

value: MII oocytes

tag: pooled numbers


title: shRIPK3#2, biological rep 1


title: 528_34_CSAA_week_8

value: liver


title: A3-41-TL

value: brain tumor derived cell line


title: CL240

description: CLL


title: CL187

description: CLL


title: 528_33_CSAA_week_8


title: A3-45-T


title: shRIPK3#1, biological rep 3


title: CL219

description: CLL


title: shRIPK3#1, biological rep 2


title: shRIPK3#1, biological rep 1


title: A3-42-T


title: A3-44-T


title: CL214

description: CLL


title: A3-43-T


title: non-targeting shRNA control, biological rep 3

value: non-targeting shRNA control


title: 528_23_CDDA_Chol_1pc_week_4

source_name: Liver CDDA Cholesterol 1pc week 4

value: CDDA Cholesterol 1pc

value: week 4


title: A3-41-T


title: 528_21_CDDA_Chol_1pc_week_4


title: CL203

description: CLL


title: A3-40-T


title: 528_22_CDDA_Chol_1pc_week_4


title: CL176

description: CLL


title: non-targeting shRNA control, biological rep 2


title: non-targeting shRNA control, biological rep 1


title: CL164

description: CLL


title: CL156

description: CLL


title: A2-49-T


title: CF patient 2 Sample visit 3

city: Braunschweig

first: Diego

last: Chaves-Moreno

address: inhoffenstrasse 7

department: Department of Medical Microbiology (MMIK)

institute: Helmholtz Centrum for Infection Research

data_processing:
Cluster generation on HiSeq SR Flow Cell v3 generated at cBot using TruSeq SR Cluster Kit v3 – HS to create single- molecule DNA templates followed by bridge amplification. Sequencing run performed at HiSeq 2500 using TruSeq SBS Kit v3 (50 cycle) to run 51 cycles and 7 cycles for the single-indexed read.
Reference genome, and features files were obtained from S. aureus strain: CFBR-105, accession:GCA_003431365.1 wich were downloaded from the ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/431/365/GCF_003431365.1_ASM343136v1
Alignment was performed with Bowtie2 (Version: 2.3.4.1) on the very sensitive mode, Sam file was later converted in to Bam for further analysis  via samtools view
R processing of the alignments, 1. Features counts (Subread R package), were loaded from  the gff file and exons were obtained. 2. Sam files were loaded and expression was quantified by the use of the function summarizeOverlaps from the R package GenomicAlignments, ran on the union mode.
RPM values were calculated by the use of the function: returnRPKM form the package systempipeR  (V. 1.16.1 ) and  TPM values were calculated with an in-house function build in R

organism: Staphylococcus aureus

source_name: sputum samples of CF patients

growth_protocol: Sputum amples were collected from CF patients at their visits

extract_protocol:
RNA was extracted using Qiagen's Rneasy Mini Kit following manufacturer's instructions, the where the samples were treated by beat beating in a solution of RLT Buffer (Qiagen) and 1% of β-mercaptoethanol.
ScriptSeq v2 RNA-Seq Library Preparation Kit for Low-input  (Epicentre) according to the manufacturer’s instructions using approximately 20 ng of input RNA
The libraries were size selected in a range of 200-500 bp using Blue Pippin

treatment_protocol: Sputolysin treatment for 30 minutes at 37 celsius degrees

tag: source

value: sputa


title: CL228

description: CLL


title: A2-45-T

tag: sample type

value: brain tumor biopsy


title: 528_24_CDDA_Chol_1pc_week_4


title: CF patient 2 Sample visit 2


title: CL146

description: CLL


title: 528_19_CDDA_Chol_1pc_week_4


title: 528_18_CDDA_Chol_1pc_week_4


title: CF patient 1 sample visit 5


title: A2-44-T


title: 528_17_CDDA_Chol_1pc_week_4


title: CF patient 1 sample visit 2


title: A2-43-T


title: A2-41-T


title: CL236

description: CLL


title: CL244

description: CLL


title: 528_7_CSAA_week_4

source_name: Liver CSAA week 4

value: CSAA


title: CL196

description: CLL


title: CL162

description: CLL

value: M


title: 528_20_CDDA_Chol_1pc_week_4


title: A2-23-T


title: A2-21-T


title: Mac THP1 Dex 5

type: RNA

city: RTP

first: NIEHS

last: Microarray Core

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description:
Cell line differentiated
Gene expression from MØ-THP1 100nM DEx 6H

hyb_protocol: NanoString protocol

scan_protocol: RNA expression was quantified on the nCounter Digital AnalyzerTM.

data_processing: Data were normalized utilizing the manufacturer’s positive and negative experimental control probes, as well as 2 housekeeping genes (HPRT1, PPIA).

label: biotin

source_name: RNA MØ-THP1 100nM Dex 6H 5

label_protocol: 50 ng of each total RNA sample was prepared as per the manufacturer’s instructions.

growth_protocol: Human Monocyte cell line THP-1 were used for differentiation into macrophages with PMA during 3 hours and a time of recovery of 24 hours. Monocytes-THP-1 and macrophages-derived monocyte-THP-1 were maintained during 24 hours with charcoal medium before the Dex treatment for 6 hours.

extract_protocol: RNA samples from all treatments groups (Mono-THP-1 Vehicle and Dex and Macro-THP-1 vehicle and Dex) will be extracted using QIAshredder and RNeasy Mini kit with DNase treatment. The RNA concentration will be determined by Nanodrop and the quality using BioAnalyzer.

treatment_protocol: Monocytes-THP-1 and THP-1-derived macrophages were stimulated with vehicle or 100nM Dexamethasone during 6 hours in stripped medium.

tag: agent

value: Dex

tag: cell type

value: macrophages-derived monocyte


title: 528_5_CSAA_week_4


title: 528_4_CSAA_week_4


title: AF22/MYCN-T58A

source_name: pre-tumor cells (cell line)

value: pre-tumor cell lines


title: 528_3_CSAA_week_4

value: male


title: CL56

description: CLL

tag: age

tag: Sex


title: HB930

source_name: stem cells (cell line)

value: embryo-derived neural stem cells


title: Mac THP1 Control 5

description:
Cell line differentiated
Gene expression from MØ-THP1 Control 6H

source_name: RNA MØ-THP1 Control 6H 5

value: Vehicle

tag: cell line


title: 528_8_CSAA_week_4

tag: animalid

value: Wistar


title: 528_2_CSAA_week_4

tag: diet


title: Mac THP1 Control 3

source_name: RNA MØ-THP1 Control 6H 3


title: CL41

description: CLL

tag: rai stage


title: Sai3

value: embryo-derived neuro-epithelial stem cells


title: 528_1_CSAA_week_4

tag: timepoint

value: liver


title: Sai2


title: Mono THP1 Dex 6

description:
Cell line
Gene expression from THP1 100nM Dex 6H

source_name: RNA-THP1 100nM Dex 6H 6

value: Monocytes


title: Mac THP1 Control 1

source_name: RNA MØ-THP1 Control 6H 1


title: Mono THP1 Dex 3

source_name: RNA-THP1 100nM Dex 6H 3


title: 528_6_CSAA_week_4

tag: gender


title: CTRL-10 NES

value: iPS-derived neuro-epithelial stem cells


title: Mac THP1 Dex 1

source_name: RNA MØ-THP1 100nM DEx 6H 1


title: SDD1.hel2.1

city: Tokyo

first: Yoshitaka

last: Matsuo

address: 4-6-1, Shirokanedai, Minato-Ku

department: IMSUT

country: Japan

institute: The University of Tokyo,

description:
Rnase I footprinting, ribosome pelleting, RNA extraction
Ribosome Profiling

data_processing:
Library strategy: Ribo-seq
Basecalling with Illumina Casava 1.8 software
3' adapter trimming with FastX-toolkit
Library sorting based on sample barcode sequence with custom script
random barcode triming with custom script
rRNA alignment with bowtie2 v2.0.6
Alignment with TopHat v2.0.7 to reporter plasmid p415GPDp-HA-SDD1-V5
Read quantitation using custom scripts
Genome_build: p415GPDp-HA-SDD1-V5
Supplementary_files_format_and_content: text files contain following columns: 1.distance from start codon [nt] ;2.counts of 28 to 30 or 29 to 31 nucleotides long reads at the given position. Asite positions of the reads are asigned.

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae

extract_protocol:
The lysate was treated with RNase I and then subjected to ultracentrifugation for ribosome profiling. Total RNA was extracted by TRIzol reagent from the ribosome pellet.
Ribosome profiling libraries were generated as described in MGlincy, N.J. and Ingolia, N.T., 2017, Methods, 126:112-129 .

tag: genetic background

value: MATa ade2 his3 leu2 trp1 ura3 can1 hel2::natMX4 p415GPD-HA-SDD1-V5


title: SDD1.hel2.2


title: CTRL-3 NES


title: CL85

description: CLL

source_name: Peripheral Blood


title: Mono THP1 Control 6

description:
Cell line
Gene expression from THP1 Control 6H

source_name: RNA-THP1 Control 6H 6


title: AF22


title: Mono THP1 Control 3

source_name: RNA-THP1 Control 6H 3


title: CL50

description: CLL


title: SDD1.WT.1

value: MATa ade2 his3 leu2 trp1 ura3 can1 p415GPD-HA-SDD1-V5


title: SDD1.WT.2


title: HB901


title: Mono THP1 Control 1

source_name: RNA-THP1 Control 6H 1


title: Mono THP1 Dex 2

source_name: RNA-THP1 100nM Dex 6H 2


title: CD45_inhibition_bottom

status: Public on Jan 26 2020

city: New York

first: Neville

last: Sanjana

address: 101 Avenue of the Americas

institute: New York Genome Center

description: sorted bottom 15% of CD45 expression

data_processing:
Samples were demultiplexed based on different biological conditions (read 1) and barcodes specific for each Cas9 variant (read 2)
20 bp sgRNA sequences were extracted from read 1 based on the 5' anchor sequence
sgRNA sequences were  mapped to the reference sgRNA library with one mismatch allowed (bowtie -v 1 -m 1).
Genome_build: hg38
Supplementary_files_format_and_content: Csv files were generated for each biological sample (mix of three Cas9 variants) by bowtie alignment to sgRNA reference sequences. Normalized counts of each sgRNA combined with each Cas9 variant are shown. The normalization was performed by adding a +1 pseudocount to each sgRNA+Cas9 variant pair, dividing each count by the sum of all counts in the sample, multiplying by 10^6 and deriving log2.

growth_protocol: Lentivirus was produced by polyethylenimine linear MW 25000 (Polysciences 23966) transfection of HEK  293FT cells with the transfer plasmid containing a barcoded Cas9 effector and sgRNA library, packaging  plasmid psPAX2 (Addgene 12260) and envelope plasmid pMD2.G (Addgene 12259). After 72 h posttransfection,  cell media containing lentiviral particles was harvested and filtered through 0.45 μm filter  Steriflip-HV (Millipore SE1M003M00). Each sgRNA library and Cas9 effector combination was  transduced into K562 cells individually, to avoid barcode swapping, and thus Cas9 misidentification, during  lentiviral integration (Xie et al., 2018). In total we produced 27 individual lentiviral libraries and transduced  them into separately into K562 cells. The transduction was performed at a multiplicity of infection (MOI)  ~ 0.4 to minimize the fraction of cells with multiple sgRNAs. We maintained 1,000× coverage of each  sgRNA library. Transduced cells were selected with 1 μg ml-1 puromycin for at least 7 days after  transduction. During the course of the screen the cells were maintained at numbers ensuring >1,000×  representation of the library. Transduced cells were maintained as 27 separate cell cultures for 14 days. At  day 14 post-transduction, cells transduced with the sgRNA library targeting the same gene and the same  CRISPR modality (but different Cas9 variants) were combined in equal numbers, resulting in 9 separate  cell pools for screening, and then analyzed and sorted via FACS.

extract_protocol:
gDNA was extracted using GeneJET DNA Purification Kit (Thermo Fisher Scientific).
All of the extracted gDNA was then used in the first PCR reaction, in multiple reactions not exceeding 10 μg gDNA per 100 uL PCR  reaction. Samples were then subjected to a second PCR to add sequencing adaptors and to barcode the samples. PCR products were run on a 2% agarose gel and the correct size band was extracted. PCR products from different samples were then pooled together in equimolar ratios. Sequencing was performed on the NextSeq 500 instrument using the MidOutput Mode v2 with 75 bp paired-end reads (Illumina).

treatment_protocol: For CRISPR library sorting, >108 cells were taken for antibody staining (~10,000× library representation).  We set aside 107 cells for the pre-sort control (~1,000× coverage). After harvesting the cells and removing  5  leftover medium by washing with PBS, the cells were stained for 5 minutes at room temperature with  LIVE/DEAD Fixable Violet Dead Stain Kit (ThermoFisher L34864). Subsequently, the cells were stained  with antibodies for 20 minutes on ice. The following antibodies were used: CD45-PE (clone 2D1), CD46-  APC (clone TRA-2-10) or CD55-APC (clone JS11). All antibodies were purchased pre-conjugated from  BioLegend. Cells were washed with PBS to remove unbound antibodies prior to sorting. Cell acquisition  and sorting was performed using a Sony SH800S cell sorter.

tag: cas9 variants

value: SpCas9, SpCas9-NG, xCas9 3.7

tag: fc antibody

value: anti-human CD45 PE-conjugated, clone 2D1


title: CD46_inhibition_bottom

description: sorted bottom 15% of CD46 expression

value: anti-human CD46 APC-conjugated, clone TRA-2-10


title: CD45_inhibition_top

description: sorted top 15% of CD45 expression


title: CD46_inhibition_presort

description: unsorted cells


title: CD55_nuclease_bottom

description: sorted bottom 15% of CD55 expression

value: anti-human CD55 APC-conjugated, clone JS11


title: CD46_activation_top

description: sorted top 15% of CD46 expression


title: CD55_activation_presort

description: unsorted cells


title: CD45_activation_bottom

description: sorted bottom 15% of CD45 expression


title: CD45_activation_presort

description: unsorted cells


title: CD46_activation_presort

description: unsorted cells


title: CD55_inhibition_presort

description: unsorted cells


title: CD45_activation_top

description: sorted top 15% of CD45 expression


title: CD55_activation_bottom

description: sorted bottom 15% of CD55 expression


title: CD55_inhibition_bottom

description: sorted bottom 15% of CD55 expression


title: CD45_inhibition_presort

description: unsorted cells


title: CD55_nuclease_presort

description: unsorted cells


title: CD46_nuclease_bottom

description: sorted bottom 15% of CD46 expression


title: CD46_nuclease_presort

description: unsorted cells


title: CD55_activation_top

description: sorted top 15% of CD55 expression


title: CD45_nuclease_bottom

description: sorted bottom 15% of CD45 expression


title: CD55_inhibition_top

description: sorted top 15% of CD55 expression


title: CD46_activation_bottom

description: sorted bottom 15% of CD46 expression


title: CD45_nuclease_top

description: sorted top 15% of CD45 expression


title: CD45_nuclease_presort

description: unsorted cells


title: ChIP-seq_K562_sgGal4_H3K27me3_rep1

city: Memphis

first: Jian

last: Xu

state: Tennessee

address: 262 Danny Thomas Place, MS 345

department: Pathology

institute: St. Jude Children's Research Hospital

data_processing:
Sequencing reads were aligned to human genome assembly hg19 (NCBI version 37) using Bowtie v2.2.8 with default parameters
The bigwig files were generated using deepTools with the following argument:  bamCoverage -b input.bam -o output.bigwig -of bigwig --effectiveGenomeSize 2864785220  --normalizeUsing RPGC --ignoreDuplicates --minMappingQuality 30 --extendReads 200
Genome_build: hg19
Supplementary_files_format_and_content: bigwig file

growth_protocol: All the leukemia cells were cultured in RPMI supplemented with 10% heat-inactivated fetal bovine serum (FBS) and 2% penicillin-streptomycin.

extract_protocol: For ChIP-seq analysis using the Illumina NextSeq500, 10-20 ng of ChIP DNA was processed for library generation using the NEBNext ChIP-seq Library Prep Master Mix following the manufacturer’s protocol (New England Biolabs). Raw reads that aligned to exactly one location in the reference human genome (hg19) were retained for downstream data analysis.

tag: cell lin

tag: chip antibody

value: H3K27me3, Millipore, Cat# 07-449 RRID:AB_310624


title: ChIP-seq_K562_enCRISPRi-LK_sgHS2_H3K27me3_rep1


title: ChIP-seq_K562_enCRISPRi-LK_sgHS2_H3K27me3_rep2


title: ChIP-seq_K562_sgGal4_H3K27me3_rep2


title: CD55_nuclease_top

description: sorted top 15% of CD55 expression


title: ChIP-seq_K562_enCRISPRi-KL_sgHS2_H3K27me3_rep2


title: ChIP-seq_K562_dCas9-KRAB_sgHS2_H3K27me3_rep2


title: Mococytes 3dpi ruxo minus A

city: Rehovot

first: Noam

last: Stern-Ginossar

address: 234 herzel

department: Molecular Genetics

country: Israel

institute: Weizmann Institute

description:
sample_barcodes.txt
ruxo_plus_vs_minus.txt

data_processing:
The MARS-seq pipeline scripts with a genome of hg19 + TB40/E were used.
In read1, the first 5 positions are ignored, the next 4 positions (6-9) are the batch barcode, and the next 37 positions (10-46) are the insert that was used for the alignment.
In read2, the first 7 positions (1-7) are the sample barcode, and the next 8 positions (8-15) are the UMI (unique molecular identifier).
Genome_build: hg19 + TB40/E (NCBI accession EF999921.1)
Supplementary_files_format_and_content: tab-delimited text files. Include number of umis for all genes, per sample.

source_name: Mococytes 3dpi ruxolitinib minus A

growth_protocol: Primary CD14+ monocytes were isolated from fresh venous blood, and cultured in X-Vivo15 media (Lonza) supplemented with 2.25mM L-glutamine at 37⁰C in 5% CO2

extract_protocol: RNA libraries were generated from samples of ~10,000 cells according to the MARS-seq protocol (Jaitin et al., 2014; Keren-Shaul et al., 2019).

treatment_protocol:
Cells were infected with HCMV strain TB40/E with SV40-GFP tag.
For the CD74 samples, cells were FACS-sorted aaccording to the cell-surface levels of CD74.
For the ruxo plus samples, Ruxolitinib was added at concentration of 4uM immediately after washing the virus

value: Mococytes 3dpi


title: Mococytes 6dpi ruxo minus A

source_name: Mococytes 6dpi ruxolitinib minus A

value: Mococytes 6dpi


title: Derived macrophages 4dpi

description:
sample_barcodes.txt
macrophages.txt

source_name: Mococytes-derived macrophages 4dpi

value: Derived macrophages 4dpi


title: Mococytes 3dpi CD74 high A

description:
sample_barcodes.txt
cd74_high_vs_low.txt

source_name: Mococytes 3dpi CD74 high A

value: Mococytes 3dpi CD74 high


title: ChIP-seq_K562_dCas9-LSD1_sgHS2_H3K27me3_rep2


title: RNA-seq_K562_enCRISPRi-LK_sgHS2_rep2

data_processing:
Sequencing reads from all RNA-seq experiments were aligned to human (hg19) reference genome by STAR 2.5.2b with the parameters: --outFilterMultimapNmax 1
The number of reads aligned to GENCODE annotated genes' exons were normalized to be of unit TPM (transcripts per million)using RSEM.
Genome_build: hg19
Supplementary_files_format_and_content: text file of gene TPM values

source_name: Human K562 cells

growth_protocol: Human K562 cells were cultured in RPMI supplemented with 10% heat-inactivated fetal bovine serum (FBS) and 2% penicillin-streptomycin.

extract_protocol: 0.1-1 ug of total RNA was processed for library generation using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB) and NEBNext Ultra II Directional RNA Library Prep Kit.

value: immortalized myelogenous leukemia cells


title: RNA-seq_K562_sgGal4_rep1


title: Mococytes 6dpi ruxo plus A

source_name: Mococytes 6dpi ruxolitinib plus A

value: Ruxolitinib


title: Mococytes 6dpi ruxo plus B

source_name: Mococytes 6dpi ruxolitinib plus B


title: RNA-seq_K562_enCRISPRi-LK_sgHS2_rep1


title: Mococytes 3dpi ruxo minus B

source_name: Mococytes 3dpi ruxolitinib minus B


title: Mococytes 3dpi CD74 high B

source_name: Mococytes 3dpi CD74 high B


title: Mococytes 3dpi CD74 low A

source_name: Mococytes 3dpi CD74 low A

value: Mococytes 3dpi CD74 low


title: ChIP-seq_K562_dCas9-LSD1_sgHS2_H3K27me3_rep1


title: RNA-seq_K562_enCRISPRi-KL_sgHS2_rep2


title: ChIP-seq_K562_dCas9-KRAB_sgHS2_H3K27me3_rep1


title: Mococytes 3dpi CD74 low B

source_name: Mococytes 3dpi CD74 low B


title: RNA-seq_K562_enCRISPRi-KL_sgHS2_rep1


title: RNA-seq_K562_dCas9-LSD1_sgHS2_rep1


title: RNA-seq_K562_dCas9-LSD1_sgHS2_rep2


title: Mococytes 6dpi ruxo minus B

source_name: Mococytes 6dpi ruxolitinib minus B


title: ChIP-seq_K562_enCRISPRi-KL_sgHS2_H3K27me3_rep1


title: RNA-seq_K562_sgGal4_rep2


title: ChIP-seq_K562_sgGal4_TAL1_rep2

data_processing:
Sequencing reads were aligned to human genome assembly hg19 (NCBI version 37) using Bowtie v2.2.8 with default parameters
The bigwig files were generated using deepTools with the following argument:  bamCoverage -b input.bam -o output.bigwig -of bigwig --effectiveGenomeSize 2864785220  --normalizeUsing RPGC --ignoreDuplicates --minMappingQuality 30 --extendReads 200
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

value: Human K562 cells

value: Santa Cruz Biotechnology,sc-12984,C1315


title: ChIP-seq_K562_sgGal4_TAL1_rep1


title: Mococytes 3dpi ruxo plus A

source_name: Mococytes 3dpi ruxolitinib plus A


title: Mococytes 3dpi ruxo plus B

source_name: Mococytes 3dpi ruxolitinib plus B


title: ChIP-seq_K562_sgGal4_H3K9me3_rep1


title: ChIP-seq_K562_sgGal4_H3K4me2_rep2


title: ChIP-seq_K562_sgGal4_H3K27ac_rep2


title: ChIP-seq_K562_sgGal4_H3K9me3_rep2


title: ChIP-seq_K562_sgGal4_H3K4me_rep1


title: ChIP-seq_K562_sgGal4_H3K4me2_rep1


title: ChIP-seq_K562_sgGal4_CTCF_rep1


title: ChIP-seq_K562_sgGal4_cas9_rep2


title: ChIP-seq_K562_sgGal4_H3K27ac_rep1


title: ChIP-seq_K562_enCRISPRi-LK_sgHS2_TAL1_rep1


title: ChIP-seq_K562_sgGal4_GATA1_rep2


title: ChIP-seq_K562_enCRISPRi-LK_sgHS2_H3K4me_rep2


title: ChIP-seq_K562_enCRISPRi-LK_sgHS2_H3K9me3_rep2


title: ChIP-seq_K562_enCRISPRi-LK_sgHS2_TAL1_rep2


title: ChIP-seq_K562_enCRISPRi-LK_sgHS2_H3K4me_rep1


title: ChIP-seq_K562_sgGal4_GATA1_rep1


title: ChIP-seq_K562_enCRISPRi-LK_sgHS2_H3K9me3_rep1


title: ChIP-seq_K562_enCRISPRi-LK_sgHS2_H3K4me2_rep2


title: RNA-seq_K562_dCas9-KRAB_sgHS2_rep1


title: ChIP-seq_K562_sgGal4_cas9_rep1


title: ChIP-seq_K562_enCRISPRi-LK_sgHS2_H3K4me2_rep1


title: ChIP-seq_K562_enCRISPRi-LK_sgHS2_H3K27ac_rep1


title: ChIP-seq_K562_enCRISPRi-LK_sgHS2_H3K27ac_rep2


title: ChIP-seq_K562_enCRISPRi-LK_sgHS2_GATA1_rep1


title: ChIP-seq_K562_enCRISPRi-LK_sgHS2_GATA1_rep2


title: ChIP-seq_K562_enCRISPRi-LK_sgHS2_CTCF_rep2


title: ChIP-seq_K562_enCRISPRi-LK_sgHS2_CTCF_rep1


title: ChIP-seq_K562_sgGal4_CTCF_rep2


title: ChIP-seq_K562_enCRISPRi-LK_sgHS2_cas9_rep2


title: ChIP-seq_K562_enCRISPRi-KL_sgHS2_H3K9me3_rep2


title: ChIP-seq_K562_sgGal4_H3K4me_rep2


title: ChIP-seq_K562_enCRISPRi-KL_sgHS2_H3K9me3_rep1


title: ChIP-seq_K562_enCRISPRi-LK_sgHS2_cas9_rep1


title: ChIP-seq_K562_enCRISPRi-KL_sgHS2_TAL1_rep2


title: ChIP-seq_K562_enCRISPRi-KL_sgHS2_TAL1_rep1


title: ChIP-seq_K562_enCRISPRi-KL_sgHS2_H3K4me_rep2


title: ChIP-seq_K562_enCRISPRi-KL_sgHS2_H3K4me_rep1


title: ChIP-seq_K562_enCRISPRi-KL_sgHS2_H3K4me2_rep2


title: ChIP-seq_K562_enCRISPRi-KL_sgHS2_GATA1_rep1


title: ChIP-seq_K562_enCRISPRi-KL_sgHS2_H3K4me2_rep1


title: ChIP-seq_K562_enCRISPRi-KL_sgHS2_cas9_rep2


title: ChIP-seq_K562_enCRISPRi-KL_sgHS2_CTCF_rep2


title: ChIP-seq_K562_dCas9-LSD1_sgHS2_TAL1_rep1


title: ChIP-seq_K562_enCRISPRi-KL_sgHS2_cas9_rep1


title: ChIP-seq_K562_enCRISPRi-KL_sgHS2_CTCF_rep1


title: ChIP-seq_K562_enCRISPRi-KL_sgHS2_H3K27ac_rep2


title: ChIP-seq_K562_dCas9-LSD1_sgHS2_H3K9me3_rep2


title: ChIP-seq_K562_enCRISPRi-KL_sgHS2_GATA1_rep2


title: ChIP-seq_K562_enCRISPRi-KL_sgHS2_H3K27ac_rep1


title: ChIP-seq_K562_dCas9-LSD1_sgHS2_H3K9me3_rep1


title: ChIP-seq_K562_dCas9-LSD1_sgHS2_TAL1_rep2


title: ChIP-seq_K562_dCas9-LSD1_sgHS2_H3K4me2_rep2


title: ChIP-seq_K562_dCas9-LSD1_sgHS2_H3K4me_rep1


title: ChIP-seq_K562_dCas9-LSD1_sgHS2_H3K4me_rep2


title: ChIP-seq_K562_dCas9-LSD1_sgHS2_H3K4me2_rep1


title: ChIP-seq_K562_dCas9-LSD1_sgHS2_H3K27ac_rep2


title: ChIP-seq_K562_dCas9-LSD1_sgHS2_H3K27ac_rep1


title: ChIP-seq_K562_dCas9-LSD1_sgHS2_GATA1_rep2


title: ChIP-seq_K562_dCas9-LSD1_sgHS2_GATA1_rep1


title: ChIP-seq_K562_dCas9-LSD1_sgHS2_cas9_rep2


title: ChIP-seq_K562_dCas9-LSD1_sgHS2_CTCF_rep2


title: ChIP-seq_K562_dCas9-LSD1_sgHS2_CTCF_rep1


title: ChIP-seq_K562_dCas9-KRAB_sgHS2_H3K9me3_rep2


title: ChIP-seq_K562_dCas9-KRAB_sgHS2_TAL1_rep1


title: ChIP-seq_K562_dCas9-KRAB_sgHS2_TAL1_rep2


title: ChIP-seq_K562_dCas9-KRAB_sgHS2_H3K9me3_rep1


title: ChIP-seq_K562_dCas9-KRAB_sgHS2_H3K4me2_rep1


title: ChIP-seq_K562_dCas9-KRAB_sgHS2_GATA1_rep1


title: ChIP-seq_K562_dCas9-KRAB_sgHS2_H3K27ac_rep2


title: ChIP-seq_K562_dCas9-KRAB_sgHS2_H3K4me_rep1


title: ChIP-seq_K562_dCas9-KRAB_sgHS2_H3K27ac_rep1


title: ChIP-seq_K562_dCas9-KRAB_sgHS2_cas9_rep1


title: ChIP-seq_K562_dCas9-KRAB_sgHS2_cas9_rep2


title: ChIP-seq_K562_dCas9-KRAB_sgHS2_GATA1_rep2


title: ChIP-seq_K562_dCas9-KRAB_sgHS2_CTCF_rep1


title: ChIP-seq_K562_dCas9-KRAB_sgHS2_H3K4me_rep2


title: ChIP-seq_K562_enCRISPRi-LK_sgGal4_HA_rep2

value: Santa Cruz, sc-805, Lot # B0810


title: ChIP-seq_K562_enCRISPRi-LK_sgGal4_HA_rep1


title: ChIP-seq_K562_enCRISPRi-LK_sgHS2_HA_rep2


title: ChIP-seq_293T_enCRISPRa_sgHS2_HA_rep1

value: Human 293T cells

value: immortalized human embryonic kidney cells


title: ChIP-seq_293T_enCRISPRa_sgHS2_HA_rep2


title: ChIP-seq_K562_dCas9-KRAB_sgHS2_CTCF_rep2


title: ChIP-seq_K562_enCRISPRi-LK_sgHS2_HA_rep1


title: ChIP-seq_293T_enCRISPRa_sgGal4_HA_rep2


title: ChIP-seq_293T_enCRISPRa_sgGal4_HA_rep1


title: ChIP-seq_K562_dCas9-LSD1_sgHS2_cas9_rep1


title: ChIP-seq_Jurkat-H3K27ac

source_name: Jurkat

value: Human Jurkat cells

value: immortalized T lymphocyte cells


title: ChIP-seq_K562_dCas9-KRAB_sgHS2_H3K4me2_rep2


title: DGF_97b1 miRNA-Seq

city: Glasgow

first: Paul

last: Shiels

address: Level 3, Wolfson Wohl Cancer Research Centre

department: Wolfson Wohl Translational Research Centre

country: United Kingdom

institute: University of Glasgow

description: Post-perfused

data_processing:
Illumina bcl2fastq software used for basecalling.
Prior to the alignment of raw sequencing reads to the human reference genome (GRCh38), a full index was built of the reference genome using subread-build index function from subread v1.4.6 (Liao, Smyth, & Shi, 2013).  Furthermore, reads does not require trimming of adapter sequences as soft clips sequences from the reads may not be properly mapped. The alignment was performed using subread-align ixing the threshold for the number of consensus subreads to 3 to allow the detection of miRNA sequences of at least 18bp or longer in each alignment.
Mapped fragment counts were summarised (as read counts) at meta-feature level of miRNA associated genes using featureCounts function (subread v1.4.6) using miRNA ids from miRBase v21
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include read counts values per transcript for each sample

source_name: Small needle biopsy

extract_protocol:
Small-needle paired renal biopsies immediately after collection were placed in RNA®later (Ambion, USA), processed and stored for further analysis.  Total RNA was isolated using TRI® reagent, on column DNase treated, further purified (Zymo Research)  and  stored at -80°C.  RNA samples with RIN>6 were used for downstream analyses.
1000 ng of total RNA and TruSeq small RNA library preparation kit (Illumina) was used to create libraries for downstream NGS. QA and QC was performed for each library.

tag: tissue

value: Kidney

tag: functional status/outcome

value: DGF


title: ATAC-seq_Jurkat

data_processing:
Sequencing reads were aligned to human genome assembly hg19 (NCBI version 37) using Bowtie v1.0.0 with the following parameters: --best --strata -k 1 -m 1. Duplicate reads were removed after the aligment with the Picard command-line tools.
The bigwig files were generated by a moving window of size 200bp. The tag count in the windown was further normalized by total read count for ATAC-seq data generated by NextSeq500.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

source_name: Human Jurkat cells

growth_protocol: Human leukemia cell lines were cultured in RPMI supplemented with 10% heat-inactivated fetal bovine serum (FBS) and 2% penicillin-streptomycin.

extract_protocol: For ATAC-seq analysis using the Illumina NextSeq500, ~50,000 cells were processed for tagmentation followed by DNA isolation and library generation. Raw reads that aligned to exactly one location in the reference human genome (hg19) were retained for downstream data analysis.

value: Jurkat


title: DGF_36b1 miRNA-Seq

description: Post-perfused


title: IGF_34b1 miRNA-Seq

description: Post-perfused

value: IGF


title: DGF_181b1 miRNA-Seq

description: Post-perfused


title: DGF_169b1 miRNA-Seq

description: Post-perfused


title: IGF_153b1 miRNA-Seq

description: Post-perfused


title: DGF_156b1 miRNA-Seq

description: Post-perfused


title: DGF_140b1 miRNA-Seq

description: Post-perfused


title: DGF_138b1 miRNA-Seq

description: Post-perfused


title: DGF_136b1 miRNA-Seq

description: Post-perfused


title: IGF_151b1 miRNA-Seq

description: Post-perfused


title: DGF_150b1 miRNA-Seq

description: Post-perfused


title: IGF_129b1 miRNA-Seq

description: Post-perfused


title: IGF_108b1 miRNA-Seq

description: Post-perfused


title: DGF_128b1 miRNA-Seq

description: Post-perfused


title: IGF_74b1 miRNA-Seq

description: Post-perfused


title: DGF_70b1 miRNA-Seq

description: Post-perfused


title: DGF_97b miRNA-Seq

description: Pre-perfused


title: DGF_106b1 miRNA-Seq

description: Post-perfused


title: DGF_70b miRNA-Seq

description: Pre-perfused


title: IGF_42b miRNA-Seq

description: Pre-perfused


title: IGF_42b1 miRNA-Seq

description: Post-perfused


title: DGF_36b miRNA-Seq

description: Pre-perfused


title: IGF_39b miRNA-Seq

description: Pre-perfused


title: IGF_34b miRNA-Seq

description: Pre-perfused


title: IGF_180b miRNA-Seq

description: Pre-perfused


title: IGF_180b1 miRNA-Seq

description: Post-perfused


title: IGF_168b1 miRNA-Seq

description: Post-perfused


title: IGF_165b1 miRNA-Seq

description: Post-perfused


title: IGF_152b1 miRNA-Seq

description: Post-perfused


title: IGF_168b miRNA-Seq

description: Pre-perfused


title: DGF_169b miRNA-Seq

description: Pre-perfused


title: IGF_165b miRNA-Seq

description: Pre-perfused


title: DGF_156b miRNA-Seq

description: Pre-perfused


title: IGF_152b miRNA-Seq

description: Pre-perfused


title: IGF_153b miRNA-Seq

description: Pre-perfused


title: IGF_74b miRNA-Seq

description: Pre-perfused


title: IGF_151b miRNA-Seq

description: Pre-perfused


title: DGF_150b miRNA-Seq

description: Pre-perfused


title: DGF_136b miRNA-Seq

description: Pre-perfused


title: DGF_138b miRNA-Seq

description: Pre-perfused


title: DGF_128b miRNA-Seq

description: Pre-perfused


title: DGF_181b miRNA-Seq

description: Pre-perfused


title: non-lesional skin3 CAGE

city: Saga

first: Satoshi

last: Nunomura

address: 5-1-1 Nabeshima

department: Department of Biomolecular Sciences

institute: Saga Medical School

data_processing:
Illumina RTA (Real Time Analysis) software was used for basecalling.
Sequenced reads were mapped to mm9 whole genome using BWA without changing any parameters.
Unmapped reads are then mapped to mm9 whole genome using HiSAT2 with the parameters set as defualt,   to map the reads that covers at least a part of exon2 as well as exon1.
Genome_build: mm9
Supplementary_files_format_and_content: A tab-delimited text file includes RPKM values for all samples

source_name: skin

extract_protocol:
Total RNA was isolated using RNeasy Mini kit (#74104, Qiagen, Hilden, Germany). Quality of total RNA was assessed by Agilent bioanalyzer to ensure that RNA integrity number is over 7.0, and A260/280 and A260/230 ratios are over 1.8.
Five micrograms of total RNAs were used for synthesis of the cDNA   using a Library Preparation kit (DNAFORM, Japan)

tag: strain

value: post natal day 28

tag: genotype

value: Control


title: IGF_129b miRNA-Seq

description: Pre-perfused


title: IGF_108b miRNA-Seq

description: Pre-perfused


title: non-lesional skin2 CAGE

tag: age


title: non-lesional skin4 CAGE


title: lesional skin1 CAGE


title: lesional skin4 CAGE


title: lesional skin3 CAGE


title: THP1 LSD1i 24h

city: milano

first: Saverio

last: Minucci

address: via Adamello 16

country: Italy

institute: European Institute of Oncology

description:
T2
RNA extracted from THP-1 cells treated with LSD1 inhibitor (0.5 μM DDP38003) for 24h

data_processing:
Illumina Casava1.8 software used for basecalling, quality check  performed with fastqc version 0.10.0
Sequenced reads were mapped to hg18 whole genome using TopHat v2.0.10  with the option --no-coverage-search
Reads counts were calculated using featureCounts v1.5.2 (Liao Y et al., 2014) from Subread package
DEGs were identified using EdgeR (Robinson MD et al., 2010)
Genome_build: hg18
Supplementary_files_format_and_content: tab-delimited text files include reads values and bigWig for UCSC visualization for each Sample

source_name: THP-1 cell line

growth_protocol: AML cells were grown in T175 flasks

extract_protocol:
AML cells were harvested, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 500ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: AML cells were treated either with vehicle or LSD1 inhibitior (DDP38003 - 0.5μM) for the indicated time points of treatment

tag: agent

value: LSD1 inhibitor (0.5 uM DDP38003)

tag: time point


title: THP1 Veh 24h

description:
T1
RNA extracted from THP-1 cells treated with vehicle for 24h

tag: cell line

value: vehicle


title: lesional skin2 CAGE


title: THP1 Veh 72h

description:
T1d3
RNA extracted from THP-1 cells treated with vehicle for 72h


title: KAS LSD1i 72h

description:
K2d3
RNA extracted from KASUMI-1 cells treated with LSD1 inhibitor (0.5 μM DDP38003) for 72h

source_name: KASUMI-1 cell line


title: DGF_140b miRNA-Seq

description: Pre-perfused


title: KAS LSD1i 6h

description:
K2
RNA extracted from KASUMI-1 cells treated with LSD1 inhibitor (0.5 μM DDP38003) for 6h


title: KAS Veh 72h

description:
K1d3
RNA extracted from KASUMI-1 cells treated with vehicle for 72h


title: RNA-seq_K562_dCas9-KRAB_sgHS2_rep2

tag: cell type

value: immortalized myelogenous leukemia cells


title: BT-TPR2_replicate3

city: New Haven

first: Qin

last: Yan

state: CT

address: Department of Pathology, PO Box 208023

institute: Yale School of Medicine

data_processing:
Raw 100-bp R1 single-end reads were mapped to human genome with Bowtie2 in local mode, which allows the reads spanning the exon-exon junctions to get mapped to one of the two exons independent of the transcriptome annotation.
The uniquely mapped reads (cutoff by MAPQ>10) were counted to ENCODE gene annotation (v24) using featureCounts
Differential gene expression were performed with DESeq2
Genome_build: hg38
Supplementary_files_format_and_content:
geneCount.csv: raw counts of sequencing reads to each gene
geneExpr.vst.csv: the gene abundance measure on log2 scale normalized with DESeq2 VarianceStabilzationTransformation

growth_protocol: Cells were grown in 10cm dishes in RPMI-1640 media supplemented with 10% FBS and 1% pen/strep to 80% confluence before harvesting.

extract_protocol:
Cell pellets were flash frozen on dry ice ethanol bath. RNA was extracted using Qiagen RNeasy Plus Mini kit according the manufacturer's protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols by the Yale Stem Cell Center Genomics Core.

tag: cell line background

value: HER2+ breast cancer cells

tag: sensitivity to her2 antibodies

value: trastuzumab + pertuzumab-resistant

tag: treatment

value: no treatment for 7 days prior to harvesting


title: BT-TPR2_replicate1


title: BT-TPR2_replicate2


title: BT-TPR1_replicate2


title: BT-TPR1_replicate1


title: BT-TPR1_replicate3


title: KAS Veh 6h

description:
K1
RNA extracted from KASUMI-1 cells treated with vehicle for 6h


title: siMESH1-7002, biological rep 2

middle: Ashley

address: 101 Science Drive, DUMC 3382

data_processing:
FastQC was used for confirming quality of sequencing reads.
Sequenced reads were mapped to hg19 reference genome using Hisat2 with default parameters
Quntification of read counts of genes were performed using HTSeq
DESeq2 were applied for differential analysis to compare gene expressions between conditions.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include results of differential analysis using DESeq2.

source_name: Human RCC4 cells with siMESH1-7002

growth_protocol: RCC4 cells were grow in DMEM media with 4.5g/L glucose and 4mM glutamine (11995-DMEM, ThermoFisher Scientific) and supplement with 10% heat-inactivated fetal bovine serum (Hyclone #SH30070.03HI) in humidified incubator, 37°C with 5% CO2

treatment_protocol: Human clear cell renal carcinoma cell line RCC4 were transfected with siRNA targeting MESH1: (target sequence CTGAAGGTCTCCTGCTAACTA, SI04167002, Qiagen), or non-targeting siRNA control (AllStars Negative Control siRNA, SI03650318). Briefly, 10^5 RCC4 cells were seeded in a well on 6-well plate with 40 pmole of siRNA and 3μL of Lipofectamine RNAiMAX (ThermoFisher Scientific, #133778150) reagent. Cells were incubated for 72 hours before collection.

value: human clear cell renal caricnoma cell line

tag: transfected with


title: siMESH1-7002, biological rep 3


title: BT-TR2_replicate3

value: trastuzumab-resistant


title: non-lesional skin1 CAGE


title: BT-TR1_replicate3


title: BT-TR2_replicate2


title: siMESH1-7002, biological rep 1


title: THP1 LSD1i 72h

description:
T2d3
RNA extracted from THP-1 cells treated with LSD1 inhibitor (0.5 μM DDP38003) for 72h


title: non-targeting siRNA control (for siMESH1-7002), biological rep 3

source_name: Human RCC4 cells with non-targeting siRNA control

value: non-targeting siRNA control


title: non-targeting siRNA control (for siMESH1-7002), biological rep 2


title: siMESH1-CDS, biological rep 3

description:
CD-L3_S7_L004
siMESH1-CDS-3
processed data file: HTSeq-DESeq2.siMESH1-CDS.siNT.out.txt

data_processing:
FastQC was used for confirming quality of sequencing reads.
Sequenced reads were mapped to hg19 reference genome using Hisat2 with default parameters
Quntification of read counts of genes were performed using HTSeq
DESeq2 were applied for differential analysis to compare gene expressions between conditions.
Genome_build: hg19
Supplementary_files_format_and_content: differential analysis results using DESeq2 (DESeq2.*out.txt); raw counts (count.txt)

source_name: Human RCC4_siMESH1-CDS

treatment_protocol: Human clear cell renal carcinoma cell line RCC4 were transfected with two independent siRNA targeting MESH1: siMESH1-CDS (D-031786-01,  Dharmacon), or siMESH1-3UTR (SI00642173, Qiagen), or non-targeting siRNA control (AllStars Negative Control siRNA, SI03650318). Briefly, 10^5 RCC4 cells were seeded in a well on 6-well plate with 40 pmole of siRNA and 3μL of Lipofectamine RNAiMAX (ThermoFisher Scientific, #133778150) reagent. Cells were incubated for 72 hours before collection.

value: human clear cell renal carcinoma cell line


title: non-targeting siRNA control (for siMESH1-7002), biological rep 1


title: BT-TR2_replicate1


title: BT-TR1_replicate1


title: siMESH1-CDS, biological rep 2

description:
CD-L20_S24_L007
siMESH1-CDS-2
processed data file: HTSeq-DESeq2.siMESH1-CDS.siNT.out.txt


title: BT474+trastuzumab+pertuzumab_replicate3

value: sensitive

value: 10 µg/mL trastuzumab + 10 µg/mL pertuzumab for 3 days


title: siMESH1-CDS, biological rep 1

description:
CD-L14_S18_L006
siMESH1-CDS-1
processed data file: HTSeq-DESeq2.siMESH1-CDS.siNT.out.txt


title: BT-TR1_replicate2


title: BT474+trastuzumab+pertuzumab_replicate2


title: non-targeting siRNA control, biological rep 3

description:
CD-L13_S17_L006
siNT-3

source_name: Human RCC4_non-targeting siRNA control


title: BT474+trastuzumab_replicate3

value: 10 µg/mL trastuzumab for 3 days


title: BT474+trastuzumab_replicate2


title: non-targeting siRNA control, biological rep 1

description:
CD-L1_S5_L004
siNT-1


title: pifq rep2

city: Stanford

first: Eunkyoo

last: Oh

state: CA

address: 260 Panama Street

department: Plant Biology

institute: Carnegie Institution

data_processing:
The quantification of transcript expression was performed using Salmon
Differential expression analysis was performed using DESeq2
Genome_build: TAIR10
Supplementary_files_format_and_content: abundance measurements

organism: Arabidopsis thaliana

source_name: pifq

growth_protocol: Seedlings were grown under white light for 5 days at 20 °C

extract_protocol:
Total RNA was extracted from seedlings using the TaKaRa MiniBEST Plant RNA Extraction Kit (Takara) according to the manufacturer’s instructions
1 µg of total RNA was processed for preparing mRNA sequencing library using MGIEasy RNA Directional Library Prep Kit (MGI) according to manufacturer’s instruction

tag: ecotype

value: pifq

value: 5-day-old whole seedlings


title: non-targeting siRNA control, biological rep 2

description:
CD-L7_S11_L005
siNT-2


title: TBX5-KO2_rep2(IonXpressRNA_003)

first: Joseph

last: Wu

state: Carlifornia

address: Stanford University School of Medicine

institute: Stanford University School of Medicine

data_processing:
WT pipeline for Ion Torrent - 1.0
Partek Flow software
Genome_build: hg19
Supplementary_files_format_and_content: excel file with Differential expression analysis results, generated by Partek Flow

extract_protocol:
RNA mini kit (Qiagen)
mRNA was isolated from total RNA (500ng) using the Ambion's mRNA direct kit (Dynabeads® mRNA Purification Kit ). Libraries were prepared with the Ion Total RNA-Seq Kit v2 according to the manufacturer's instructions. ERCC were spiked-in before the mRNA isolation.

treatment_protocol: CM differentiation (small molecule approach)

tag: differentiation status

value: Day 30 post differentiation

value: iPSC-CM


title: TBX5-KO2_rep1(IonXpressRNA_003)


title: TBX5-KO1_rep3(IonXpressRNA_002)


title: TBX5-KO2_rep3(IonXpressRNA_003)


title: pifq rep1


title: BT474+trastuzumab_replicate1


title: TBX5-KO1_rep2(IonXpressRNA_002)


title: BT474_replicate3


title: SUC2-PIF4 rep1


title: SUC2-PIF4 rep2


title: TBX5-KO1_rep1(IonXpressRNA_002)


title: Parental_rep3 (IonXpressRNA_001)

value: wildtype (parental)


title: BT474_replicate2


title: Parental_rep2 (IonXpressRNA_001)


title: BT474_replicate1

data_processing:
Raw 100-bp R1 single-end reads were mapped to human genome with Bowtie2 in local mode, which allows the reads spanning the exon-exon junctions to get mapped to one of the two exons independent of the transcriptome annotation.
The uniquely mapped reads (cutoff by MAPQ>10) were counted to ENCODE gene annotation (v24) using featureCounts
Differential gene expression were performed with DESeq2
Genome_build: hg38
Supplementary_files_format_and_content:
geneCount.csv: raw counts of sequencing reads to each gene
geneExpr.vst.csv: the gene abundance measure on log2 scale normalized with DESeq2 VarianceStabilzationTransformation function


title: ML1-PIF4 rep2


title: preB-KO (0826)

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

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

source_name: pre-B cells derived from STAP-2 knockout (KO) BM 1 month after transplantation (Tx)

extract_protocol:
Total RNA samples were prepared by miRNeasy-Kit (Qiagen, Valencia, CA, USA) in accordance with the manufacturer’s instructions.
Library preparation was performed using a TruSeq stranded mRNA sample prep kit (Illumina, San Diego, CA) according to the manufacturer’s  instructions.

value: pre-B cells

tag: genotype/variation


title: Parental_rep1 (IonXpressRNA_001)


title: BT474+trastuzumab+pertuzumab_replicate1


title: preB-WT (0826)

source_name: pre-B cells derived from wildtype (WT) BM 1 month after transplantation (Tx)


title: ML1-PIF4 rep1


title: Col-0 rep2

value: wildtype


title: preB-Tg (0901)

source_name: pre-B cells derived from STAP-2 transgenic (Tg) BM under steady-state


title: Col-0 rep1


title: Monocytes 5dpi ruxo at 3dpi  B

description:
sample_barcodes.txt
ruxo_kinetics.txt

source_name: Monocytes 5dpi ruxo at 3dpi  B

extract_protocol:
RNA libraries were generated from samples of ~10,000 cells according to the MARS-seq protocol (Jaitin et al., 2014; Keren-Shaul et al., 2019).
The library is 3' RNA-seq

value: ruxolitinib


title: preB-WT (0901)

source_name: pre-B cells derived from wildtype (WT)  BM under steady-state

value: wildtype (WT)  BM under steady-state


title: Monocytes 5dpi ruxo at 2dpi  B

description:
sample_barcodes.txt
ruxo_kinetics.txt

source_name: Monocytes 5dpi ruxo at 2dpi  B


title: Monocytes 5dpi ruxo at 2dpi  A

description:
sample_barcodes.txt
ruxo_kinetics.txt

source_name: Monocytes 5dpi ruxo at 2dpi  A


title: Monocytes 5dpi ruxo at 1dpi  A

description:
sample_barcodes.txt
ruxo_kinetics.txt

source_name: Monocytes 5dpi ruxo at 1dpi  A


title: Monocytes 5dpi ruxo at 1dpi  B

description:
sample_barcodes.txt
ruxo_kinetics.txt

source_name: Monocytes 5dpi ruxo at 1dpi  B


title: PHH treated with Rimonabant upon infection with HBV

description: primary human hepatocytes treated with Rimonabant upon infection with HBV

data_processing:
Sequencing was performed on an Illumina HiSeq 2500 platform in a 75-base single-end mode.
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were mapped to the human reference genome sequences (hg19) using TopHat v2.0.13 in combination with Bowtie2 ver. 2.2.3 and SAMtools ver. 0.1.19.
The fragments per kilobase of exon per million mapped fragments (FPKMs) was calculated using Cuffnorm version 2.2.1.
Genome_build: hg19
Supplementary_files_format_and_content: FPKM

extract_protocol:
Total RNA was extracted from PHH using the PureLink RNA Mini Kit (Thermo Fisher Scientific).
RNA libraries were prepared for sequencing using the TruSeq Stranded Total RNA with Ribo-Zero kit (Illumina, San Diego, CA, USA). according to the manufacturer’s instructions.

value: primary human hepatocytes (PHH)


title: PHH

description: primary human hepatocytes

source_name: PHH

value: mock


title: PHH treated with DMSO upon infection with HBV

description: primary human hepatocytes treated with DMSO upon infection with HBV


title: Monocytes 5dpi no ruxo B

description:
sample_barcodes.txt
ruxo_kinetics.txt

source_name: Monocytes 5dpi no ruxo B


title: RNA-Seq Blo2705-1

city: Gifu

first: Tomoya

last: Kozakai

address: Yanagido 1-1

institute: Gifu university

description:
treated with Ribo-Zero rRNA removal Kit
Sample 1

data_processing:
Basecalls performed using CASAVA (Illumina)
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to B. longum NCC2705 (NC_004307.2) whole genome using CLC Genomics Workbench
Reads Per Kilobase of exon per Million mapped reads (RPKM) were calculated using CLC Genomics Workbench
Genome_build: NC_004307.2
Supplementary_files_format_and_content: Excel file include RPKM values for each sample

organism: Bifidobacterium longum NCC2705

source_name: Bacteria

extract_protocol:
The total RNA were extracted from MRS culture in OD660 0.5, treated with Ribo-Zero rRNA Removal Kit (Illumina) to deplete the ribosomal RNA, and then reverse transcribed.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: phase

tag: media

value: MRS

value: wild type


title: RNA-Seq Blo2705-2

description:
treated with Ribo-Zero rRNA removal Kit
Sample 2


title: RNA-Seq Blo2705-3

description:
treated with Ribo-Zero rRNA removal Kit
Sample 3


title: Monocytes 5dpi ruxo at 3dpi  A

description:
sample_barcodes.txt
ruxo_kinetics.txt

source_name: Monocytes 5dpi ruxo at 3dpi  A


title: normal adrenal gland-1

city: Guangzhou

first: Yinghua

last: Chen

state: Guangdong

address: 1023 South Shatai  Road

department: Department of Histology and Embryology

country: China

institute: Southern Medical University

hyb_protocol: DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm at 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: Scanned on an Agilent G2565CA scanner.

data_processing: Feature Extraction v10.7 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and genespring software was used to analyze the raw data, which are normalized by percentile normalization.

source_name: tissue from normal adrenal gland

label_protocol: cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. This procedure has been previously described, and the procedure has been improved by using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio) for producing higher yields of labeled cDNA.

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer.

tag: gender

value: male

tag: tissue

value: tissue from normal adrenal gland


title: normal adrenal gland-2


title: Monocytes 5dpi no ruxo A

description:
sample_barcodes.txt
ruxo_kinetics.txt

data_processing:
The MARS-seq pipeline scripts with a genome of hg19 + TB40/E were used.
In read1, the first 5 positions are ignored, the next 4 positions (6-9) are the batch barcode, and the next 37 positions (10-46) are the insert that was used for the alignment.
In read2, the first 7 positions (1-7) are the sample barcode, and the next 8 positions (8-15) are the UMI (unique molecular identifier).
Genome_build: hg19 + TB40/E (NCBI accession EF999921.1)
Supplementary_files_format_and_content: tab-delimited text files. Include number of umis for all genes, per sample.

source_name: Monocytes 5dpi no ruxo A


title: aldosterone producing adenoma-1

source_name: tissue from aldosterone producing adenoma

value: female


title: aldosterone producing adenoma-3

value: tissue from aldosterone producing adenoma


title: MTAI2 [miRNA-seq]

status: Public on Jan 25 2020

city: Tianjin

first: Ming

last: Cui

address: 238 Baidi Road

department: Institute of Radiation Medicine,

institute: Chinese Academy of Medical Sciences and Peking Union Medical College

data_processing:
Raw data (raw reads) of fastq format were firstly processed through custom perl and python scripts. In this step, clean datas(clean reads) were obtained by removing reads containing ploy-N, with 5’ adapter contaminants, without 3’ adapter or the insert tag, containing ploy A or T or G or C and low quality reads from raw data. At the same time, Q20, Q30, and GC-content of the raw datas were calculated. Then, chose a certain range of length from clean reads to do all the downstream analyses.
The small RNA tags were mapped to reference sequence by Bowtie (Langmead et al., 2009) without mismatch to analyze their expression and distribution on the reference.
Position 2~8 of a mature miRNA were called seed region which were highly conserved. The target of a miRNA might be different with the changing of nucleotides in this region. In our analysis pipeline, miRNA which might have base edit could be detected by aligning all the sRNA tags to mature miRNA, allowing one mismatch.
Exploring the occurrence of miRNA families identified from the samples in other species. In our analysis pipeline, known miRNA used miFam.dat (http://www.mirbase.org/ftp.shtml) to look for families; novel miRNA precursor was submitted to Rfam (http://rfam.sanger.ac.uk/search/) to look for Rfam families.
miRNA expression levels were estimated by TPM (transcript per million) through the following criteria (Zhou et al., 2010):Normalization formula: Normalized expression = mapped readcount/Total reads*1000000
Genome_build: ensembl 90
Supplementary_files_format_and_content: Excel file include TPM values for each Sample.

source_name: MTAI_small intestine

extract_protocol:
Small intestine were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. NEBNext® UltraTM RNA Library Prep Kit was used with 3 ug of total RNA for the construction of sequencing libraries.
Sequencing libraries were generated using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (NEB, USA.)

tag: strain

tag: Sex

value: total abdominal irradiation

value: small intestine


title: MT3 [miRNA-seq]

source_name: MT_small intestine

value: total abdominal irradiation combined with simvastatin treatment


title: Mcon3 [miRNA-seq]

source_name: Mcon_small intestine

value: without irradiation


title: Ffat3 [miRNA-seq]

source_name: Ffat_small intestine

value: total abdominal irradiation combined with high fat diet


title: Ffat2 [miRNA-seq]


title: aldosterone producing adenoma-2


title: Ffat1 [miRNA-seq]


title: MT2 [miRNA-seq]


title: FTAI3 [miRNA-seq]

source_name: FTAI_small intestine


title: FTAI2 [miRNA-seq]


title: Fcon3 [miRNA-seq]

source_name: Fcon_small intestine


title: MT1 [miRNA-seq]


title: MTAI3 [miRNA-seq]


title: FTAI1 [miRNA-seq]


title: Mcon2 [miRNA-seq]


title: Day 8

city: Macau

first: Ren

last: Zhili

address: Avenida da Universidade

institute: University of Macau

hyb_protocol: cRNA was hybridized onto HumanHT-12 v4 Expression BeadChip (Illumina) using standerd protocol.

scan_protocol: BeadChips were scanned with the iScanner (Illumina).

data_processing:
Data was normalized by quantile normalization.
www.arrayanalysis.org computed the normalized signal intensity.

source_name: Human embryonic stem cell H1

label_protocol: RNA was converted to cRNA using the TargetAmp™-Nano Labeling Kit for Illumina Expression BeadChip (Epibio).

growth_protocol: Human ESCs (H1) were maintained in E8 medium on matrigel-coated plates with daily medium change.

extract_protocol: Toatal RNA was isolated by Qiagen Rneasy kit.

treatment_protocol: Human PSCs were cultured as above until 30% confluence, then switched to differentiation medium (DMEM/F12, L-ascorbic acid, selenium, transferrin, insulin, 1x chemically defined lipid concentrate. From Day 0 to Day 8, cells were cultured in differentiation medium with the following treatments: Day 0-6, 10 µM SB431542; Day 1-6, 5 µM CHIR99021; Day 1-8, 10 ng/ml BMP4 (R&D 314-BP-01M); Day 4-8, 5 µM DAPT (Tocris 2634). From Day 9 to Day 11, the medium was changed to low-calcium differentiation medium (containing 0.06 mM calcium) supplemented with BMP4/DAPT/EGF (10 ng/ml). The resulting stage Ⅲ keratinocyte were then maintained in low-calcium differentiation medium supplemented with 0.7% BSA, 2.4 ng/ml adenine, 0.4 µg/ml hydrocortisone, 5 µg/ml NKH477, 10 ng/ml EGF .

tag: time

value: Day 8


title: Day 11

value: Day 11


title: Day 26

value: Day 26


title: Day 6

value: Day 6


title: Day 4

value: Day 4


title: Mcon1 [miRNA-seq]


title: normal adrenal gland-3


title: Day 1

value: Day 1


title: Day 0

value: Day 0


title: Fcon2 [miRNA-seq]

value: wild type


title: Fcon1 [miRNA-seq]


title: TN09-29_infected_Rep2 (RNA-seq)

city: Knoxville

first: Sarbottam

last: Piya

address: 2431 Joe Johnson Dr.

department: Plant Science

institute: University of Tennessee

data_processing:
Quality of paired-ended reads was accessed using FastQC (version 0.11.4).
Adapter sequences and low-quality reads were removed using Trimmomatic (version 0.35).
TOPHAT v.2.0.13 was used to map the reads to the soybean reference genome (Wm82.a2.v1).
Reads mapped to multiple loci were discarded and numbers of uniquely mapped reads per gene were determined using HTSeq.
Differentially expressed genes were identified the R package edgeR.
Python-based package QoRTs was used for counting sequencing reads spanning exons for every gene.
Differentially spliced transcripts were identified using R package JunctionSeq.
Genome_build: Wm82.a2.v1
Supplementary_files_format_and_content: counts

organism: Glycine max

source_name: Root

growth_protocol: Soybean seeds of TN09-16, TN09-29, Fowler and Anand were washed under running water for 30 minutes followed by soaking in 10% bleach for 10 minutes. After surface sterilization, the seeds were washed again for 30 minutes to remove bleach remnants. The seeds were germinated on wet germination paper by keeping in dark at 26 degrees for three days.

extract_protocol:
mRNA was isolated using magnetic mRNA isolation kit (NEB).
RNA-seq libraries were prepared using NEBnext mRNA library prep master mix (NEB) following manufacturer’s protocol.

treatment_protocol: Soybean seedlings of 3-days old TN09-16 and TN09-29 were treated with 3000 freshly hatched second stage juveniles (J2s) of SCN HG type 0 (race 3) by spreading the nematodes across the whole root of a seedling. Control plants were set up in the exact same way, except mock inoculations were performed using 0.1% (w/v) agarose per seedling. The two parental lines (Fowler and Anand) were only mock-inoculated. Root tissues of all in the samples were collected five days after nematode treatment.

tag: line

tag: phenotype

value: Soybean cyst nematode  resistant

value: Root

tag: age

value: 8 days

tag: infection

value: Soybean cyst nematode infected root tissue


title: TN09-29_infected_Rep1 (RNA-seq)


title: TN09-29_infected_Rep3 (RNA-seq)


title: TN09-29_noninfected_Rep3 (RNA-seq)

value: Mock treated root tissue


title: TN09-29_noninfected_Rep1 (RNA-seq)


title: TN09-16_infected_Rep3 (RNA-seq)

value: Soybean cyst nematode susceptible


title: TN09-16_infected_Rep2 (RNA-seq)


title: TN09-16_infected_Rep1 (RNA-seq)


title: TN09-16_noninfected_Rep1 (RNA-seq)


title: TN09-16_noninfected_Rep3 (RNA-seq)


title: Fowler_noninfected_Rep1 (MethylC-Seq)

data_processing:
Adapters and low quality reads below phred threshold of 33 were removed using Trimmomatic.
Reads were aligned to the soybean reference genome (Wm82.a2.v1) using Bismark.
Differentially methylated cytosines were identified using R bioconductor package methylKit.
Differentially methylated regions were mapped to various genic regions using R Bioconductor package rtracklayer.
Genome_build: Wm82.a2.v1
Supplementary_files_format_and_content: methlyation calls

extract_protocol:
Genomic DNA of root tissues were extracted using DNeasy Plant Mini Kit (Qiagen).
Whole genome methylC-seq libraries were constructed following the protocol from Illumina TruSeq Library Prep kit (Illumina, San Diego, CA)

value: Fowler

value: parental


title: Fowler_noninfected_Rep3 (MethylC-Seq)


title: TN09-16_noninfected_Rep2 (RNA-seq)


title: Fowler_noninfected_Rep2 (MethylC-Seq)


title: TN09-29_noninfected_Rep2 (RNA-seq)


title: Anand_noninfected_Rep3 (MethylC-Seq)

value: Anand