title: shCTRL_NET_seq_rep2

data_processing:
Adaptor sequences and library tails were removed by Cutadapt. Low-quality bases were trimmed using Trimmomatic. Reads shorter than 10 nt were discarded.
The remaining reads were mapped to hg19 (human) through Tophat249 with default parameters. Mapping quality less than 20 were removed by samtools.
Then the remaining mapped reads were split into forward/plus R-loop reads and reverse/minus reads by samtools.
Genome_build: hg19
Supplementary_files_format_and_content: The splited bam files were converted to normalized BigWig files, with coverage normalized to 1× sequencing depth (Reads Per Genomic Content).

extract_protocol:
The chromatin fraction was isolated from 5x107 HeLa cells. Chromatin was digested in 100 mL of MNase (40 units/ mL ) reaction buffer for 3 min at 37 °C in a thermomixer (1,400 rpm). After addition of 10 L EGTA (25mM) to inactivate MNase, soluble digested chromatin was collected by 13,000 rpm centrifuge for 5 min. 10 mg of Pol II antibody was conjugated to magnetic protein A beads. The supernatant was diluted with 400 mL of NET-2 buffer and pSer2-Pol II antibody-conjugated beads were added. Incubated the IP reaction at 4 °C for 1 hr. The beads were washed with 1 mL of NET-2 buffer six times and 100 mL of 1xPNKT (1xPNK buffer and 0.05% Triton X-100) buffer once. Washed beads were incubated in 50 mL PNK reaction mix (1xPNKT, 1 mM ATP and 0.05 U/ml T4 PNK (NEB)) in Thermomixer at 37 °C, 1,400 rpm for 6 min. Beads were washed with 1 mL of NET-2 buffer once and RNA was extracted with Trizol reagent. RNA was suspended in urea Dye (7M Urea, 1xTBE, 0.1% BPB and 0.1% XC) and resolved on 6% TBU gel (Invitrogen) at 200 V for 5 min. Gels with 30-160 nt RNAs were collected. 0.2 mL tube was prepared with holes made with 25G needle and placed in a 1.5 mL tube. Gel fragments were placed in the layered tube and broken down by centrifugation at 12,000 rpm for 1 min. The small RNAs were eluted from gel using RNA elution buffer (1 M NaOAc and 1 mM EDTA) at 25 °C for 1 hr in Thermomixer (900 rpm). Eluted RNA was puriﬁed with SpinX column (Coster) with 2 glass ﬁlters (Millipore) and the ﬂow-through RNA was ethanol precipitated.
RNA libraries were prepared according to manual of SMARTer smRNA-Seq Kit for Illumina (Clontech, 635031).

value: anti- Pplymerase II CTD ser2p


title: CA_shCTRL_meRIP_rep1

status: Public on Oct 15 2019

type: SRA

city: Beijing

first: Bao-Fa

last: Sun

address: Da-Tun Road

country: China

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

description:
caRNA
CA_shCTRL_meRIP_rep1

library_source: transcriptomic

data_processing:
For meRIP-seq (IP) and RNA-seq (input), adaptor sequences and library tails were removed by Cutadapt. Low-quality bases were trimmed using Trimmomatic48. Reads shorter than 18 nt were discarded. The remaining reads were mapped to hg19 (human) through Tophat2 with default parameters. Mapping quality less than 20 were removed by samtools. MACS2 (version 2.0.10) was used to call peaks between IP and input with the parameters --keep-dup all, --nomodel and -- extsize 100.
For miCLIP-seq data, fastx_clipper was used to remove adaptor sequences. R2 reads were transformed to reverse complementary sequences and merged with R1 reads. PolyA tails were trimmed by Cutadapt. Duplicated reads were removed by fastq2collapse. stripBarcode.pl was used to strip barcodes of remaining reads. The low-quality bases were trimmed and reads shorter than 18 nt were discarded. The remaining reads were mapped to hg19 (human) by BWA (version 0.7.10) with the parameter: -n 0.06. parseAlignment.pl (--map-qual 1 --min-len 18) and tag2collapse.pl (-EM 30 --seq-error-model alignment) were used to extract mutation information and remove PCR duplicates. The coverage (k) of mutation site and transition number (m) were calculated by CIMS.pl. The mutation sites with k ≥ 10, m ≥ 2, k/m ≥ 0.01 and k/m ≤ 0.5 were kept.
Genome_build: hg19
Supplementary_files_format_and_content: m6C sites generated by miCLIP-seq

molecule: total RNA

organism: Homo sapiens

source_name: HeLa cell

extract_protocol:
Cells were washed with cold PBS twice and scraped from the plates, then centrifuged at 1000 rpm for 5 min to pellet cells. Washed cells were lysed with 400 L of cell lysis buffer (10 mM Tris-HCl pH7.5, 150 mM NaCl, 0.15% NP-40 and proteinase inhibitor cocktail) and incubated on ice for 10 min. The suspension was carefully add at the top of sucrose buffer (10 mM Tris-HCl pH7.5, 150 mM NaCl, 24% sucrose), and centrifuged at 3200g for 10 min to collect nuclear pellets. Pellets were resuspended in 250 L of Glycerol buffer (20 mM Tris-HCl pH7.5, 75 mM NaCl, 0.5 mM EDTA pH8.0, 50% glycerol), then then immediately add 250 μl Nuclear lysis buffer (10 mM Tris-HCl pH7.5, 300 mM NaCl, 7.5 mM MgCl2, 0.2 mM EDTA pH8.0, 1% NP-40, 1M urea). Mix by vortexing for 4 s and incubate on ice for 2 min. Centrifuge the lysate at 13,000 × g for 2 min to precipitate the chromatin–RNA complex. Brieﬂy rinse the chromatin pellets with PBS-EDTA. RNA was extracted with Trizol reagent.
RNA libraries were prepared according to manual of SMARTer smRNA-Seq Kit for Illumina (Clontech, 635031).

tag: cell type

value: HeLa cell

tag: antibody

value: anti- m6A (abcam, ab151230)


title: gata2a- runx1+

city: Kanazawa

first: Isao

last: Kobayashi

state: Ishikawa

address: Kakumamachi

country: Japan

institute: Kanazawa University

data_processing:
Illumina RTA software was used for base-calling.
Sequence reads were mapped to the zebrafish reference genome (GRCz11) using HiSAT2 (version 2.1.0).
Reads per million (RPM) were calculated using the Subread (ver. 1.6.4).
Genome_build: GRCz11
Supplementary_files_format_and_content: Reads per million (RPM) values for each sample.

organism: Danio rerio

source_name: erythroid- and/or myeloid-primed progenitors

extract_protocol:
Total RNAs were extracted from sorted cells using RNeasy Mini Kit (QIAGEN).
Cells were directly sorted in a lysis buffer containing 1 μg/mL of polyinosinic-polycytidylic acid, and total RNA was extracted using RNeasy Mini Kit. Reverse transcription (RT) was performed using Super Script III (Thermo Fisher Scientific) and an RT primer, which contains oligo-dT, T7 promoter, and PCR target region sequences. After digestion of remaining RT primers by exonuclease I (Takara), a poly-A tail was added to the 3’ ends of the first-strand cDNAs using terminal transferase (Sigma). The second-strand DNA was then synthesized using MightyAmp DNA polymerase (Thermo Fisher Scientific) and a tagging primer, which contains oligo-dT and PCR target region sequences. PCR amplification was performed using a suppression primer, which allow to amplify small-size DNA that contains complementary sequences at both ends of the template DNA. The amplified double-strand cDNA was purified using QIAquick PCR Purification Kit (Qiagen). Library preparation was performed using Nextera XT DNA Library Preparation Kit (illumina).

tag: tissue

value: Sorted cells from the kidney

value: gata2a- runx1+

tag: age

value: adult

tag: genotype

value: wild type


title: shMETTL3_WT_ssDRIP_rep2

library_source: genomic

data_processing:
Adaptor sequences were trimmed off by Cutadapt (version 1.16). Both first and last seven (the tails of ssDNA library) and low-quality bases were discarded for both R1 and R2 reads. Only reads with length longer than 50 bp were kept.
The remaining reads were aligned to the hg19 (human) reference genomes by using Bowtie2 (version 2.2.9)43 with default parameters.
Low mapping quality reads and duplicated reads were removed by samtools (version 1.3.1) and Picard tools (http://broadinstitute.github.io/picard) (version 2.16.0) separately.
Then the remaining mapped reads were split into forward/plus R-loop reads and reverse/minus R-loop reads by samtools.
Genome_build: hg19
Supplementary_files_format_and_content: The splited bam files were converted to normalized BigWig files, with coverage normalized to 1× sequencing depth (Reads Per Genomic Content).

molecule: genomic DNA

extract_protocol:
gDNA was estracted and digested with cocktail of restrict enzymes MseI, DdeI, AluI, MboI, incubated at 37°C for 6 h. After purified by phenol/chloroform extraction, fragmented DNA was resuspended by TE, and quantified by Qubit 3.0 (Invitrogen). For each sample, 20 μg input DNA was immunoprecipitated overnight at 4°C in a shaker, with 1× DRIP binding buffer (10 mM NaPO4 pH 7.0, 140 mM NaCl, 0.05% Triton X-100) and 10 μg S9.6 antibody (ATCC, HB-8730). After adding 50 μl Dynabeads Protein G (Invitrogen, 10004D) and incubated for 4 h, the beads with antibody were washed by 1× DRIP binding buffer for 4 times at room temperature, each wash takes 10 min. Added 250 μl elution buffer (50 mM Tris pH 8.0, 10 mM EDTA, 0.5% SDS) and 5 U Proteinase K to beads/antibody complexes, incubated for 40 min in an Eppendorf ThermoMixer at 55°C, 1,000 rpm. Purified by phenol/chloroform extraction, and moved supernatant to a new tube, followed by adding 1/10 volume 3 M NaAc, 1 μl GlycoBlue (Invitrogen) and 1 volume isopropanol, precipitated at -20°C for 3 h and then centrifuged. After washed by 70% ethanol and dried, the DRIPed DNA pellet was resuspended by 75 μl low EDTA TE buffer (10 mM Tris-HCl 8.0, 0.1 mM EDTA). NGS libraries were constructed using Accel-NGS® 1S Plus DNA Library Kit (Swift Biosciences).
DRIPed DNA sample was fragmented to an average size of 250 bp with an S220 Focused-ultrasonicator (Covaris, Woburn, MA, USA). The sonicated DNA was denatured into ssDNA at 98°C for 2 minutes and placed on ice for another 2 min. Accel-NGS® 1S Plus DNA Library Kit (Swift Biosciences, 10096) was used. The truncated adapter 1 was ligated to 3’ end of ssDNA first, followed by extension. The truncated adapter 2 was ligated to 5’ end. After 12 cycles PCR reaction, libraries were purified by VAHTS DNA Clean Beads (Vazyme, N411).
single strand DNA library

value: HeLa


title: CA_shCTRL_input_rep1

description:
caRNA
CA_shCTRL_input_rep1


title: shMETTL3_WT_ssDRIP_rep1


title: shMETTL3_NET_seq_rep1


title: shMETTL3_NET_seq_rep2


title: shMETTL3_mut_ssDRIP_rep2


title: shCTRL_NET_seq_rep1


title: shMETTL3_mut_ssDRIP_rep1


title: shMETTL3_EV_ssDRIP_rep2


title: shMETTL3_EV_ssDRIP_rep1


title: s9P_NS human liver cancer adjacent tissue

type: RNA

city: Shanghai

first: Ji-Min

last: Zhu

address: 180 Fenglin Road, Shanghai, China

institute: Zhongshan Hospital of Fudan University

description: Microarray profile of miRNA in the adjacent tissue of Hepatocellular carcinoma

hyb_protocol: Each slide was hybridized with 100ng Cy3-labeled RNA using miRNA Complete Labeling and Hyb Kit (Cat # 5190-0456, Agilent technologies, Santa Clara, CA, US) in hybridization Oven (Cat # G2545A, Agilent technologies, Santa Clara, CA, US) at 55°C，20 rpm for 20 hours according to the manufacturer’s instructions, hybridization section. After hybridization, slides were washed in staining dishes (Cat # 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit (Cat #5188-5327, Agilent technologies, Santa Clara, CA, US).

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat # G2565CA, Agilent technologies, Santa Clara, CA, US) and Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US) with default settings. Raw data were normalized by Quantile algorithm, Gene Spring Software 12.6 (Agilent technologies, Santa Clara, CA, US).

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, GeneSpring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

source_name: human liver cancer adjacent tissue

label_protocol: miRNA molecular in total RNA was labeled by miRNA Complete Labeling and Hyb Kit (Cat # 5190-0456, Agilent technologies, Santa Clara, CA, US) followed the manufacturer’s instructions, labeling section.

extract_protocol: Total RNA was extracted and purified using mirVanaTM miRNA Isolation Kit without phenol (Cat # AM1561, Ambion, Austin, TX, US), following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

treatment_protocol: 7 pairs of HCC and matched adjacent tumor-free tissues were collected during the surgery from HCC patients admitted to Zhongshan Hospital of Fudan University between 2008 and 2009 and All tissue samples were stored at -80℃ immediately after surgery

tag: disease state

value: hepatocellular carcinoma matched adjacent tissue

tag: gender

value: Male


title: s10T_NS human liver cancer tissue

source_name: human liver cancer tissue

value: hepatocellular carcinoma tissue


title: shMETTL3_ssDRIP_rep2


title: shCTRL_EV_ssDRIP_rep1


title: shMETTL3_ssDRIP_rep1


title: shCTRL_ssDRIP_rep3


title: MCF7-ATAC-shCTRL

first: Guojuan

last: Jiang

state: Shanghai

address: Ruijin er road

department: School of Medicine

institute: Shanghai Jiaotong University

data_processing:
Reads were filtered with trimmomatic (version 0.32).
Bowtie version 2.2.4 was used to align the reads against the hg19 reference genome.
Samtools 1.9 to remove PCR duplicates
MACS2 to do peak calling on all files
Genome_build: hg19
Supplementary_files_format_and_content: wig and peak files for each sample

source_name: Breast

growth_protocol: The MCF-7 cells were maintained in DMEM supplemented with 10% fetal bovinw serum at 37℃ incubator

extract_protocol:
50,000 sorted cells were washed with cold PBS and suspended in lysis buffer for 10-15 min on ice.  DNA was purified using MinElute PCR Purification Kit (Qiagen). Transposed DNA was amplified using NEB Next High-Fidelity 2X PCR Master Mix and libraries were sequenced on HiSeq 4000
DNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: DNA of MCF-7 cells with WT and NR2F2 KO were extracted using standard Illumina protocals.

tag: cell line

value: breast cancer cell line

tag: genotype/variation

value: shCTRL


title: NR2F2-KO+E2 rep1

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using tophat2 and cufflinks.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using cufflinks. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Hg19
Supplementary_files_format_and_content: RPKM values for each Sample

growth_protocol: The MCF-7 cells were maintained in DMEM supplemented with 10% fetal bovinw serum at 37℃ incubator.

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The MCF-7 cells were grown in the phenol red-free medium supplement with 10% charcoal/dextran-treated fetal bovine serum for 3 days, followed by treatment of vehicle or 10 nM estrogen for 12 hours.

value: breast cell line

value: NR2F2 KO

tag: treatment

value: 10 nM estrogen for 12hr


title: s9T_NS human liver cancer tissue


title: shCTRL_ssDRIP_rep2


title: MCF7-ATAC-shNR2F2


title: shCTRL_ssDRIP_rep1


title: CON+E2 rep2


title: CON+E2 rep1


title: NR2F2-KO rep1

value: vehicle for 12hr


title: MCF7-E2-NR2F2_ChIPSeq

data_processing:
Data were filtered using trimmomatic (version 0.32)
ChIP-seq reads were aligned to the hg19 genome assembly using bowtie2 with the default configurations
Samtools were used to remove PCR duplicated reads and sort aglined reads.
Peaks were called using MACS version 2.1.2 with the following setting: macs2 callpeak -t treatfile -c confile -n name -p 1e-6 -f BAM -g hs -m 10 40.
Genome_build: hg19
Supplementary_files_format_and_content: wig files were generated using igvtools.jar version 2.4.17; Peak files were generated by MACS2.

growth_protocol: The MCF-7 cells were maintained in DMEM supplemented with 10% fetal bovinw serum at 37℃ incubator. Cells were incubated in Phenol red-free DMEM containing 2.5% charcoal/dextran treated FBS for three days.

extract_protocol:
Lysates were clarified form sonicated nuclei and protein-DNA complexes were isolated with antibody.
The Chromatin immunoprecipitated DNA fragments (approx.10 ng in 30 µl water) are end repaired by using T4 DNA polymerase, Klenow DNA polymerase and T4 polynucleotide kinase in the presence of dNTPs. And an ‘A’ base is added to the 3’end of the blunt phosphorylated DNA fragments, using the polymerase activity of Klenow fragment. Then, adaptors (Adaptor oligo mix, Illumina) are ligated to the ends of the DNA fragments. The resulting DNA fragments are purified by MinElute column (QIAGEN). 300 ~ 500 bp DNA fragments are purified by using E-Gel SizeSelect agarose Gels (Invitrogen) according to manufacturer’s instruction. Size selected adaptor-modified DNA fragments are amplifiedand the resulting PCR products are purified by MinElute column (QIAGEN). The size and amount of DNA fragments (libraries) are validated by Bioanalyzer (Agilent)

treatment_protocol: MCF-7 cells were treated with vehicle or estrogen 10 nM for 12 h.

tag: chip antibody

value: NR2F2 (active motif, 61213，Lot 10216002)


title: MCF7-E2-Input_ChIPSeq


title: CON rep1

source_name: CON


title: MCF7-vehicle-NR2F2_ChIPSeq


title: MCF7-vehicle-Input_ChIPSeq


title: MCF7-shNR2F2-FOXA1_ChIPSeq


title: MCF7-shNR2F2-H3K4me3_ChIPSeq


title: MCF7-shNR2F2-H3K4me1_ChIPSeq


title: shCTRL_EV_ssDRIP_rep2


title: shMETTL3_ssDRIP_rep3


title: MCF7-shNR2F2-ER_ChIPSeq

value: ERa (santa cruze, sc-543x,Lot # E3014 )


title: MCF7-shCTRL-H3K4me1_ChIPSeq


title: MCF7-shNR2F2-Input_ChIPSeq


title: MCF7-shCTRL-H3K27ac_ChIPSeq


title: MCF7-shCTRL-H3K4me3_ChIPSeq


title: MCF7-shCTRL-Input_ChIPSeq


title: MCF7-shCTRL-ER_ChIPSeq


title: MCF7-shNR2F2-H3K27ac_ChIPSeq


title: aGvHD1

first: Aijie

last: Huang

address: 168, Changhai road

institute: Changhai Hospital

data_processing:
Image analysis and base calling were conducted by the HiSeq Control Software (HCS) + OLB + GAPipeline-1.6 (Illumina) on the HiSeq instrument.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, and all sequencing reads were mapped to Human genome using tophat.
The mapped results were processed using cufflinks, producing Fragments per Kilobase of transcript per Million mapped reads data matrix, and with htseq-count(http://www-huber.embl.de/users/anders/HTSeq/doc/count.html), producing the raw hit counts data matrix. The raw hit counts gene matrixes were transformed using DESeq variance stabilization algorithm and normalized using quantile normalization function built into the Bioconductor Limma package. The normalized data matrix was then analyzed using Limma and SAMR algorithms.
Genome_build: hg19
Supplementary_files_format_and_content: text file with RPKM

source_name: MNC

extract_protocol:
Mononucleated cells was isolated from the peripheral blood. Total RNA of each sample was extracted using TRIzol Reagent (Invitrogen)/RNeasy Mini Kit (Qiagen)/other kits. Total RNA of each sample was quantified and qualified by Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), NanoDrop (Thermo Fisher Scientific Inc.) and 1% agrose gel. 1 μg total RNA with RIN value above 7 was used for following library preparation. Next generation sequencing library preparations were constructed according to the manufacturer’s protocol (NEBNext® Ultra™ RNA Library Prep Kit for Illumina®). Whole transcriptome sequencing libraries (3 pairs of aGvHD and controls, 6 libraries in total) were prepared following the manufacturer’s instructions for the Whole Transcriptome Sample Prep Kit (Illumina) by GENEWIZ Company.
RNA libraries were prepared following the manufacturer’s instructions for the Whole Transcriptome Sample Prep Kit (Illumina) by GENEWIZ Company.  The poly(A) mRNA isolation was performed using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB) or Ribo-Zero™ rRNA removal Kit (illumina). The mRNA fragmentation and priming was performed using NEBNext First Strand Synthesis Reaction Buffer and NEBNext Random Primers. First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase and the second-strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix. The purified double-stranded cDNA（by AxyPrep Mag PCR Clean-up (Axygen)was then treated with End Prep Enzyme Mix to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using AxyPrep Mag PCR Clean-up (Axygen), and fragments of ~360 bp (with the approximate insert size of 300 bp) were recovered. Each sample was then amplified by PCR for 11 cycles using P5 and P7 primers, with both primers carrying sequences which can anneal with flow cell to perform bridge PCR and P7 primer carrying a six-base index allowing for multiplexing. The PCR products were cleaned up using AxyPrep Mag PCR Clean-up (Axygen), validated using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), and quantified by Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA, USA).

value: peripheral blood mononucleated cells

tag: disease

value: acute leukemia

tag: agvhd status

value: with


title: aGvHD3


title: NR2F2-KO rep2


title: Control1

value: without


title: Control3


title: Control2


title: MCF7-shCTRL-FOXA1_ChIPSeq


title: aGvHD2


title: CMV-QKO tumor [17.CMVCre]

city: Madrid

first: Corina

last: Lorz

state: Madrid

address: Avda. Complutense 40

country: Spain

institute: Ciemat (Centro de Investigaciones Energeticas Mediambientales y Tecnologicas)

description: Gene expression data form tumours from Ad5-CMVCre treated Rb1F/F;Trp53F/F; PtenF/F p107−/− mice

hyb_protocol: Following fragmentation, 3.5 ug of ssDNA were hybridizedon Mouse Gene 2.0 ST Chip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station according to the manufacturer's instructions.

scan_protocol: GeneChips were scanned using the Affymetrix system.

data_processing: The data were analyzed with RMA using Gene Expression Console.

label: biotin

organism: Mus musculus

source_name: Lung tumors from Ad5-CMVCre treated Rb1F/F;Trp53F/F; PtenF/F p107−/− mice

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Extraction of total RNA was performed with miRNeasy Mini Kit Qiagen according to the manufacturer's instructions.

value: tumor (lung)

tag: agent

value: Rb1F/F;Trp53F/F; PtenF/F p107-/- mice


title: CMV-QKO tumor [18.CMVCre]


title: K5-QKO tumor [9.K5Cre]

description: Gene expression data form tumours from Ad5-K5Cre treated Rb1F/F;Trp53F/F; PtenF/F p107−/− mice

source_name: Lung tumors from Ad5-K5Cre treated Rb1F/F;Trp53F/F; PtenF/F p107−/− mice


title: adjacent normal tissue [N1318]

city: Harbin

first: Yanan

state: Heilongjiang

address: No. 246, Baojian Road

department: The Second  Affiliated Hospital, Harbin Medical University

institute: Department of Otorhinolaryngology, Head and Neck Surgery

description: Gene expression in human sinonasal squamous cell carcinomas

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Human lncRNA Arrays (4x44K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with the Agilent Scanner  G2565BA.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v11.5.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 8 out of 10 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through Volcano Plot filtering. Hierarchical Clustering was performed using the Agilent GeneSpring GX software (version 11.5.1). GO analysis and Pathway analysis were performed in the standard enrichment computation method.

source_name: adjacent normal tissue

label_protocol: Total RNA from each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method.

growth_protocol: sinonasal squamous cell carcinomas tissue and matched non-tumor tissues

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions

treatment_protocol: Tissues from sinonasal squamous cell carcinomas surgery and promptly frozen in liquid nitrogen.

value: adjacent normal tissue

value: male


title: Normal lung [5.Lung]

description: Gene expression data from normal lung

source_name: Normal lung

value: normal lung

value: normal


title: K5-QKO tumor [7.K5Cre]


title: CMV-QKO tumor [16.CMVCre]


title: Normal lung [4.Lung]

description: Gene expression data from normal lung


title: CMV-QKO tumor [15.CMVCre]


title: K5-QKO tumor [10.K5Cre]


title: K5-QKO tumor [12.K5Cre]


title: Normal lung [2.Lung]

description: Gene expression data from normal lung


title: cancerous tissue [C712]

source_name: cancerous tissue

value: sinonasal squamous cell carcinomas tissue

value: female


title: adjacent normal tissue [N16]


title: adjacent normal tissue [N2530]


title: adjacent normal tissue [N1924]


title: CMV-QKO tumor [14.CMVCre]


title: Input_Tip60cKO

city: Goettingen

first: Vakhtang

last: Elerdashvili

address: Von-Siebold Str.3a

country: Germany

institute: German Center for Neurodegenerative Diseases

data_processing:
Base calling and fastq conversion were performed using Illumina pipeline scripts.
Reads were mapped to mouse genome mm10.
Duplicates were removed from BAM files by rmdup function of samtools.
Peaks were called using MACS2 with q-value < 0.1.
Genome_build: mm10
Supplementary_files_format_and_content: BAM files and peak files.

source_name: Hippocampal neurons

extract_protocol:
Chromatin immunoprecipitation was performed from fixed neuronal nuclei sorted by FACS.
Libraries for ChIP-Seq were prepared using NEBNext Ultra II DNA Library Preparation Kit from Illumina.

value: Hippocampal neurons

value: 3 months (adult)

tag: Sex

value: Male

tag: strain

value: input


title: cancerous tissue [C1318]


title: cancerous tissue [C16]


title: Normal lung [3.Lung]

description: Gene expression data from normal lung


title: H4K12ac_Control_5

value: control


title: CMV-QKO tumor [13.CMVCre]


title: Input_Control


title: K5-QKO tumor [8.K5Cre]


title: Normal lung [6.Lung]

description: Gene expression data from normal lung


title: cancerous tissue [C1924]


title: cancerous tissue [C2530]


title: adjacent normal tissue [N712]


title: H4K12ac_Control_4


title: Normal lung [1.Lung]

description: Gene expression data from normal lung


title: H4K12ac_Control_1


title: H4K12ac_Tip60cKO_5


title: H4K12ac_Control_3


title: H4K12ac_Tip60cKO_2


title: H4K12ac_Tip60cKO_1


title: H4K12ac_Tip60cKO_3


title: H4K12ac_Control_2


title: Spleen sample, day42 post infection, untreated [S3]

city: York

first: Paul

last: Kaye

address: Wentworth way

country: United Kingdom

institute: University of York

data_processing:
Adaptor sequences were removed using cutadapt version 1.8.3
Reads were further trimmed and quality scored using sickle v 1.2 with a q value of 20 and minimum length of 20bp. Unpaired reads were seperated into an R0 file
Reads were mapped to the Mus musculus version 89 reference using STAR v 2.5.1b
Reads were assigned to genes using Htseq count with the union algorithm
Differential gene expression was identified using edgeR using a generalised linear model
Genome_build: ENSEMBL v89 mus musculus

extract_protocol: Qiagen RNeasy column kit and polyA selection followed by the NEB next ultra II RNA kit

treatment_protocol: All individuals were infected with M. bovis

value: BALB/c

value: 6-8 weeks

value: infected with BCG-SSI; untreated

value: spleen


title: Spleen sample, day42 post infection, untreated [S5]


title: Spleen sample, day42 post infection, untreated [S1]


title: Spleen sample, day42 post infection, ambisome treated [S9]

value: infected with BCG-SSI; ambisome treated


title: Spleen sample, day42 post infection, untreated [S2]


title: Spleen sample, day42 post infection, untreated [S4]


title: Spleen sample, day42 post infection, ambisome treated [S6]


title: Spleen sample, day42 post infection, ambisome treated [S7]


title: Liver sample, day42 post infection, untreated [L19]

value: liver


title: Spleen sample, day42 post infection, ambisome treated [S8]


title: Liver sample, day42 post infection, untreated [L17]


title: Liver sample, day42 post infection, untreated [L18]


title: Liver sample, day42 post infection, untreated [L16]


title: Liver sample, day42 post infection, ambisome treated [L23]


title: Liver sample, day42 post infection, ambisome treated [L22]


title: Liver sample, day42 post infection, ambisome treated [L20]


title: Liver sample, day42 post infection, ambisome treated [L21]


title: Liver sample, day42 post infection, ambisome treated [L24]


title: H4K12ac_Tip60cKO_4


title: 950 PPs BCL2 Hel+

city: San Diego

first: Ashima

last: Shukla

state: CA

address: 10901 N Torrey Pines Rd, La Jolla, La Jolla

country: USA

institute: Sanford Burham Prebys Medical Discovery

description: Sample 21

data_processing:
Sequenced reads were trimmed for adaptor sequence, and mapped against the UCSC mouse genome mm10 using STAR with the default parameters, using GALAXY interface
Exons from all isoforms of a gene were merged to create one meta-transcript using HTseq using default parameters
Raw counts were input into DESeq2 and paired-wise comparisons were performed.
Supplementary_files_format_and_content: Raw counts of every sample (column), separated by tabs

source_name: Peyers Patches

growth_protocol: All the mice from same group were cagged together

extract_protocol:
Spleen, mLNS and PPs were isolated cells were directly sorted into tubes containing TRIzol and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
cDNA libraries were prepared using Nextera XT Library Prep Kit (Illumina) and libraries were sequenced on an Illumina HiSeq 2500 with single-end 50-bp reads

treatment_protocol: Cells were sorted directly into Trizol

value: BCL2 HEL pos B cells

value: 8-12 weeks


title: 950 mLNs BCL2 Hel+

description: Sample 20

source_name: Mesenteric Lymph Nodes


title: 950 Spl BCL2 Hel+

description: Sample 19

source_name: Spleen


title: 926 PPs BCL2 Hel+

description: Sample 18


title: 922 mLNs BCL2 Hel+

description: Sample 14


title: 926 mLNs BCL2 Hel+

description: Sample 17


title: 926 Spl BCL2 Hel+

description: Sample 16


title: 922 PPs BCL2 Hel+

description: Sample 15


title: 399PPs Hel+

description: Sample 12

value: HEL pos B cells


title: 399 mLNs Hel+

description: Sample 11


title: 922 Spl BCL2 Hel+

description: Sample 13


title: 392 mLNs Hel+

description: Sample 8


title: 392 PPs Hel+

description: Sample 9


title: Pool PPs Hel+

description: Sample 6


title: 392 Spl Hel+

description: Sample 7


title: Pool PPs Hel-

description: Sample 5

value: HEL neg B cells


title: Pool mLNs Hel+

description: Sample 4


title: 399 Spl Hel+

description: Sample 10


title: Pool Spl Hel-

description: Sample 1


title: Pool mLNs Hel-

description: Sample 3


title: RNA-seq TfhKO2

city: Nanjing

first: jingjing

last: chen

address: 101 Longmian Road

institute: Nanjing Medical University

data_processing:
We used Trim_galore(version 0.4.4_dev) to remove low quality sequence and adapter sequence contamination in raw RNA-seq data, then discard reads shorter than 30bp.
Filtered reads were mapped to mouse transcriptome(mm10) using the hisat2 with default parameters.
We used HTSeq-count from the HTSeq python package to calculate reads count on each transcript, then differential expressed genes were identified by DESeq2,packages(log2(fold change)>0.5 or <-0.5 and padj<0.05).
We used FPKM_count in RSeQC(An RNA-seq Quality Control Package) to calculate FPKM value for every single gene.
Genome_build: mm10
Supplementary_files_format_and_content: xlsx, gene expression value

source_name: RNA-seq TfhKO

extract_protocol:
Follicular helper T cells from wt/ko spleens were sorted by BD Aria then extracted in Tizol
The sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer's recommdendations

tag: strain background

tag: genotoype/variation

value: CD4Cre+Nsd2fl/fl (KO)

value: spleens

value: Follicular helper T cells


title: RNA-seq TfhWT1

source_name: RNA-seq TfhWT

value: wild type

tag: cell type


title: RNA-seq TfhKO1

tag: tissue


title: WT4 M95

city: Cambridge

first: Ayush

middle: T

last: Raman

state: MA

address: 75 Ames St

department: Epigenomics Program

institute: Broad Institute of MIT and Harvard

description:
Sample_45134
WT_Sample4
Processed data file: raw-counts_mm9.txt

data_processing:
RNA sequencing was performed using Illumina HiSeq 2500. All sequencing was done by the Genomic and RNA Profiling Core at the Baylor College of Medicine. For each sample, about 40 to 60 million of 101bp pair-end reads were generated. The quality of raw reads was assessed using FastQC. The average per base quality score across all the files were > 34 and had passed all the major tests.
The raw reads were aligned to the Mus musculus genome (Gencode Version M1 -- Ensembl 65/NCBIM37) using STAR v2.4.2a. The mappability of unique reads for each sample was above 89%. The htseq-count function in HTSeq with union mode (-m union) was used to accumulate the number of aligned reads that falls under the exons of the gene. The obtained read counts are analogous to the expression level of each gene across all the samples.
Normalization and differential gene expression analysis were carried out using the DESeq2 package in R.
Genome_build: MM9 (MGSCv37) or Gencode Version M1 -- Ensembl 65/NCBIM37
Supplementary_files_format_and_content: raw-counts_mm9.txt: Tab-delimited text file includes raw counts.

source_name: Hippocampus

growth_protocol: All mice used in this study were B6.129 F1-hybrids. They were group-housed with up to five mice per cage. They were maintained on a 14h light:10h dark cycle (light on at 06:00) with standard mouse chow and water ad libitum in our AAALAS-accredited facility. All research and animal care procedures were approved by the Baylor College of Medicine Institutional Animal Care and Use Committee.

extract_protocol:
We performed RNA extraction and purification from the hippocampus of male mice 3 months of age (four biological replicates of wild type and Nr2f1 het) using the miRNeasy Mini Kit (Qiagen 217004) per the manufacturer’s instructions. Genomic DNA was eliminated using an on-column DNase digestion step. RNA quality was assessed using the Agilent 2100 Bioanalyzer system prior to library preparation for deep sequencing.
Using NuGEN Ovation RNA-Seq System v2, purified double-stranded cDNA was generated from 10 ng of total RNA and amplified using both 3’ poly (A) selection and random priming. ERCC RNA Spike-In Mix 1 or 2 (Thermo Fisher) was added to the samples prior to library preparation according to the manufacturers instructions. 2 µg of each sample was sheared using the Covaris S2 focused-ultrasonicator following the manufacturer’s protocol to obtain a final library with insert size of 400 bp. The sheared samples were quantified using the NanoDrop ND-1000 spectrophotometer and Invitrogen Qubit 2.0 DNA quantitation assay. The fragment sizes were confirmed on the Agilent Bioanalyzer to verify proper shearing. A double-stranded DNA library was produced using Illumina TruSeq DNA library preparation system and the sequencing was run on a HiSeq 2500 system.

tag: strain/background

value: B6.129 F1-hybrid

value: WT

tag: age

value: 3 months

value: Male

value: Hippocampus


title: Liver sample, day42 post infection, untreated [L15]

value: BALB/c

value: 6-8 weeks

value: infected with BCG-SSI; untreated


title: Pool Spl Hel+

description: Sample 2


title: Nr2f1 het4 M97

description:
Sample_45130
HET_Sample4
Processed data file: raw-counts_mm9.txt

value: Nr2f1 het


title: WT3 M93

description:
Sample_45133
WT_Sample3
Processed data file: raw-counts_mm9.txt


title: WT2 M88

description:
Sample_45132
WT_Sample2
Processed data file: raw-counts_mm9.txt


title: Nr2f1 het3 M96

description:
Sample_45129
HET_Sample3
Processed data file: raw-counts_mm9.txt


title: Nr2f1 het2 M94

description:
Sample_45128
HET_Sample2
Processed data file: raw-counts_mm9.txt


title: Nr2f1 het1 M87

description:
Sample_45127
HET_Sample1
Processed data file: raw-counts_mm9.txt


title: WT1 M86

description:
Sample_45131
WT_Sample1
Processed data file: raw-counts_mm9.txt


title: PKCi knockdown mTS

city: Kansas City

first: Bhaswati

last: Bhattacharya

state: Kansas

address: 3901 Rainbow Blvd

department: Pathology and Laboratory Medicine

institute: University of Kansas Medical Center

data_processing:
bcl2fastq Conversion Software v1.8.4 from illumina was used to generate fastq files
reads were  mapped to the mouse GRCm38 genome with STAR-2.5.2b --genomeDir GRCm38 --readFilesIn R1.fastq R2.fastq --runThreadN 16 --outSAMstrand  Field intronMotif --outSAMattrIHstart 0 --outSAMattributes All --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM GeneCounts
differential gene expression was deterimined using stringtie-1.3.0.Linux_x86_64/ Aligned.sortedByCoord.out.bam -p 16 -o .gtf -G Mus_musculus.GRCm38.86.gtf , cuffmerge v1.0.0 -g Mus_musculus.GRCm38.86.gtf -p 16 -s mouse/WholeGenomeFasta/genome.fa assembly_GTF_list.txt, HTSeq-0.6.1p1/scripts/htseq-count -f bam -r pos -s no -t exon -i gene_id -m union Aligned.sortedByCoord.out.bam stringtie_mer  ged.gtf > htcount.out
Genome_build: GRCm38
Supplementary_files_format_and_content: Gene-level differential expression. Tests differences in the summed CPM of transcripts sharing each gene_id EdgeR v 3.12.1 fit <- glmFit(firstglm,design)

source_name: trophoblast stem cells

growth_protocol: Mouse TS cells were routinely cultured under stem condition using standard protocol which consists of 20% FBS in the presence of FGF4 & heparin (1µg/ml) in MEF conditioned media.

extract_protocol:
Total RNA from the whole cell-extract was isolated using RNeasy Mini Kit (#74104) from Qiagen per the manufacturer’s protocol with on column DNase digestion.  RNA concentrations were quantified using a NanoDrop Spectrophotometer at a  wavelength of 260nm. Integrity of the total RNA samples was evaluated using an Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Santa Clara, CA) and the samples with RNA integrity values above 9.0  were used for the sequencing experiments.
Total RNA was used to construct RNA-seq libraries using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit according to manufacturer's instructions.

treatment_protocol: Mouse TS cells were treated with lentiviral supernatants for 24 hours either containing scrambled or shRNA against Prkci mRNA and transduced colonies were selected using 1µg/ml puromycin.

value: trophoblast stem cells


title: Scramble Control mTS


title: RNA-seq TfhWT2


title: KO DES Replicate 2

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: Gene expression in corn oil vehicle treated or DES treated Six1 wildtype or conditional knockout mice.

hyb_protocol: For each sample, 1.65ug of Cy3 labeled cRNAs were fragmented and hybridized for 17 hours in a rotating hybridization oven.

scan_protocol: Slides were washed and then scanned with an Agilent Scanner.

data_processing: Data was obtained using the Agilent Feature Extraction software (v12), using the 1-color defaults for all parameters.

source_name: Uterine tissue, KO DES, replicate 2

label_protocol: Starting with 400ng of total RNA, Cy3 labeled cRNA was produced following the manufacturer’s protocol.

extract_protocol: RNA was isolated from frozen uterine horn tissue using the RNeasy Mini Kit (Qiagen, Hilden, Germany) following the manufacturer’s recommendations. The protocol includes lysis of uterine cells, and an on-column DNase digestion. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Female Six1+/+ and Six1d/d pups were given daily subcutaneous injections (0.02 ml) of 1 mg/kg diethylstilbestrol (DES) in corn oil or corn oil (CO) alone as a vehicle control on the day of birth (postnatal day 1, PND1) through PND5. Mice were euthanized by CO2 asphyxiation at 6 mos and uterine horn tissue was collected and frozen at -80C for molecular analysis.

value: uterine horn tissue

tag: treatment group

value: DES

tag: genotype


title: WT CON Replicate 4

source_name: Uterine tissue, WT CON, replicate 4

value: Corn oil vehicle

value: Six1 wildtype


title: D226G H3K27 ChIP-Seq 2

city: Boston

first: Changmeng

last: Cai

state: Massachusetts

address: 100 William T. Morrissey Blvd.

institute: University of Massachusetts Boston

description:
technical replicate in cell line overexpressing D226G FOXA1
LN_H3K27ac_D226G_ATTACTCG_peaks.narrowPeak
LN_H3K27ac_D226G_ATTACTCG_treat_pileup.bw

data_processing:
Raw reads were aligned to hg19 using bwa (version 0.7.2-r351)
sam files are converted to bam with samtools (version 0.1.18 (r982:295))
MACS2 (version 2.0.10.20131216) was used to call peak on the bam files
bedGraph files containing signal per million reads produced from MACS2 was converted to bigwig files with ucsctool kit (315)
Genome_build: GRCh37
Supplementary_files_format_and_content: bigWig and narrowPeak files containing normalized signal and peak intervals

source_name: LNCaP

growth_protocol: LNCap derived tetracycline-inducible FOXA1 overexpressing stable cells were maintained in RPMI-1640 with 10% tetracycline-free FBS

extract_protocol: Libraries construction was performed using ThruPLEX DNA-seq 48D Kit (Rubicon Genomics)

treatment_protocol: LNCaP stable cells grown in RPMI1640 with 5% CSS were treated with doxycycline for 2 days

value: prostate cancer cell line


title: KO CON Replicate 3

source_name: Uterine tissue, KO CON, replicate 3


title: M253K H3K27 ChIP-Seq 1

description:
technical replicate in cell line overexpressing M253K FOXA1
LN_H3K27ac_M253K_ATTACTCG_peaks.narrowPeak
LN_H3K27ac_M253K_ATTACTCG_treat_pileup.bw


title: WT H3K27 ChIP-Seq 1

description:
technical replicate in cell line overexpressing WT FOXA1
LN_H3K27ac_WT_ATTACTCG_peaks.narrowPeak
LN_H3K27ac_WT_ATTACTCG_treat_pileup.bw


title: D226G H3K27 ChIP-Seq 1


title: M253K H3K27 ChIP-Seq 2


title: KO CON Replicate 2

source_name: Uterine tissue, KO CON, replicate 2


title: M253K FOXA1 ChIP-Seq 2

description:
technical replicate for overexpressing M253K FOXA1
LN_V5FOXA1_M253K_CGCTCATT_peaks.narrowPeak
LN_V5FOXA1_M253K_CGCTCATT_treat_pileup.bdg.bw


title: WT H3K27 ChIP-Seq 2


title: WT DES Replicate 4

source_name: Uterine tissue, WT DES, replicate 4


title: WT DES Replicate 3

source_name: Uterine tissue, WT DES, replicate 3


title: WT CON Replicate 1

source_name: Uterine tissue, WT CON, replicate 1


title: KO DES Replicate 4

source_name: Uterine tissue, KO DES, replicate 4


title: WT CON Replicate 3

source_name: Uterine tissue, WT CON, replicate 3


title: KO DES Replicate 3

source_name: Uterine tissue, KO DES, replicate 3


title: KO CON Replicate 4

source_name: Uterine tissue, KO CON, replicate 4


title: WT DES Replicate 1

source_name: Uterine tissue, WT DES, replicate 1


title: KO DES Replicate 1

source_name: Uterine tissue, KO DES, replicate 1


title: M253K FOXA1 ChIP-Seq 1


title: WT CON Replicate 2

source_name: Uterine tissue, WT CON, replicate 2


title: KO CON Replicate 1

source_name: Uterine tissue, KO CON, replicate 1


title: KO mice arteries, biological rep2

city: Wuhan

first: Hongliang

last: Li

state: Hubei

address: JieFang Road 238, Wuhan

department: Department of Cardiology

institute: Renmin Hospital of Wuhan University

description: Gene expression data from KO mice artery sufferd from wire injury

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45℃.

scan_protocol: GeneChips were scanned using the Scanner 7G.

data_processing: The data were analyzed with Expression Console using Affymetrix default analysis settings and global scaling as normalization method. RMA analysis was employed to evaluate the gene expression

source_name: mice artery sufferd from wire injury

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 400ng total RNA

growth_protocol: The mice were exposed to a 12-h light/dark cycle with controlled temperature and humidity. Food and water were provided ad libitum.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Mice were treated with wire-injury operation, and the arteries were collected at 14 days post-injury and were immediately put in RNAlatter reagent.

value: IRF4 KO


title: WT mice arteries, biological rep1

description: Gene expression data from WT mice artery sufferd from wire injury


title: WT DES Replicate 2

source_name: Uterine tissue, WT DES, replicate 2


title: KO mice arteries, biological rep1


title: WT mice arteries, biological rep3


title: WT mice arteries, biological rep2


title: KO mice arteries, biological rep3


title: D226G FOXA1 ChIP-Seq 1

description:
technical replicate for overexpressing D226G FOXA1
LN_V5FOXA1_D226G_TCCGGAGA_peaks.narrowPeak
LN_V5FOXA1_D226G_TCCGGAGA_treat_pileup.bdg.bw


title: D226G DHT 3

description:
technical replicate in cell line overexpressing M253K FOXA1, under DHT condition
RNA-seq_FOXA1_mutants_DHT.xlsx

data_processing:
raw reads were submitted to usegalaxy.org for analysis via Tophat pipeline, and differential gene expression files were downloaded from galaxy
Genome_build: GRCh37
Supplementary_files_format_and_content: excel  file for gene level RPKM

extract_protocol:
RNA was extracted with TRIzol Reagent (Invitrogen) based on manufacturer’s protocol
TruSeq® Strnd Total RNA LT (Illumina) was used for library construction

treatment_protocol: LNCaP stable cells grown in RPMI1640 with 5% CSS were treated with doxycycline for 2 days, then DHT or EtOH for 16hours


title: WT FOXA1 ChIP-Seq 2

description:
technical replicate for overexpressing WT FOXA1
LN_V5FOXA1_WT_ATTACTCG_peaks.narrowPeak
LN_V5FOXA1_WT_ATTACTCG_treat_pileup.bdg.bw


title: D226G EtOH 1

description:
technical replicate in cell line overexpressing D226G FOXA1, under EtOH condition
RNA-seq_FOXA1_mutants_EtOH.xlsx


title: D226G FOXA1 ChIP-Seq 2


title: D226G EtOH 2


title: D226G DHT 4


title: H69AR-replicate1

city: New York

first: Hideo

last: Watanabe

state: NY

address: One Gustave L. Levy Place

department: Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Aligned to hg19 with Bowtie2 with a setting of -X 2000 and defalut parameters.
Blacklist (Buenrostro and chrM) is filtered out from aligned data and duplicate reads are removed. Triplicates data are merged into a single bam file.
Two fragment ends were shifted +4bp for + strand and -5bp for - strand, and trimmed to 9bp length.
Peaks were called using MACS2 with parameters --nomodel --extsize 100 --shift 50 -g hs -B --nolambda --keep-dup all.
Genome_build: hg19
Supplementary_files_format_and_content: BED files with peaks

source_name: Small Cell Lung Cancer

growth_protocol: H69 and H69AR cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum.

extract_protocol:
Sorted cells were washed once in cold PBS and lysed in cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). Lysed nuclei were incubated in Tn5 transposition reaction mix and purified using MinElute Reaction Cleanup kit (Qiagen).
ATAC-seq fragments from one set of replicates for H69 and H69AR cells were size selected for fragments between 115 and 600 bp using Pippin Prep 2% Agarose Gel Cassettes and the Pippin Prep DNA Size Selection System (Sage Science). Post size-selection, ATAC libraries were amplified and Nextera sequencing primers ligated using Polymerase Chain Reaction (PCR). Finally, PCR primers were removed using Agencourt AMPure XP bead cleanup (Beckman Coulter/Agencourt) and library quality was verified using a Tapestation machine. High quality ‘multiplexed’ DNA libraries were sequenced on the Illumina HiSeq 2000.

value: Small Cell Lung Cancer

tag: passages

tag: experimental conditions

value: Basal conditions 48h


title: D226G DHT 1

description:
technical replicate in cell line overexpressing D226G FOXA1, under DHT condition
RNA-seq_FOXA1_mutants_DHT.xlsx

source_name: LNCaP


title: M253K EtOH 2

description:
technical replicate in cell line overexpressing M253K FOXA1, under EtOH condition
RNA-seq_FOXA1_mutants_EtOH.xlsx


title: WT FOXA1 ChIP-Seq 1


title: M253K EtOH 1


title: H69-replicate2


title: D226G DHT 2


title: WT DHT 2

description:
technical replicate in cell line overexpressing WT FOXA1, under DHT condition
RNA-seq_FOXA1_mutants_DHT.xlsx


title: WT EtOH 1

description:
technical replicate in cell line overexpressing WT FOXA1, under EtOH condition
RNA-seq_FOXA1_mutants_EtOH.xlsx


title: H69-replicate3


title: H69AR-replicate2


title: H69AR-replicate3


title: H69-replicate1


title: BMPC

city: Clayton

first: Wei

last: Shi

state: VIC

address: 15 Innovation Walk

department: Department of Biochemistry and Molecular Biology

country: Australia

institute: Monash University

data_processing:
The Mouse and Human RNA-seq samples were mapped to the mm10 and hg38 genomes respectively, by using Subread-1.6.0. Only uniquely mapped fragments were retained. Genewise counts were obtained using featureCounts. Only the genes that had a CPM (counts per million mapped fragments) value greater than 0.5 in at least 2 libraries, and Immunoglobulin genes were removed from the Mouse data.
Counts were converted to log2 CPM, quantile-normalized, and precision-weighted with the voom function of the limma package, along with a few samples from public data sets (GSE60927 and GSE70981, see the manuscript for details). Log2 CPM values were then converted to log2 FPKM (fragments per kilobase of transcript per million mapped fragments) values.
Two linear models were fitted on the log2 FPKM values of each gene in the Mouse and Human samples respectively, and empirical Bayes moderated t-statistic was used to assess differences in expression. Genes were called differentially expressed (DE) if they achieved a false discovery rate (FDR) of 0.05 or less (for the Mouse genes), or an FDR of 0.2 or less (for the Human genes).
Genome_build: mm10 and hg38 for Mouse and Human samples
Supplementary_files_format_and_content: TAB-delimited text files including normalized log2-FPKM values for each library. The supplementary files, ‘MM10_Supp_Counts.txt’ and ‘HG38_Supp_Counts.txt’, include raw fragment counts of genes in each Mouse/Human library (before CPM/Ig gene filtering).

source_name: Bone marrow

growth_protocol: Bone marrow from IRF4 flox/+ [Irf4het] or Irf4flox/- [Irf4Hom]  were transferred into congenically marked host mice with uMT bone marrow, which were subsequently treated with tamoxifen and days 1,2,7 and 8 and harvested on day 14. Donor plasma cells were sorted from mice spleen and used for RNA sequencing. Bone marrow plasma cells and follicular B cells (spleen) were used as control.  Additionally two cell lines MPC-11 (mouse plasmacytoma) and MM1.S (human myeloma) were infected with Cas9 and either sgRNA against Irf4 or empty vector and treated with doxycycline and sorted on day 3 after deletion.

extract_protocol:
RNA purification was performed following the manufacturer’s protocol using the RNeasy Plus Mini Kit (Qiagen).
mRNA reverse transcription and cDNA libraries were prepared using the Nextera DNA Library preparation kit (Illumina) following the manufacturer’s instructions.

treatment_protocol: Cells were washed twice with PBS prior to RNA extraction.

tag: cell line

value: plasma cells

value: WT


title: WT DHT 1


title: MPC.11.sgRNA.IRF4KO.Rep1

source_name: Lymph node

value: plasmacytoma


title: MPC.11.empty.vec.Rep2


title: WT EtOH 2


title: MPC.11.empty.vec.Rep1


title: IRF4.flox.pos.Rep2

source_name: Spleen

value: Irf4 flox/+


title: IRF4.flox.pos.Rep1


title: IRF4.flox.neg.Rep1

value: Irf4 flox/-


title: IRF4.flox.neg.Rep2


title: tcx2 x CYCD6:GFP rep 1

city: Ames

first: Natalie

middle: M

last: Clark

state: IA

address: Advanced Teaching and Research Building 2213 Pammel Drive

department: Plant Pathology and Microbiology

institute: Iowa State University

description:
processed data file:
tcx2mutant_cellspecific_FPKM.csv
name in processed data file:
TCXC61

data_processing:
Reads were aligned to TAIR10 genome using Bowtie2 and Cufflinks
Reads were mapped using Rsubread
FPKM values were calculated using edgeR
Genome_build: TAIR10
Supplementary_files_format_and_content: Comma separated variable file containing FPKM values for each gene in each sample

organism: Arabidopsis thaliana

source_name: Root

growth_protocol: Arabidopsis thaliana seedlings were grown on plates supplmeneted with 1x MS, 1% sucrose on top of Nitex mesh for 5 days at 22C in 16hr light/8hr dark cycle

extract_protocol:
Roots were protoplasted and sorted for GFP-positive cells. RNA was extracted from collected cells using Qiagen RNEasy Micro Prep Kit
Libraries were constructed using Clontech SMARTer® Stranded RNA-Seq Kit

value: root

value: GFP-positive cells

tag: genotype/variation

value: tcx2 x CYCD6:GFP


title: FoB

value: Follicular B cells


title: tcx2 x WOX5:GFP rep 2

description:
processed data file:
tcx2mutant_cellspecific_FPKM.csv
name in processed data file:
TCXW52

value: tcx2 x WOX5:GFP


title: tcx2 x TMO5:3xGFP rep 1

description:
processed data file:
tcx2mutant_cellspecific_FPKM.csv
name in processed data file:
TCXT1

value: tcx2 x TMO5:3xGFP


title: tcx2 x WOX5:GFP rep 3

description:
processed data file:
tcx2mutant_cellspecific_FPKM.csv
name in processed data file:
TCXW53


title: tcx2 x TMO5:3xGFP rep 2

description:
processed data file:
tcx2mutant_cellspecific_FPKM.csv
name in processed data file:
TCXT2


title: tcx2 x FEZ:FEZ-GFP rep 2

description:
processed data file:
tcx2mutant_cellspecific_FPKM.csv
name in processed data file:
TCXF2

value: tcx2 x FEZ:FEZ-GFP


title: tcx2 x CYCD6:GFP rep 2

description:
processed data file:
tcx2mutant_cellspecific_FPKM.csv
name in processed data file:
TCXC62


title: tcx2 mutant replicate 3

data_processing:
Reads were aligned using Bowtie and FPKM values were obtained using Cufflinks.
Differential expression was calculated using PoissonSeq
Genome_build: TAIR10
Supplementary_files_format_and_content: FPKM values for each gene in WT and tcx2 mutant samples (csv format)

source_name: root tissue

growth_protocol: Roots were grown for 5 days on Nitex mesh on 1X MS, 1% sucrose agar on long day (16 hr light/8 hr dark) cycle at 22C

extract_protocol:
Approximately 1mm of root was sectioned and collected in RLT buffer+beta mercaptoethanol. Total RNA was extracted using the Qiagen MicroRNEasy kit.
Libraries were constructed using the NEBNext Ultra II Directional RNA Library Prep Kit.

value: 5 days old

value: tcx2 mutant


title: tcx2 x FEZ:FEZ-GFP rep 1

description:
processed data file:
tcx2mutant_cellspecific_FPKM.csv
name in processed data file:
TCXF1


title: MPC.11.sgRNA.IRF4KO.Rep2


title: tcx2 mutant replicate 1


title: WT replicate 1

value: wild type


title: tcx2 x FEZ:FEZ-GFP rep 3

description:
processed data file:
tcx2mutant_cellspecific_FPKM.csv
name in processed data file:
TCXF3


title: tcx2 x TMO5:3xGFP rep 3

description:
processed data file:
tcx2mutant_cellspecific_FPKM.csv
name in processed data file:
TCXT3


title: WT replicate 3


title: tcx2 x WOX5:GFP rep 1

description:
processed data file:
tcx2mutant_cellspecific_FPKM.csv
name in processed data file:
TCXW51


title: PET111:GFP-negative cells 5 days 16 hours rep 1

data_processing:
Filtered samples using fastq-mcf from eautils
Mapped filtered samples to Arabidopsis genome using Tophat
Assembled transcriptomes using Cufflinks and Cuffmerge
Extracted FPKM for each gene using Tablemaker and Ballgown
Genome_build: TAIR10
Supplementary_files_format_and_content: Comma separated FPKM values for each gene in each sample

growth_protocol: PET111:GFP seeds were sterilized using bleach and HCl for 2 hours, imbibed and vernalized at 4C for 48 hours before plating. Seeds were plated on top of Nitex mesh on plates containing 1xMS, 1% sucrose. Seeds were grown for 4-6 days on 16hr light/8hr dark at 22C.

extract_protocol:
Approximately 1mm of the root tips were collected and protoplasted. Protoplasts were sorted using a MoFlo cell sorter, and GFP-negative cells were collected in a solution of RLT buffer and beta-mercaptoethanol. Total RNA was extracted using the Qiagen RNeasy Micro Kit.
Libraries were synthesized and multiplexed using the Illumina TruSeq Stranded mRNA kit

value: 5 days 16 hours

value: PET111:GFP-negative cells


title: PET111:GFP-negative cells 6 days rep 2

source_name: PET111:GFP-negative cells 6 days

value: 6 days


title: PET111:GFP-negative cells 5 days 16 hours rep 2


title: WT replicate 2


title: PET111:GFP-negative cells 6 days rep 1


title: PET111:GFP-negative cells 5 days 8 hours rep 2

value: 5 days 8 hours


title: PET111:GFP-negative cells 5 days 8 hours rep 1


title: PET111:GFP-negative cells 5 days rep 3

source_name: PET111:GFP-negative cells 5 days

value: 5 days


title: tcx2 x CYCD6:GFP rep 3

description:
processed data file:
tcx2mutant_cellspecific_FPKM.csv
name in processed data file:
TCXC63


title: tcx2 mutant replicate 2


title: PET111:GFP-negative cells 5 days rep 2


title: PET111:GFP-negative cells 4 days 8 hours rep 1

value: 4 days 8 hours


title: PET111:GFP-negative cells 6 days rep 3


title: PET111:GFP-negative cells 4 days rep 3

source_name: PET111:GFP-negative cells 4 days

value: 4 days


title: PET111:GFP-negative cells 4 days 16 hours rep 2

value: 4 days 16 hours

value: root


title: PET111:GFP-negative cells 4 days rep 2


title: PET111:GFP-negative cells 4 days 16 hours rep 1


title: PET111:GFP-negative cells 4 days rep 1


title: PET111:GFP-negative cells 4 days 16 hours rep 3


title: PET111:GFP-negative cells 4 days 8 hours rep 2


title: PET111:GFP-negative cells 5 days rep 1


title: AGL42:GFP negative rep 1

data_processing:
cDNA libraries were sequenced using an Illumina HiSeq 2500 sequencing machine
Adapters and low quality reads were filtered out using ea-utils software. Reads longer than 30bp with a quality score was greater than 30 were kept.
Clean reads were mapped against the TAIR 10 reference genome using the TopHat v2.0.13
Transcripts were assembled using Cufflinks (version 2.1.1). Normalized reads (FPKM values) were calculated at this step.
Genome_build: TAIR 10 reference genome
Supplementary_files_format_and_content: FPKM values for each gene in each sample. Rows are genes, columns are samples.

source_name: AGL42:GFP seedlings

growth_protocol: Seeds were sterilized using 50% bleach. Seeds were imbibed in water and vernalized at 4C for 2 days. Seeds were plated on mesh squares on media containing 1xMS salts and 1% sucrose. Seeds were grown for 5 days

extract_protocol:
Roots were cut and protoplasted. GFP positive (negative for the AGL42:GFP negative samples) cells were collected using a MoFlo cell sorter in RLT buffer and beta mercaptoethanol. RNA was extracted from sorted cells using the Qiagen RNeasy Micro Kit
cDNA synthesis and amplification was performed using the SMARTer Low Input RNA Kit for sequencing. Fragmentation was done using Covaris ultrasonicator. Libraries were prepared using the Low Input Library Prep Kit.

tag: ecotype

value: meristematic non stem cells (NS)

value: root tip


title: WOX5:GFP rep 2

source_name: WOX5:GFP seedlings

value: quiescent center (QC)


title: TMO5:3xGFP rep 4

source_name: TMO5:3xGFP seedlings

value: xylem stem cells


title: WOX5:GFP rep 1


title: WOX5:GFP rep 3


title: AGL42:GFP negative rep 3


title: TMO5:3xGFP rep 1


title: TMO$:3xGFP rep 2


title: J2341:GFP rep 3

source_name: J2341:GFP seedlings

value: columella stem cells (CSC)


title: J2341:GFP rep 2


title: TMO5:3xGFP rep 3


title: FEZ:FEZ:GFP rep 3

source_name: FEZ:FEZ:GFP seedlings

value: epidermis/lateral root cap (Epi/LRC)


title: J2341:GFP rep 1


title: FEZ:FEZ:GFP rep 2


title: FEZ:FEZ:GFP rep 1


title: CVP2:NLS:VENUS rep 4

source_name: CVP2:NLS:VENUS seedlings

value: protophloem


title: AGL42:GFP negative rep 4


title: AGL42:GFP negative rep 2


title: CVP2:NLS:VENUS rep 3


title: CVP2:NLS:VENUS rep 1


title: CYCD6:GFP rep 2

source_name: CYCD6:GFP seedlings

value: cortex endodermis initial (CEI)


title: CYCD6:GFP rep 1


title: CYCD6:GFP rep 3


title: AGL42:GFP rep 4

value: stem cell niche (SCN)


title: AGL42:GFP rep 3


title: AGL42:GFP rep 1


title: AGL42:GFP rep 2


title: CHLA-90_shREST_1

first: Emily

last: Bernstein

address: 1470 Madison Avenue, 6th floor Rm 302

department: Oncological Sciences

institute: Mount Sinai School of Medicine

description:
CHLA90_shREST_FPKM.txt
C90shREST5.R1

data_processing:
Reads were aligned using STAR (Dobin et al., 2013) amd featureCounts.
The log2 fold change was calculated with DESeq2 (Varet et al., 2016) and differentially expressed genes were identified with a log2 fold-change >0.8-1 and p value<0.05.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: fastq - raw illumina reads.  txt - gene expression in FPKM

source_name: Cell Culture

growth_protocol: grown in DMEM supplemented with 20% FBS, penicillin and streptomycin

extract_protocol:
RNA was extracted using RNeasy mini kit (Qiagen, #74104)
Poly-A RNA was isolated using NEXTFLEX® Poly(A) Beads and libraries prepared with the NEXTFLEX® Rapid Directional RNA-Seq Library Prep Kit (PerkinElmer).

tag: cell line or tissue

tag: cell or tissue type

value: CHLA-90 ATRX in-frame fusion metastatic neuroblastoma control RNA-seq

tag: treatment

value: shREST


title: CHLA-90_control_2

description:
CHLA90_shREST_FPKM.txt
C90shSCR.R2

value: control


title: CHLA-90_control_1

description:
CHLA90_shREST_FPKM.txt
C90shSCR.R1


title: CHLA-90_shREST_2

description:
CHLA90_shREST_FPKM.txt
C90shREST5.R2


title: Trans10_H2O2 shock_10 min_rep3

city: Beijing

first: Yongliang

last: Yan

state: Haidian

address: 12th Zhongguancun Nanjie

institute: Chinese Academy of Agricultural Sciences

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Escherichia coli Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

organism: Escherichia coli

source_name: E.coli Tans10 after H2O2 shock for 10 min

label_protocol: cDNA was synthesized from 10 µg total RNA using One-Cycle Target Labeling and Control Reagents (Affymetrix) to produce biotin-labeled cDNA. The quality and quantity of the original RNA samples and of the cDNA probes generated for array hybridization were determined with NanoDrop ND-2000 Spectrophotometer (Thermo Scientific)

growth_protocol: E. coli Trans10 and the derivatives strain Trans10-nfiS were cultured in LB broth at 30 °C overnight and then transferred into fresh LB broth the next day till the OD600 was raised to 0.6.

extract_protocol: Total RNA samples were extracted from the 3 pairs of WT and Trans10-nfiS strain using the Qiagen RNeasy Mini Kit (Qiagen)

treatment_protocol: 20 mM H2O2 was added into the medium and incubated at 30 °C, 220 rpm for 10 min.

tag: strain


title: SK-N-FI-MS2-NLS-ATRX-helicase_2

description:
SKNFI_MS2_FPKM.txt
FI.MS2.IFF.R2

growth_protocol: grown in DMEM supplemented with 10% FBS, penicillin and streptomycin

value: SK-N-FI

value: SK-N-FI ATRX wild-type metastatic neuroblastoma control RNA-seq

value: expressing MS2-NLS-ATRX-helicase


title: CVP2:NLS:VENUS rep 2


title: Trans10-nfiS_H2O2 shock_10 min_rep1

source_name: Recombinant E.coli strain Tans10-nfiS after H2O2 shock for 10 min


title: Trans10-nfiS_H2O2 shock_10 min_rep3


title: Trans10_H2O2 shock_10 min_rep1


title: Trans10-nfiS_H2O2 shock_10 min_rep2


title: knockout, sample2

city: Berlin

first: Fritz

last: Rathjen

address: Robert-Roessle-str. 10

institute: Max-Delbrueck-Center

description: Gene expression data from CAR knockout E10.5 embryonic hearts

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

source_name: CAR knockout E10.5 hearts

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: CAR +/- mice were breed and female, pregnant mice were dissected accordingly to embryonic developmental day E10.5. After embryos were collected, hearts were frozen in liquid nitrogen.

extract_protocol: RNA isolation was performed as described in Rneasy MiniKit by Qiagen.

treatment_protocol: No treatment, hearts were collected and RNA was isolated.

value: heart

tag: developmental stage

value: CAR KO


title: wild type, sample5

description: Gene expression data from CAR wild type E10.5 embryonic hearts

source_name: CAR wild type E10.5 hearts

value: wild type


title: SK-N-FI-MS2-NLS-ATRX-helicase_1

description:
SKNFI_MS2_FPKM.txt
FI.MS2.IFF.R1


title: SK-N-FI-MS2-NLS_2

description:
SKNFI_MS2_FPKM.txt
FI.MS2.R2

value: expressing MS2-NLS-control


title: knockout, sample5


title: SK-N-FI-MS2-NLS_1

description:
SKNFI_MS2_FPKM.txt
FI.MS2.R1


title: Trans10_H2O2 shock_10 min_rep2


title: knockout, sample4


title: wild type, sample3


title: wild type, sample2


title: wild type, sample4


title: wild type, sample1


title: knockout, sample3


title: knockout, sample1


title: CD3+ cells, Naïve (3' V(D)J scRNASeq)

city: Toronto

first: Jastaranpreet

last: Singh

state: Ontario

address: 2075 Bayview Avenue

country: Canada

institute: University of Toronto

data_processing:
I1 read: contains the sample index.
R1 read: contains the cell barcode (first 16 nt) and UMI (next 10 nt).
R2 read: contains the RNA sequence.
Filtering (Immunarch using R software)
Genome_build: hg19
Supplementary_files_format_and_content: CSV file containing individual cells (marked by unique barcodes), and their expression of V, D, J and CDR3 genes.

source_name: CD3+ cells

growth_protocol: All mice were maintained in specific pathogen free conditions.

extract_protocol:
Splenic CD3+ cells were FACS sorted.
10x sample preparation - Samples were prepared as outlined by 10x genomics Single Cell V(D)J Reagent Kits v1 user guide. 31.7ul of the cell suspension was loaded onto the 10x single cell A chip targeting 2400 cells per sample. After droplet generation, samples were transferred onto a pre-chilled 96 well plate (Eppendorf), heat sealed and incubated overnight in a Veriti 96-well thermos cycler (Thermo Fisher) for the reverse transcriptase (RT) and template switching (TS) reactions. Following the RT and TS reaction, cDNA was recovered using the Recovery Agent provided by 10x and subsequently cleaned up using a Silane DynaBead (10x Genomics) mix as outlined by the user guide. Purified cDNA was amplified,cleaned up using SPRIselect beads (Beckman). Samples were run undiluted on a Bioanalyzer (Agilent Technologies) to determine cDNA concentration. For TCR libraries, 2ul of cDNA library was diluted in 33ul of nuclease-free water before undergoing a series of target enrichment reactions. These enriched libraries were then fragmented, ligated and indexed as described in the user guide. For the gene expression library, samples were prepared as outlined by the Single Cell V(D)JReagent Kits v1 user guide with modifications to the PCR cycles based on the calculated cDNA concentration.
Sequencing - The molarity of each library was calculated based on library size as measured bioanalyzer (Agilent Technologies) and qPCR amplification data (Roche). Samples were pooled and normalized to 10 nM, then diluted to 2 nM using elution buffer (Qiagen) with 0.1% Tween20 (Sigma). Each 2 nM pool was denatured using 0.2N NaOH at equal volumes for 5 minutes at room temperature. Library pools were further diluted to 20 pM using HT-1 (Illumina) before being diluted to a final loading concentration of 1.8 pM. 1300ul from the 1.8 pM pool was loaded into Nextseq Midoutput cartridge (Illumina) for cluster generation. 5' expression libraries were sequenced on a Nextseq with the following run parameters: Read 1 - 26 cycles, read 2 - 98 cycles, index 1 - 8 cycles. The enriched V(D)J libraries were sequence paired-end 150 cycles, index 1-8 to a targeted depth of 5,000 read pairs/target cell while the gene expression libraries were sequenced to a targeted depth of 40,000 read pairs/cell.

treatment_protocol: Bulk CD7+ progenitor T-cells (proT-cells) sorted from day 13-14 naïve- or SR1-CD34+/OP9-DL1 cultures were intrahepatically injected into non-irradiated 2-5 day old immunodeficient neonatal mice. Splenocytes were harvested from mice 10–12 weeks after intrahepatic injection proT-cells.

value: CD3+ cells


title: CD3+ cells, SR1 (3' V(D)J scRNASeq)


title: CD3+ cells, SR1 (5' scRNAseq)

data_processing:
I1 read: contains the sample index.
R1 read: contains the cell barcode (first 16 nt) and UMI (next 10 nt).
R2 read: contains the RNA sequence.
Filtering (Seurat using R software)
Normalization (Seurat using R software)
Scaling (Seurat using R software)
Genome_build: hg19
Supplementary_files_format_and_content: Text file containing matrix of individual cells (marked by unique barcodes) and their expression values for genes.


title: Day 4 CNTF Rep 4 [LAN-5]

city: Frankfurt

first: Sebastian

last: Lobentanzer

address: Max-von-Laue-Str. 9

department: Pharmacology

institute: Johann-Wolfgang-von-Goethe University

description:
48-LA5CN4-4_S48
Small RNA sequencing
processed data file: mirexpress2_counts_raw.csv

data_processing:
Adapter trim and quality filtering using flexbar 3.4.0, miRBase alignment: miRExpress 2.1.4: Data parse (“Raw_data_parse”), statistics generation (“statistics_reads”), alignment (“alignmentSIMD”, “analysis”).
Count readout for all alignments: R/Rsubread 1.28.1
Genome_build: miRBase v21
Supplementary_files_format_and_content: mirexpress2_counts_raw.csv: Comma-delimited text file contains raw count values. Row names in miRExpress file contain mature human miR name.

source_name: LAN-5 neuroblastoma

growth_protocol: Cells were grown in 50/50 mixture of DMEM and RPMI media, with 20% FCS added, under 8% CO2 atmosphere. Cell splitting was performed weekly at 80% confluency.

extract_protocol:
Total RNA was extracted by TRIzol lysis with 1 ml of TRIzol per well. RNA was precipitated with pure Ethanol and washed with 85% Ethanol, according to the manufacturers instructions.
An even amount of 150 ng RNA per sample was used for small-RNA library construction using the New England BioLabs NEB-next multiplex small-RNA library construction kit. The library was size selected based on DNA 1000 LabChip kits by 2100 Bioanalyzer (Agilent Technologies) results to 146 bp long transcripts which include the barcodes, adaptors and ca. 20 bp long miRs. This ensures that sequenced transcripts are in the maximum length of 30 bp only. Libraries were quantified using the highly sensitive fluorescent dye-based Qubit® ds DNA HS Assay Kit (Invitrogen). Sequencing was run in The NextSeq Series desktop sequencing system of the Illumina platform (all 48 samples on one chip). The number of Pass Filter reads per sample was at the range of (13-14*10^6 reads). Read counts and quality for each sample were evaluated with the BaseSpace Sequencing QC report tool.

treatment_protocol: Cells were treated once with 100 ng/ml (LA-N-2) or 10 ng/ml (LAN-5) of CNTF in deionized water, 24h after seeding. CNTF (or pure water for control) was added to existing medium. Medium was not changed for the duration of the experiment (max. 5 days). For short periods (30 and 60 minutes), samples were incubated at Day 2 and compared to Day 2 controls.

value: Immortalized human nervous cell

tag: rin

tag: Sex

value: Male

value: CNTF

tag: time point

value: Day 4


title: CD3+ cells, Naïve (5' scRNAseq)

tag: cell type


title: 8_alb-SREBP-1c

city: Duesseldorf

first: Birgit

last: Knebel

address: Auf'm Hennekamp 65

department: Cinical Biochemistry and Pathobiochemistry

institute: German Diabetes Center

description: RMA expression value derived from TAC software; RMA gene analysis

hyb_protocol: Amplified cDNA was hybridized on Affymetrix Mouse Gene ST 1.0 arrays (Affymetrix)

scan_protocol: Detection of probe intensities was performed using a GeneChip scanner 3000 7G (GDAS 1.4 package, Affymetrix).

data_processing: The data were analyzed with Affymetrix Expression  Console  using default analysis settings for RMA analyses  for  gene default and exon default .CHP files.

source_name: C57Bl6-TgN alb-HA-hSREBP-1c-NT

label_protocol: 150 ng total RNAwas amplified using the Ambion WT Expression Kit and the WT Terminal Labeling Kit (Affymetrix, Freiburg, Germany).

extract_protocol: Total RNA extraction was made with RNeasy mini kit (Qiagen, Hilden, Germany) including DNAse digestion according to the manufacturer's instructions. RNA quality was evaluated using an Agilent 2100 Bioanalyzer and only high quality RNA (RIN > 8) was used for microarray analysis.

treatment_protocol: C57Bl6 (C57Bl6) and B6-TgN(alb-HA-SREBP-1cNT) (alb-SREBP-1c) [18] mice were bred and maintained under standard conditions (12h light/dark cycle; 22°C ± 1°C, 50% ± 5% humidity). At 6 weeks of age, male littermates of each genotype were kept under standardized conditions with free access to water and regular laboratory chow (13.7 mJ/kg: 53% carbohydrate, 36% protein, 11% fat (Ssniff, Soest, Germany)). Mice were sacrificed by CO2 asphyxiation (7:00 am) at 24 weeks of age. Blood samples were collected by left ventricular puncture, and liver were removed. The Animal Care Committee of the University Duesseldorf approved animal care and procedure (Approval#84-02.04.2015.A424; 02. April 2015).

value: C57Bl6-TgN alb-HA-hSREBP-1c-NT

tag: gender

value: male

tag: age

value: 24 weeks


title: 7_alb-SREBP-1c


title: skn-1gf + paraquat rep 4

city: Los Angeles

first: Sean

last: Curran

address: 3715 McClintock Ave

department: Davis School of Gerontology

institute: University of Southern California

description:
fpkm.txt
J_PQ_4
J_PQvsJ_188.Differential_analysis_results.txt

data_processing:
Raw reads were first cleaned by removing reads containing adapter, reads contraining poly-N , and low quality reads. Base quality and phred score relationship with CASAVA v1.8 software from Illumina was used for QC.
Index of reference genome was built using Bowtie v2.2.3 on files available publicly and paired-end clean reads were aligned to reference genome using TopHat v2.0.12.
HTSeq v0.6.1 was used to count reads numbers mapped to each gene. FPKM of each gene was calculated based on length of gene and reads count mapped. FPKM is most commonly used currently (Trapnell, Cole, et al., 2010).
Differential expression analysis of two conditions/groups was performed using DESeq R package (1.18.0). Resulting p-values were adjusted using Benjamini and Hochberg's approach.
Genome_build: ce11
Supplementary_files_format_and_content: txt file contains fpkm for all samples. Txt files contain DESeq results with normalized read counts comparing WT and skn-1gf, WT and wdr-5, skn-1gf and wdr-5;skn-1gf, skn-1gf and skn-1gf + PQ .

organism: Caenorhabditis elegans

source_name: whole worms

growth_protocol: Worms were egg prepped and eggs were allowed to hatch overnight. Next day, synchronized L1s were dropped on NGM plates seeded with concentrated OP50. 48 and 120 hrs post drop, L4 animals and day 3 adult animals, respectively, were washed 3 times with M9 and frozen in TRI Reagent at -80°C.

extract_protocol:
Animals are homogenized in Trizol and RNA extraction is performed following protocol in Zymo Direct-zol RNA Isolation Kit. 1ug of RNA was used per sample for library construction using NEBNext® UltraTM RNA Library Prep Kit  for Illumina® (NEB, USA).
Sequencing libraries were generated following manufacturer's recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: skn-1gf  + paraquat samples had skn-1gf worms grown on NGM plates supplemented with 75µM paraquat for entire life

value: N2 Bristol

value: Day 3 adult

tag: genotype

tag: agent

value: paraquat

tag: tissue

value: whole worms


title: Day 4 CNTF Rep 3 [LAN-5]

description:
47-LA5CN4-3_S47
Small RNA sequencing
processed data file: mirexpress2_counts_raw.csv

tag: cell line

tag: passages


title: 3_alb-SREBP-1c


title: 2_alb-SREBP-1c


title: Day 4 CNTF Rep 2 [LAN-5]

description:
46-LA5CN4-2_S46
Small RNA sequencing
processed data file: mirexpress2_counts_raw.csv


title: 5_alb-SREBP-1c


title: 8_C57BL6


title: skn-1gf + paraquat rep 3

description:
fpkm.txt
J_PQ_3
J_PQvsJ_188.Differential_analysis_results.txt


title: Day 4 CNTF Rep 1 [LAN-5]

description:
45-LA5CN4-1_S45
Small RNA sequencing
processed data file: mirexpress2_counts_raw.csv


title: 4_alb-SREBP-1c


title: skn-1gf + paraquat rep 2

description:
fpkm.txt
J_PQ_2
J_PQvsJ_188.Differential_analysis_results.txt


title: skn-1gf + paraquat rep 1

description:
fpkm.txt
J_PQ_1
J_PQvsJ_188.Differential_analysis_results.txt


title: 7_C57BL6


title: 6_alb-SREBP-1c


title: 2_C57BL6


title: 1_alb-SREBP-1c


title: 3_C57BL6


title: 4_C57BL6


title: wdr-5;skn-1gf rep 3

description:
fpkm.txt
J_W188_3
J_W188vsJ_188.Differential_analysis_results.txt


title: wdr-5;skn-1gf rep 1

description:
fpkm.txt
J_W188_1
J_W188vsJ_188.Differential_analysis_results.txt


title: wdr-5;skn-1gf rep 2

description:
fpkm.txt
J_W188_2
J_W188vsJ_188.Differential_analysis_results.txt


title: 6_C57BL6


title: Day 4 Control Rep 3 [LAN-5]

description:
43-LA5CO4-3_S43
Small RNA sequencing
processed data file: mirexpress2_counts_raw.csv

value: Control


title: skn-1gf rep 4

description:
fpkm.txt
J_188
J_188vsJ_N2.Differential_analysis_results.txt


title: skn-1gf rep 3

description:
fpkm.txt
J_188_3
J_188vsJ_N2.Differential_analysis_results.txt


title: 1_C57BL6


title: 5_C57BL6


title: WT rep 3

description:
fpkm.txt
J_N2_3
J_188vsJ_N2.Differential_analysis_results.txt

value: wildtype


title: WT rep 1

description:
fpkm.txt
J_N2_1
J_188vsJ_N2.Differential_analysis_results.txt


title: WT rep 2

description:
fpkm.txt
J_N2_2
J_188vsJ_N2.Differential_analysis_results.txt


title: WT rep 4

description:
fpkm.txt
J_N2
J_188vsJ_N2.Differential_analysis_results.txt


title: Day 2 CNTF Rep 4 [LAN-5]

description:
40-LA5CN2-4_S40
Small RNA sequencing
processed data file: mirexpress2_counts_raw.csv

value: Day 2


title: Day 4 Control Rep 4 [LAN-5]

description:
44-LA5CO4-4_S44
Small RNA sequencing
processed data file: mirexpress2_counts_raw.csv


title: 60 Minutes CNTF Rep 4 [LAN-5]

description:
36-LA5CN60-4_S36
Small RNA sequencing
processed data file: mirexpress2_counts_raw.csv

value: 60 minutes


title: Day 2 CNTF Rep 1 [LAN-5]

description:
37-LA5CN2-1_S37
Small RNA sequencing
processed data file: mirexpress2_counts_raw.csv


title: Day 2 CNTF Rep 2 [LAN-5]

description:
38-LA5CN2-2_S38
Small RNA sequencing
processed data file: mirexpress2_counts_raw.csv


title: skn-1gf rep 2

description:
fpkm.txt
J_188_2
J_188vsJ_N2.Differential_analysis_results.txt


title: Day 4 Control Rep 2 [LAN-5]

description:
42-LA5CO4-2_S42
Small RNA sequencing
processed data file: mirexpress2_counts_raw.csv


title: 60 Minutes CNTF Rep 3 [LAN-5]

description:
35-LA5CN60-3_S35
Small RNA sequencing
processed data file: mirexpress2_counts_raw.csv


title: skn-1gf rep 1

description:
fpkm.txt
J_188_1
J_188vsJ_N2.Differential_analysis_results.txt


title: Day 4 Control Rep 1 [LAN-5]

description:
41-LA5CO4-1_S41
Small RNA sequencing
processed data file: mirexpress2_counts_raw.csv


title: 60 Minutes CNTF Rep 1 [LAN-5]

description:
33-LA5CN60-1_S33
Small RNA sequencing
processed data file: mirexpress2_counts_raw.csv


title: 30 Minutes CNTF Rep 4 [LAN-5]

description:
32-LA5CN30-4_S32
Small RNA sequencing
processed data file: mirexpress2_counts_raw.csv

value: 30 minutes


title: Day 2 CNTF Rep 3 [LAN-5]

description:
39-LA5CN2-3_S39
Small RNA sequencing
processed data file: mirexpress2_counts_raw.csv


title: GTR0010 PRXB [200764720061_K]

city: Candiolo

first: Enzo

last: Medico

state: TO

address: Strada Prov. 142, km 3,95

department: Oncology

country: Italy

institute: Candiolo Cancer Institute, University of Torino

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data were normalized with loess normalization with lumi package (beadscan and HiScanSQ independently, amnd then scaled on the basis of common samples)

label: biotin-SA Cy3

source_name: Gastric Cancer | PRX

label_protocol: Synthesis of cDNA and biotinylated cRNA were performed using the Illumina Total-Prep RNA Amplification Kit (Ambion, Austin, TX, USA, cat. no. IL1791), according to the manufacturer’s protocol, for which hybridization was carried out on Illumina HumanHT-12 V4 arrays

growth_protocol: Tumor were collected upon surgical resection and stored in liquid nitrogen

extract_protocol: RNA was extracted using the Trizol Plus purification Kit (Invitrogen, Frederick, MD, USA, cat. no.12183555), according to the manufacturer’s protocol. Quantification and quality analysis of RNA was performed on a Bioanalyzer 2100 (Agilent, Santa Clara, CA, USA).

treatment_protocol: Cryostatic section of the frozen specimens were cut for RNA extraction

value: Gastric Cancer

tag: sample type

value: PRX


title: 30 Minutes CNTF Rep 3 [LAN-5]

description:
31-LA5CN30-3_S31
Small RNA sequencing
processed data file: mirexpress2_counts_raw.csv

value: Immortalized human nervous cell

value: Male


title: 30 Minutes CNTF Rep 2 [LAN-5]

description:
30-LA5CN30-2_S30
Small RNA sequencing
processed data file: mirexpress2_counts_raw.csv

value: CNTF


title: GTR0287 PRX [200764720038_H]


title: GTR0263 PRX [200764720038_L]


title: GTR0289 PRX [200764720038_I]


title: GTR0271 PRX [200764720038_E]


title: 60 Minutes CNTF Rep 2 [LAN-5]

description:
34-LA5CN60-2_S34
Small RNA sequencing
processed data file: mirexpress2_counts_raw.csv


title: GTR0264 PRX [200764720038_D]


title: GTR0398 PRX [200764720061_H]


title: GTR0257 PRX [200764720038_B]


title: 30 Minutes CNTF Rep 1 [LAN-5]

description:
29-LA5CN30-1_S29
Small RNA sequencing
processed data file: mirexpress2_counts_raw.csv


title: GTR0255 PRX [200764720038_K]


title: GTR0286 PRX [200764720038_G]


title: GTR0272 PRX [200764720038_F]


title: GTR0248 PRX  [200764720053_K]


title: Day 2 Control Rep 4 [LAN-5]

description:
28-LA5CO2-4_S28
Small RNA sequencing
processed data file: mirexpress2_counts_raw.csv


title: GTR0258 PRX [200764720038_C]


title: GTR0015 PRX0A [200764720061_I]


title: GTR0249 PRX [200764720038_J]


title: GTR0233 PRX [200764720061_D]


title: PET111:GFP-negative cells 5 days 8 hours rep 3

tag: genotype/variation

value: 5 days 8 hours

value: root

value: PET111:GFP-negative cells


title: GTR0042 PRX [200764720061_L]


title: GTR0108 PRX [200764720064_B]


title: GTR0256 PRX [200764720038_A]


title: Day 2 Control Rep 3 [LAN-5]

description:
27-LA5CO2-3_S27
Small RNA sequencing
processed data file: mirexpress2_counts_raw.csv


title: GTR0254 PRX [200764720053_L]


title: GTR0164 PRX [200764720061_F]


title: Day 2 Control Rep 1 [LAN-5]

description:
25-LA5CO2-1_S25
Small RNA sequencing
processed data file: mirexpress2_counts_raw.csv


title: Day 2 Control Rep 2 [LAN-5]

description:
26-LA5CO2-2_S26
Small RNA sequencing
processed data file: mirexpress2_counts_raw.csv


title: GTR0041 PRH [200764720061_J]

source_name: Gastric Cancer | PR

value: PR


title: Day 4 CNTF Rep 4 [LA-N-2]

description:
24-LA2CN4-4_S24
Small RNA sequencing
processed data file: mirexpress2_counts_raw.csv

source_name: LA-N-2 neuroblastoma

value: Female

value: Day 4


title: GTR0037 PRH [3998720035_K]


title: Day 4 CNTF Rep 2 [LA-N-2]

description:
22-LA2CN4-2_S22
Small RNA sequencing
processed data file: mirexpress2_counts_raw.csv


title: Day 4 CNTF Rep 1 [LA-N-2]

description:
21-LA2CN4-1_S21
Small RNA sequencing
processed data file: mirexpress2_counts_raw.csv


title: GTR0221 ORG [200143170012_L]

source_name: Gastric Cancer | Organoids

value: Organoids


title: GTR0060B ORG [200143170010_E]


title: GTR0044 ORG [200143170012_C]


title: GTR0219B ORG [200143170012_H]


title: GTR0165 ORG [200143170010_H]


title: Day 4 Control Rep 4 [LA-N-2]

description:
20-LA2CO4-4_S20
Small RNA sequencing
processed data file: mirexpress2_counts_raw.csv

value: Control


title: GTR0165 ORG [200764720061_E]


title: GTR0221 CELLS [200143170012_K]

source_name: Gastric Cancer | Cells

value: Cells


title: GTR0181 ORG [200143170010_L]


title: GTR0181 CELLS [200143170010_K]


title: Day 4 Control Rep 3 [LA-N-2]

description:
19-LA2CO4-3_S19
Small RNA sequencing
processed data file: mirexpress2_counts_raw.csv


title: GTR0219 CELLS [200143170012_G]


title: GTR0032 ORG [200143170010_B]


title: Day 4 Control Rep 2 [LA-N-2]

description:
18-LA2CO4-2_S18
Small RNA sequencing
processed data file: mirexpress2_counts_raw.csv


title: Day 4 Control Rep 1 [LA-N-2]

description:
17-LA2CO4-1_S17
Small RNA sequencing
processed data file: mirexpress2_counts_raw.csv


title: Day 4 CNTF Rep 3 [LA-N-2]

description:
23-LA2CN4-3_S23
Small RNA sequencing
processed data file: mirexpress2_counts_raw.csv


title: GTR0165 CELLS [200143170010_I]


title: Day 2 CNTF Rep 4 [LA-N-2]

description:
16-LA2CN2-4_S16
Small RNA sequencing
processed data file: mirexpress2_counts_raw.csv

value: Day 2


title: GTR0044 CELLS [200143170012_D]


title: GTR0032A CELLS [200143170010_C]


title: GTR0060B CELLS [200143170010_F]


title: GTR0010 CELLS [3998720068_D]


title: Day 2 CNTF Rep 2 [LA-N-2]

description:
14-LA2CN2-2_S14
Small RNA sequencing
processed data file: mirexpress2_counts_raw.csv


title: Day 2 CNTF Rep 1 [LA-N-2]

description:
13-LA2CN2-1_S13
Small RNA sequencing
processed data file: mirexpress2_counts_raw.csv


title: Day 2 CNTF Rep 3 [LA-N-2]

description:
15-LA2CN2-3_S15
Small RNA sequencing
processed data file: mirexpress2_counts_raw.csv


title: 60 Minutes CNTF Rep 3 [LA-N-2]

description:
11-LA2CN60-3_S11
Small RNA sequencing
processed data file: mirexpress2_counts_raw.csv

value: 60 minutes


title: 60 Minutes CNTF Rep 4 [LA-N-2]

description:
12-LA2CN60-4_S12
Small RNA sequencing
processed data file: mirexpress2_counts_raw.csv


title: GTR0025PRX0A

description: Sample name: 3998720099_L

data_processing: Data were not normalized. Illumina's raw AVG_Signal is provided in the sample tables and in the supplementary file on the series record (with detection pvalues).

source_name: Gastric Cancer | PDX

label_protocol: Synthesis of cDNA and biotinylated cRNA were performed using the Illumina Total-Prep RNA Amplification Kit (Ambion, Austin, TX, USA, cat. no. IL1791), according to the manufacturer’s protocol, for which hybridization was carried out on Illumina HumanHT-12 V3 arrays

value: gastric cancer

value: PDX

tag: patient id


title: GTR0015PRX0A

description: Sample name: 3998720099_J


title: 60 Minutes CNTF Rep 2 [LA-N-2]

description:
10-LA2CN60-2_S10
Small RNA sequencing
processed data file: mirexpress2_counts_raw.csv

tag: treatment


title: GTR0024PRX0B

description: Sample name: 3998720099_K


title: GTR0013PRX0A

description: Sample name: 3998720099_I


title: GTR0011PRX0A

description: Sample name: 3998720099_H


title: GRT0277PDX

description: Sample name: 3998720099_A


title: GTR0078PRX0B

description: Sample name: 3998720096_J


title: GRT0399PDX

description: Sample name: 3998720099_D


title: 60 Minutes CNTF Rep 1 [LA-N-2]

description:
09-LA2CN60-1_S9
Small RNA sequencing
processed data file: mirexpress2_counts_raw.csv


title: GRT040P5PDX

description: Sample name: 3998720099_F


title: GRT0409PDX

description: Sample name: 3998720099_G


title: GRT0398PDX

description: Sample name: 3998720099_C


title: GRT0403PDX

description: Sample name: 3998720099_E


title: GTR0085PRX0A

description: Sample name: 3998720096_K


title: GRT0392PDX

description: Sample name: 3998720099_B


title: GTR0009 CELLS [3998720068_A]

value: Gastric Cancer


title: GTR0096PRX0A

description: Sample name: 3998720096_L


title: GTR0062PRX0A

description: Sample name: 3998720096_H


title: GTR0071PRX0B

description: Sample name: 3998720096_I


title: GTR0060PRX0B

description: Sample name: 3998720096_G


title: 30 Minutes CNTF Rep 4 [LA-N-2]

description:
08-LA2CN30-4_S8
Small RNA sequencing
processed data file: mirexpress2_counts_raw.csv

value: Immortalized human nervous cell

value: 30 minutes


title: GTR0048PRX0A

description: Sample name: 3998720096_F


title: GTR0042PRX0A

description: Sample name: 3998720096_E


title: 30 Minutes CNTF Rep 3 [LA-N-2]

description:
07-LA2CN30-3_S7
Small RNA sequencing
processed data file: mirexpress2_counts_raw.csv

value: CNTF


title: 30 Minutes CNTF Rep 2 [LA-N-2]

description:
06-LA2CN30-2_S6
Small RNA sequencing
processed data file: mirexpress2_counts_raw.csv


title: 30 Minutes CNTF Rep 1 [LA-N-2]

description:
05-LA2CN30-1_S5
Small RNA sequencing
processed data file: mirexpress2_counts_raw.csv


title: Day 2 Control Rep 4 [LA-N-2]

description:
04-LA2CO2-4_S4
Small RNA sequencing
processed data file: mirexpress2_counts_raw.csv


title: GTR0032PRX0B

description: Sample name: 3998720096_B


title: Day 2 Control Rep 3 [LA-N-2]

description:
03-LA2CO2-3_S3
Small RNA sequencing
processed data file: mirexpress2_counts_raw.csv


title: GTR0035PRX0A

description: Sample name: 3998720096_C


title: Day 2 Control Rep 1 [LA-N-2]

description:
01-LA2CO2-1_S1
Small RNA sequencing
processed data file: mirexpress2_counts_raw.csv


title: GTR0036PRX0B

description: Sample name: 3998720096_D


title: GTR0019PRH

description: Sample name: 3998720068_K

value: primary tumor


title: GTR0181 CELLS [200764720061_G]


title: GTR0015PRH

description: Sample name: 3998720068_H


title: GTR0019PRXA

description: Sample name: 3998720068_L


title: ATRX in-frame fusion neuroblastoma, patient MSK4343 RNA-seq

description:
Processed data file: MSKCC_NB_patient_gene_exp.txt
MSK4343

data_processing:
[ChIP-seq] Sequence reads were aligned to the GRCh37 (hg19) assembly using Bowtie v1.0.0 with the following parameters: For 100nt reads: -M 10 -k 1 -n 2 --trim5 5 -l 80 --best. Redundant reads were eliminated using the macs2 (v2.1.0) filterdup option with default parameters. The optimal normalization factor between ChIP and Input samples was calculated with the R NCIS package v1.0.1 using a shift size of 75bp.
[ChIP-seq] Peak calling was performed with macs2 callpeak using the following options: --ratio X --broad --bdg -q 1x10-5 OR 1x10-15 OR 0.05 OR 0.005 or 0.0005 --broad-cutoff 1x10-5 OR 1x10-15, where X is the normalization factor estimated by NCIS. ChIP/Input fold enrichment pileups were created with the macs2 bdgcmp tool using the -m FE option and converted to bigWig files using the bedGraphToBigWig program (v4) from the UCSC binaries.
[RNA-seq] Reads were aligned using STAR (Dobin et al., 2013)
[RNA-seq] Transcriptome assemblies in FPKM, and differential expression ratios were computed using the featureCounts program from the Rsubread package (v1.20.6) in R. The FPKM was calculated using the fpkm function from the edgeR package (v 3.12.1). Genes with a count per million < 1 were marked as not transcribed.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: fastq - raw illumina reads. Bam - aligned reads. bigwig - aligned reads pileup. txt - gene expression in FPKM

source_name: Tumor Tissue

extract_protocol:
Tissue was homogenized at 17000 rpm for 30 seconds with a tissue homogenizer (Polytron, PT10-35GT). RNA was prepared using TRIzol (Life Technologies) and cleaned using RNeasy Plus Mini kit (Qiagen #74134)
Total RNA was processed into sequencing libraries using the Illumina TruSeq Stranded Total RNA Library Prep Kit following manufacturer’s protocol.

value: ATRX in-frame fusion neuroblastoma (patient MSK4343)

value: none (untreated)


title: MM1S.sgRNA.IRF4KO.Rep2

source_name: Bone marrow

tag: strain

value: Human

value: myeloma


title: ATRX in-frame fusion neuroblastoma, patient MSK4297 RNA-seq

description:
Processed data file: MSKCC_NB_patient_gene_exp.txt
MSK4297

value: ATRX in-frame fusion neuroblastoma (patient MSK4297)


title: GTR0029PRX0B

description: Sample name: 3998720096_A


title: MM1S.sgRNA.IRF4KO.Rep1


title: GTR0015PRXB

description: Sample name: 3998720068_I


title: GTR0010PRXB

description: Sample name: 3998720068_F


title: GTR0010PRH

description: Sample name: 3998720068_E


title: ATRX Mutant neuroblastoma, patient MSK3374 RNA-seq

description:
Processed data file: MSKCC_NB_patient_gene_exp.txt
MSK3374

value: ATRX Mutant neuroblastoma (patient MSK3374)


title: Day 2 Control Rep 2 [LA-N-2]

description:
02-LA2CO2-2_S2
Small RNA sequencing
processed data file: mirexpress2_counts_raw.csv

value: Female

value: Control


title: GTR0041PRH

description: Sample name: 3998720067_K


title: GTR0041PRXA

description: Sample name: 3998720067_L


title: GTR0009PRXB

description: Sample name: 3998720068_C


title: GTR0009PRH

description: Sample name: 3998720068_B


title: GTR0023PRXA

description: Sample name: 3998720067_F


title: GTR0026PRH

description: Sample name: 3998720067_H


title: GTR0026PRXA

description: Sample name: 3998720067_I


title: MM1S.empty.vec.Rep2

value: WT


title: Serum, C6

city: Lublin

first: Marta

last: Rusek

address: Radziwillowska 11

department: Dept. of Dermatology

country: Poland

institute: Medical University of Lublin

description: Gene expression data from serum of healthy control

hyb_protocol: Samples were hybridized overnight to the Affymetrix GeneChip miRNA array (P/N 901326).

scan_protocol: The arrays were washed and stained using standard Affymetrix protocols and scanned using the Affymetrix GCS 3000 7G Scanner. Feature intensities were extracted using the miRNA_4.0 library files.

data_processing: For microarray data analysis, Affymetrix Transcriptome Analysis Console (TAC) Software v4.0 was used.

source_name: Control group

label_protocol: RNA samples were obtained from starting material (200 µL of serum), then a total of 16 samples from patients and healthy controls were labeled using the FlashTag™ Biotin HSR RNA Labeling Kit (Affymetrix, Santa Clara, CA, USA).

growth_protocol: Whole blood (5–10 mL) was collected in BD Monovette plastic tubes (Sarstedt, Germany). The samples were stored on ice and processed within 1 hour of the draw. Serum was isolated by centrifugation at 3 000 x g for 10 min at 4 ºC and stored at -80 ºC, in the absence of freeze-thaw cycles, until analysis.

extract_protocol: RNA was extracted from 100 µL serum using the miRNeasy Serum/Plasma Kit (Qiagen, Germany) following the manufacturer’s protocol. Briefly, after Qiazol solution (1 mL) was added and mixed by vortexing, samples were incubated at room temperature for 5 min, the addition of chloroform was useful to achieve aqueous and organic phase separation. In the next step, the aqueous phase was applied to an RNeasy spin column. The purified RNA was eluted in 14 µL RNase-free water, split into single-use aliquots and stored at -80 ºC.

tag: disease state

value: healthy control

value: serum


title: Serum, C5


title: ATRX Mutant neuroblastoma, patient MSK2140 RNA-seq

description:
Processed data file: MSKCC_NB_patient_gene_exp.txt
MSK2140

value: ATRX Mutant neuroblastoma (patient MSK2140)


title: ATRX in-frame fusion neuroblastoma, patient MSK832 RNA-seq

description:
Processed data file: MSKCC_NB_patient_gene_exp.txt
MSK832

value: ATRX in-frame fusion neuroblastoma (patient MSK832)


title: MM1S.empty.vec.Rep1