title: Ribo-seq_P4003

city: Shenzhen

first: Rihong

last: Zhai

state: Guangdong

address: 1066 Xueyuan Ave.

institute: Shenzhen University School of Medicine

data_processing:
Library strategy: Ribosome sequencing
Basecalls performed using Illumina Casava version 1.8
Data were filtered using the following specifications:1) reads with 5’ adapter; 2) reads without 3’ adapter or insert sequence; 3) reads with more than 10% N; 4) reads with more than 50% nucleotides with Qphred<=5;Adapter trimming for the removal of adapter sequences from the 3’ ends of reads was also performed. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Clean reads were mapped to human genome database (GRCh38) using the TopHat2 software.
Quantification of mapped results to gene level was carried out using HTSeq.
Genome_build: GRCh38
Supplementary_files_format_and_content: count and fpkm

source_name: Cells exposed to PM2.5

growth_protocol: Cells were cultured in DEME medium containing 10% FBS in a humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
Sample was treated with specific lysis buffer with cycloheximide (50mg/mL) to acquire the lysate.
Cells were treated with specific lysis buffer of cycloheximide to stop translation. Then, cell lysate was treated with unspecific endoribonuclease RNase to digest the free RNAs other than ribosome-protected fragments (RPFs). The RNA samples were then treated with rRNA depletion kit to remove rRNA contamination.  Small RNA (< 200 bp) was resolved by PAGE, and the RPFs bands (~30nt) were cut for RNA extraction, cDNA transcription, and PCR amplification.

treatment_protocol: BEAS-2B cells were exposed to PM2.5 or PBS, respectively.

tag: cell type

value: epithelial cell

value: exposed to PM2.5 for 24h


title: NCoR2_control_RNA-seq_rep1

status: Public on Jul 27 2022

type: SRA

city: Philadelphia

first: Mitchell

last: Lazar

state: PA

address: 3400 Civic Center Blvd

department: Perelman School of Medicine

country: USA

institute: University of Pennsylvania

library_source: transcriptomic

data_processing:
RNA-seq
RNA-sequencing output, including published HDAC3 BAT-KO data (23), was analyzed in tandem using the DIYTranscriptomics course pipeline (61). Briefly, this pipeline uses Kallisto to align and quantify reads, EnemblDB to annotate data, edgeR to normalize read counts, and Limma to determine DEGs. Cut-offs used for these analyses were a CPM of 1 in a minimum of 4 of 31 total samples to identify a transcript as expressed and a log2FC>|0.58| and adjusted p-value <0.05 for all DEGs per mouse line.
ChIP-seq
FASTQ files were aligned to the GRCm38 (mm10) reference genome using bowtie2 v2.4.2 aligner with the following parameters: -N 1. Duplicate reads were removed with samtools rmdup. Then tag directories were made with Homer v4.11.1. HDAC3 peaks in Control and NCoR1/2 dKO were called using Homer from pooled replicates, using HDAC3 KO as background. findPeaks was used with default parameters, which sets the cutoff to 4-fold minimum enrichment over the background.
Assembly: mm10
Supplementary files format and content: RNA-seq: abundance files in Kallisto’s .h5 format
Supplementary files format and content: RNA-seq: gene ID and log2 fold change in CSV format
Supplementary files format and content: ChIP-seq: peak files in bed format

molecule: total RNA

organism: Mus musculus

source_name: brown adipose tissue

growth_protocol: all male mice between 11-14 weeks old

extract_protocol:
RNA-seq
RNA was isolated from snap-frozen BAT as previously described (23) using TRIzol-chloroform extraction followed by RNeasy Mini spin columns (Qiagen) and on-column DNase-digestion
Novogene or TruSeq
ChIP-seq
Chromatin immunoprecipitation (ChIP) was done as previously described with minor modifications (23). Total protein for each sonicated sample was quantified by BCA and normalized to 1.5mg of protein for each ChIP prior to incubation with antibody overnight. 5% input was saved prior to antibody incubation and used as input control. Antibodies used were HDAC3 (Genetex GTX109679) and rabbit IgG (CST 2729S) and immunoprecipitated with BSA blocked Protein A agarose beads (Invitrogen 15918014). ChIP DNA was isolated using phenol/chloroform extraction and treated with RNAse A prior to sequencing library preparation.
The NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB #E7645S) with AMPure XP Beads (Beckman Coulter, Inc. #A63881) was used to amplify and size select ChIP DNA. Agilent High Sensitivity DNA Kit (5007-4626) KAPA Library Quantification Kit (KR0405) were used to quantify libraries and fragment sizes prior to sequencing.
An n=3 was sequenced for NCoR1/2 Control and NCoR1/2 BAT-dKO groups, n=2 for HDAC3 BAT-KO, and n=1 each for input and IgG. The sequencing was done at the Next-Generation Sequencing Core at the University of Pennsylvania on a NextSeq platform (Illumina) at 100SR for a total of 30 million reads per sample.

treatment_protocol: 2 weeks housing at 30C

tag: strain

tag: allele

tag: temperature

value: 14 days 30°C

tag: tissue

value: brown adipose tissue


title: ES - SOX17 Rep1

city: Cincinnati

first: Shreyasi

last: Mukherjee

state: OH

address: 3333 Burnet Ave

department: Developmental Biology

institute: Cincinnati Children's Hospital Medical Center

library_source: genomic

data_processing:
For RNA-Seq experiments, raw reads were quality-checked using  FASTQC and adapters were trimmed using cutadapt.
Reads were pseudo-aligned to the hg19 reference index using salmon.
The tximport package was then used for downstream analysis to convert transcript-level counts to gene-level estimates. Differential gene expression analysis was performed using DESeq2 using default parameters
For ChIP-Seq experiments, Reads were aligned to the hg19 genome using bowtie2
Duplicates were marked using Picard and removed using samtools
A consensus set of peaks were called for each TF at each stage using HOMER getDifferentialPeaksReplicates.pl using stage-matched input samples as background and -style factor.
For ATAC-Seq, trimmed paired-end reads were aligned to the hg19 genome using bowtie2 and the parameters -X 2000 -very-sensitive-local
Peaks were called on replicates using Genrich and the parameters j -r -e -v -q 0.1
Genome_build: hg19
Supplementary_files_format_and_content: .bw' files are bigWig files for visualization of ChIP-Seq and ATAC-Seq data
Supplementary_files_format_and_content: .csv' files are TPM matrices from RNA-Seq experiment

molecule: genomic DNA

organism: Homo sapiens

source_name: Induced pluripotent stem cells

growth_protocol: iPS72.3 cells were routinely maintained in mTesr. CRISPRi-SOX2 cells were maintained in Essential 8 medium.

extract_protocol:
For RNA-Seq experiments, Total RNA was extracted using the Nucleospin RNA Extraction kit.For ChIP-Seq experiments, after differentiation to the desired stage, cells were dual crosslinked in plate with 1.5mM EGS and 1% formaldehyde. The fixation was then quenched with 125mM glycine. Cells were then washed twice and scraped in ice-cold PBS and resuspended in sonication buffer.For ATAC-Seq experiments, 50,000 cells were collected following differentiation to the desired stage, and lysed in 50ul of ATAC-lysis buffer (10mM Tris-HCl, pH 7.4. 10mM NaCl, 3mM MgCl2, 0.1% NP-40) to obtain a crude nuclei prep
For RNA-Seq experiments, 300ng of total RNA was poly-A selected and reverse transcribed using Illumina’s TruSeq stranded mRNA library preparation kit (Illumina; 20020595). For ChIP-Seq experiments, DNA libraries were prepared using 1-5 ng of starting material using the SMARTer ThruPLEX DNA-Seq kit (Takara; R400674) according to manufacturer’s instructions. For ATAC-Seq, the eluted DNA was amplified in a reaction with 25ul NEBNext High-Fidelity 2x PCR Mastermix (NEB; M0541L) and custom 25um Nextera PCR Primers (Ad1_noMx universal primer, 0.5um Ad2.x indexing primer). PCR was performed as follows: 1 cycle of 72C for 5min, 98C for 30s, 5 cycles of 98C for 10s, 63C for 30s, 72C for 1min. 5ul of the amplified DNA was then used to perform qPCR to determine the optimal number of additional cycles to prevent amplification saturation of DNA libraries. In all cases, either 4 or 5 additional cycles of PCR was performed at: 98C for 10s, 63C for 30s and 72C for 1 min. Double size selection of amplified libraries (0.5x – left sided, 1.8x – right sided) was performed using AMPure XP beads
ChIP-Seq, RNA-Seq and ATAC-Seq

treatment_protocol: DE differentiation was carried out in RPMI-1640 media supplemented with non-essential amino acids Cells were treated with 100ng/ml Activin A and 2um CHIR99021 for 24hrs. In the next two days, cells were treated with 100ng/ml Activin A and 2um CHIR99021 in RPMI-1640 with increasing concentrations (0.2% on Day 2, 2% on Day 3) of ES-grade FBS . For NMP differentiation, cells were passaged using E8. The following day, media was changed to Essential 6 Medium. 24 hours later, cells were treated with 200ng/ml FGF8b in E6 media. After a further 24 hours, cells were treated with 200ng/ml FGF8b and 3um CHIR99021 in E6 media

tag: developmental stage

value: pluripotent ES cells

tag: chip antibody

value: SOX17 R&D AF1924


title: Veh_liver_rep3

city: San Antonio

first: Xiaoli

last: Sun

state: TX

address: 7703 Floyd Curl Dr

department: Pharmacology

institute: University of Texas Health Science Center at San Antonio

description: mRNA

data_processing:
FASTQ files from sequencing experiments were mapped to the mouse mm10 genome. STAR with default parameters was used to map RNA-seq experiments.
To compare differential gene expression between indicated groups, HOMER’s analyzeRepeats with the option rna and the parameters -condenseGenes, -noadj, and -count exons was used on two-three replicates per condition.
Assembly: mm10
Supplementary files format and content: *.txt: Tab-delimited text files include TPM values and differential expressed genes for each Sample.

source_name: Liver

extract_protocol:
RNA was harvested using Quick RNA mini prep kit (Life Technologies). 1ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Ldlr-/- mice were fed on Western diet for 11 weeks. Starting at week 3 of the feeding period, mice were orally gavaged 25mg/kg amlexanox or vehicle for 8 weeks until end point.

value: Liver

tag: genotype

value: Ldlr-/-

tag: diet

value: Western diet

tag: diet duration

value: 11 weeks

tag: treatment

value: Vehicle

tag: treatment duration

value: 8 weeks


title: Ribo-seq_P4002

country: China

tag: cell line


title: Ribo-seq_C03

source_name: Control cells

value: untreated


title: XCS03

city: San Juan de Alicante

first: Guillermina

last: López-Bendito

state: Alicante

address: Av Ramon y Cajal s/n, Campus de San Juan

department: Instituto Neurociencias CSIC-UMH

country: Spain

institute: Universidad Miguel Hernández (UMH)

description: Bulk Tissue

data_processing:
Quality control of the raw data was performed with FastQC (v.0.11.9).
RNA-seq reads were mapped to the Mouse genome (GRCm39/mm10 Ensembl release 104, May 2021) using STAR (v2.7.9d) (Dobin et al., 2013) and SAM/BAM files were further processed using SAMtools v1.14 (Li et al., 2009).
Aligned reads were counted and assigned to genes using Ensembl release 104 gene annotation and FeatureCounts, Subread (v2.0.1) (Liao et al., 2014).
Genome_build: GRCm39/mm10 Ensembl release 104, May 2021
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include Gene Counts values for each Sample.

source_name: Superior Colliculus Superficial layer

extract_protocol:
Total RNA was isolated from the bulk tissue using the RNeasy® Micro Kit (Qiagen, #74004) according to manufacturer’s instructions.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.
The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Then the quantified libraries were pooled and sequenced for 150pb paired-read and performed on an Illumina Novaseq6000 platform using 2x150 sequencing to read depth of > 40 million reads per sample at Novogene Co. Ltd. genomics core facility (Cambridge, UK).

treatment_protocol: For the pharmacological ablation of retinal waves in vivo, mice were anesthetized on ice and a small incision was made into each eyelid to expose the eyeball. A pulled glass micropipette was used to pressure-inject 0.3-0.5 μL of 1 mM epibatidine (epb, Merck, E1145), 50 mM carbenoxolone (cbx, Merck, C4790) or saline into the vitreous humor of the eye.

value: Superior Colliculus (Superficial layer)

tag: age

value: Post natal day 6

value: Cbx injected at P0-1


title: XCS02

description: Bulk Tissue


title: Amx_aorta_rep2

source_name: Aorta

value: Aorta

value: Amlexanox


title: Veh_liver_rep2

description: mRNA


title: Amx_aorta_rep1


title: Ribo-seq_P4001

value: epithelial cell

value: exposed to PM2.5 for 24h


title: Ribo-seq_C02


title: Veh_liver_rep1

description: mRNA


title: XCD04

description: Bulk Tissue

source_name: Superior Colliculus Deep layer

value: Superior Colliculus (Deep layer)


title: Veh_aorta_rep1


title: XCS01

description: Bulk Tissue


title: Ribo-seq_C01


title: NCoR2_control_RNA-seq_rep2

value: 14 days 30°C

value: brown adipose tissue


title: Veh_aorta_rep3


title: XCD03

description: Bulk Tissue


title: PM2_5_400_3

data_processing:
Basecalls were performed using Illumina Casava version 1.8
Data were filtered using the following specifications:1) reads with 5’ adapter; 2) reads without 3’ adapter or insert sequence; 3) reads with more than 10% N; 4) reads with more than 50% nucleotides with Qphred<=5;Adapter trimming for the removal of adapter sequences from the 3’ ends of reads was also performed. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Clean reads were mapped to human genome database (GRCh38) using the HISAT2 v2.0.5.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Genome_build: GRCh38
Supplementary_files_format_and_content: count, fpkm

source_name: PM2.5 expsoure to BEAS-2B cells 24 hours

extract_protocol:
Total RNA was extracted from cells using the TRIzol Reagent.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: PM2.5 or PBS were exposured to BEAS-2B cells.

value: exposure to PM2.5 24h


title: PM2_5_400_2


title: XCD02

description: Bulk Tissue


title: Veh_aorta_rep2

value: Ldlr-/-


title: PM2_5_400_1


title: XCD01

description: Bulk Tissue


title: XCS04

description: Bulk Tissue


title: SCS03

description: Bulk Tissue

value: Saline injected at P0-1


title: PM2_5_0_2


title: SCS02

description: Bulk Tissue


title: LiverILC2_rep2.fastq.gz

city: Boston

first: Masanori

last: Fujimoto

state: MA

address: Center for Life Sciences 3 Blackfan Circle, Room CLS730

department: Division of Endocrinology

institute: Beth Israel Deaconess Medical Center, Harvard Medical School

data_processing:
The libraries were sequenced for 60 cycles (single-end reads) on an Illumina Nextseq 500 instrument.
The sequenced reads in the ChIP-seq experiment were mapped to the UCSC mouse genome (mm10) using Bowtie 1.2.2, and duplicate reads were removed with Picard tools.
Peak calling and motif analyses were performed using HOMER software (http://homer.salk.edu/homer/index.html), which was also used to identify differential peaks.
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph

growth_protocol: Wild type BALB/c mice received daily i.p. injections of rIL-33 (0.5 µg) for 5 days. Then, liver (1.7x106) and lung (0.5x106) ILC2s were sorted using flow cytometry ARIA III [gating: Lin− (CD3e−Ly6G−Ly6c−CD11b−CD45R−TER119−TCRb−) CD127+Thy1+ST2+]

extract_protocol:
Lysates were clarified fromsonicated nuclei and GATA3-DNA complexes were isolated with antibody.
ChIP-seq libraries were constructed using the NEBNext® ChIP-Seq Library Preparation Kit according to the manufacturer’s instructions.

treatment_protocol: described in growth protocol

value: BALB/c

value: wild type

tag: celltype

value: liver ILC2s from IL-33-treated mice

tag: antibody


title: mESCS-C3_BGI-2

city: Brisbane

first: Christian

last: Nefzger

state: Queensland

address: 306 Carmody Road

department: Institute for Molecular Biology

country: Australia

institute: The University of Queensland

data_processing:
ATAC-seq: Peak calling was performed using the MACS2 callpeak command with the following parameters “-g mm –shift -100 –extsize 200 –nomodel –call-summits –nolambda –keep-dup all -p 0.01” [34], [35]. Then, peak summits were extended by 250 bp on both sides  to a final width of 501 bp. Peaks were filtered for mm10 blacklisted regions [36]  (https://www.encodeproject.org/annotations/ENCSR636HFF/).
As in Corces et al. 2020 per sample overlapping peaks were handled using an iterative removal approach. That is in case of two overlapping peaks the most significant peak is kept and the other removed. This process is performed in an iterative manner, so all peaks have been kept or removed based on their overlap and significance score. This method results in a set of fixed-width peaks per sample.
Next, significance peak scores “(-log10(p-value))” were converted to a score per million value by dividing each individual peak score by the sum of all of the peak scores in the given sample divided by 1 million.  This normalized score per million value corrects the original peak calling scores for sample sequencing depth and quality, as higher quality samples yield higher number of peaks and higher significance scores overall. Thus, scores per million allow the direct comparison of peaks across biological replicates.
Next, we compiled a condition - MEF, mESC- and sequencer specific - BGI, Illumina - peak set containing reproducible peaks observed in a particular cell type and sequencing platform. For that, we generated a cumulative peak set per cell type and sequencing platform and performed the same iterative approach as mentioned above. Therefore, maintaining the peak with the highest significance or score per million. Only peaks with a score per million value >=3 observed in at least two samples (minimal overlap 50%) were further considered.
Assembly: mm10
Supplementary files format and content: bigwig for ATAC-seq samples, called peaks in (.gtf) format and counts per peak in .txt format.

source_name: mouse embryonic stem cells

extract_protocol: OMNI-ATACseq libraries were generated from FACS purified cells (in case of MEFs: Thy1+ ; in case of mESCs: Thy1-/Ssea1+/Epcam+)  according to the standard protocol (see doi: 10.1038/nmeth.4396). Afterwards, libraries were purified using a QIAGEN MinElute PCR purification kit (QIAGEN, Cat#28004) followed by Agencourt AMPure XP beads (Beckman Coulter, Cat#A63880) according to the manufacturer’s recommendations. Library fragments ranging from 150 to 700 bp were enriched and the final elution volume was 21 ul. The finalized libraries were provided to BGI for sequencing. HiSeqX10 sequencing was performed in 150bp PE mode followed by read trimming to 100bp PE for analysis. In case of sequencing on the DNBSEQ-G400 instrument libraries were converted to nanoballs and sequenced according to established workflows in 100bp PE mode (see doi: 10.1093/nargab/lqaa034).

value: mouse embryonic stem cells

value: C57/Bl6 background


title: mESCS-C1_BGI_3-


title: PM2_5_0_1

value: untreated


title: SCS01

description: Bulk Tissue

value: Superior Colliculus (Superficial layer)

value: Post natal day 6


title: L1_F_NVR_3

city: New York

first: Zeguo

address: 1468 Madison Avenue

institute: Ichan School of Medicine at Mount Sinai

data_processing:
Raw sequencing data was aligned to hg38 reference using STAR 2.5.3a (Dobin et al., 2013) and HTseq 0.11.2 (Anders et al., 2015) was used to quantify the gene-sample expression profile.
Genome_build: hg38
Supplementary_files_format_and_content: tab delimited xls file of raw counts of  gene expression profile

source_name: lung squamous cell carcinoma cell line

growth_protocol: H520 cells were routinely cultured in RPMI1640 containing 10% FBS and 1% penicillin/streptomycin.

extract_protocol:
Cells were collected 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.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For 12-LOX inhibitor treatment experiments, ML355 was dissolved in DMSO to make stock regent. 5h after cells seeded, ML355 was diluted to 10 μM, followed by replacing the cell medium. For L1 inhibitor treatment experiments, NVR was dissolved in DMSO to make stock regent. 5h after cells seeded, NVR was diluted to 450 μM, followed by replacing the cell medium. The same DMSO volume (0.2% final concentration) was added to control cells.

value: treated with NVR


title: LiverILC2_rep1.fastq.gz


title: MEFS-C2_BGI-6

source_name: mouse embryonic fibroblasts

value: mouse embryonic fibroblasts


title: P0 Mouse Cortex - H3.3 Emx1 dKO 4

city: Ann Arbor

first: Kenneth

last: Kwan

state: MI

address: 4909 Buhl Building, 1241 E. Catherine St.

department: Human Genetics

institute: University of Michigan

description: cDNA from rRNA-depleted RNA

data_processing:
Processed reads were aligned to mm10 with STAR.
Reads were deduplicated according to UMI using UMI-tools.
Read counts were obtained with htseq-count with intersection-nonempty mode
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample

source_name: cortex

extract_protocol:
Fresh cortex was lysed in trizol using a bullet blender
Libraries were constructed usind ClickSeq (Routh et. al. 2015)

value: H3.3 Emx1 dKO

value: cortex


title: SCD03

description: Bulk Tissue

value: Superior Colliculus (Deep layer)


title: L1_F_NVR_2


title: mESCS-C5_BGI-1


title: SCD02

description: Bulk Tissue


title: Wt Mab ATCC19977 - Rif16 - Replicate 2

city: Albany

first: Pallavi

last: Ghosh

state: NY

address: 150 New Scotland Ave

department: New York State Department of Health

institute: Wadsworth Center

data_processing:
Processed files were generated using Rockhopper
SAM files of each sample were generated by Rockhopper
Supplementary files format and content: Excel File showing RPKM vvalues and normalized expression of each sample

organism: Mycobacteroides abscessus

growth_protocol: Bacteria were grown to an OD of 0.6 in Middle brook 7H9 + OADC

extract_protocol:
RNA prepared using Qiagen kit, 2 microgm total RNA samples were treated with the Ribo-ZeroTM rRNA,
NEBNext Ultra II RNA Library Prep kit

treatment_protocol: 16mg/L) of RIF for 30 mins

value: bacteria

value: Wt Mab

value: OD=0.6, Rif 16ug/mL , 30 mins


title: MEFS-C1_BGI-7


title: P0 Mouse Cortex - H3.3 Emx1 dKO 3

description: cDNA from rRNA-depleted RNA


title: PM2_5_0_3

value: epithelial cell


title: P0 Mouse Cortex - H3.3 Emx1 dKO 2

description: cDNA from rRNA-depleted RNA


title: CTRL_DMSO_3

value: treated with DMSO


title: L1_F_NVR_1


title: Bone Marrow Mononuclear Cells, VDJ

city: Bethesda

first: Shouguo

last: Gao

state: MD

address: 9000 Rockville Pike

department: NHLBI

institute: National Institutes of Health

data_processing:
Library strategy: VDJ-seq
Binary Base Call (BCL) files were demultiplexed into FASTQ files was performed using 10x cellranger mkfastq.
The raw data was processed using cellranger multi.
Metadata for hashed samples including HTO oligo sequence is available in the file "GEO_upload_seq_HTO.xlsx"
Paired-end reads were mapped to the mm10 genome with cellranger for gene-level read counts
Paired-end reads were mapped to protein feature sequence with cellranger for protein-level read counts
Cell Ranger VDJ pipeline (10xGenomics) under default parameters was performed to generate scTCR annotations on the assembled contigs and on the clonotype consensus sequences
Genome_build: mm10
Supplementary_files_format_and_content: VDJ_filtered_contig_annotations.csv
Supplementary_files_format_and_content: GEO_upload_seq_HTO.xlsx (metadata details)

source_name: Bone Marrow

extract_protocol: Libraries were generated using Chromium Next GEM Single Cell V(D)J Reagent Kits v1.1 from 10XGenomics.

tag: markers

value: BMMNCs

value: Bone Marrow

tag: Sex

value: Female

value: 2-5 months

tag: subject

value: mixed samples (five C.B10 BM failure control mice and five bone marrow failure mice treated with G-MDSCs)


title: Wt Mab ATCC19977 - Rif16 - Replicate 1

tag: strain

tag: cell type


title: P0 Mouse Cortex - H3.3 Emx1 dKO 1

description: cDNA from rRNA-depleted RNA

tag: tissue


title: LungILC2_rep1.fastq.gz

value: BALB/c

value: wild type

value: lung ILC2s from IL-33-treated mice


title: CTRL_DMSO_2


title: MEFS-C4_BGI-4

value: mouse embryonic fibroblasts

value: C57/Bl6 background


title: Wt Mab ATCC19977 - Rif - Replicate 2

value: OD=0.6, No Rif


title: CTRL_DMSO_1


title: Wt Mab ATCC19977 - Rif - Replicate 1


title: L1_F_ML355_3

value: treated with ML355


title: P0 Mouse Cortex - H3.3 Neurod6 dKO 3

description: cDNA from rRNA-depleted RNA

value: H3.3 Neurod6 dKO

value: cortex


title: P0 Mouse Cortex - H3.3 Neurod6 dKO 4

description: cDNA from rRNA-depleted RNA


title: Bone Marrow Mononuclear Cells, GEX

data_processing:
Binary Base Call (BCL) files were demultiplexed into FASTQ files was performed using 10x cellranger mkfastq.
The raw data was processed using cellranger multi.
Metadata for hashed samples including HTO oligo sequence is available in the file "GEO_upload_seq_HTO.xlsx"
Paired-end reads were mapped to the mm10 genome with cellranger for gene-level read counts
Paired-end reads were mapped to protein feature sequence with cellranger for protein-level read counts
Cell Ranger VDJ pipeline (10xGenomics) under default parameters was performed to generate scTCR annotations on the assembled contigs and on the clonotype consensus sequences
Genome_build: mm10
Supplementary_files_format_and_content: RNA_counts* files (cell ID is barcode-#.  # is the mouse ID, from mouse1 to mouse10)
Supplementary_files_format_and_content: GEO_upload_seq_HTO.xlsx (metadata details)


title: Bone Marrow Mononuclear Cells, ADT

data_processing:
Binary Base Call (BCL) files were demultiplexed into FASTQ files was performed using 10x cellranger mkfastq.
The raw data was processed using cellranger multi.
Metadata for hashed samples including HTO oligo sequence is available in the file "GEO_upload_seq_HTO.xlsx"
Paired-end reads were mapped to the mm10 genome with cellranger for gene-level read counts
Paired-end reads were mapped to protein feature sequence with cellranger for protein-level read counts
Cell Ranger VDJ pipeline (10xGenomics) under default parameters was performed to generate scTCR annotations on the assembled contigs and on the clonotype consensus sequences
Genome_build: mm10
Supplementary_files_format_and_content: ADT_counts* files (cell ID is barcode-#.  # is the mouse ID, from mouse1 to mouse10)
Supplementary_files_format_and_content: GEO_upload_seq_HTO.xlsx (metadata details)

molecule: protein


title: L1_F_ML355_2


title: P0 Mouse Cortex - H3.3 Neurod6 dKO 2

description: cDNA from rRNA-depleted RNA


title: HepatocytePBS

description: HepatocytePBS

data_processing:
Sequencing was performed using the Illumina Novaseq6000 on a paired-end read flow cell, and sequenced on R1 (10× barcode and the UMIs), followed by eight cycles of the I7 index (sample index) and 89 based on R2 (transcript).
The 10× Genomics Cell Ranger Single Cell Software was used for sample demultiplexing, alignment to the mouse reference genome (mm10), filtering, UMI counting, single-cell 3ʹ-end gene counting, and quality control, according to the manufacturer’s parameters.
Genome_build: mm10
Supplementary_files_format_and_content: barcodes.tsv.gz
Supplementary_files_format_and_content: features.tsv.gz
Supplementary_files_format_and_content: matrix.mtx.gz

source_name: primary hepatocyte

growth_protocol: Mice received daily i.p. injections of PBS or rIL-33 (0.5 µg) for 5 days. Primary hepatocyte were isolated with two step-digestion method and approximately 14000-16000 hepatocyte were loaded on ChIP G.

extract_protocol:
The cells were encapsulated into single droplets using Chromium Controller (10x Genomics) according to manufacturer's protocol.
Libraries were prepared using Chromium Single Cell 3' Reagent Kits v3.1 according to the manufacturer's protocol.

value: primary hepatocyte from PBS-treated mice


title: SCD01

description: Bulk Tissue

value: Superior Colliculus (Deep layer)

value: Post natal day 6

value: Saline injected at P0-1


title: P0 Mouse Cortex - H3.3 Neurod6 dKO 1

description: cDNA from rRNA-depleted RNA


title: CtLiverILC2

growth_protocol: Mice received daily i.p. injections of PBS or rIL-33 (0.5 µg) for 5 days. Then, liver and lung ILC2s were sorted using flow cytometry ARIA III [gating: Lin− (CD3e−Ly6G−Ly6c−CD11b−CD45R−TER119−TCRb−) CD127+Thy1+ST2+]. Approximately 10000-20000 ILC2s were loaded on 10x Chromium ChIP G.

value: liver ILC2s from PBS-treated mice


title: CtLungILC2

value: lung ILC2s from PBS-treated mice


title: P0 Mouse Cortex - Control 4

description: cDNA from rRNA-depleted RNA

value: control


title: P0 Mouse Cortex - Control 3

description: cDNA from rRNA-depleted RNA


title: L1_F_DMSO_3

value: treated with DMSO


title: IL1403_vs_IL594_Glu_S

type: RNA

city: Warszawa

first: Marek

last: Skoneczny

email: kicia@ibb.waw.pl, mrksknc@gmail.com

address: Pawińskiego 5A

country: Poland

institute: Institute of Biochemistry and Biophysics PAS

hyb_protocol: Labeled probes were hybridized to custom designed microarrays in 8x15k format, made by Agilent (Design ID: 084868) using Gene Expression Hybridization Kit, Hybridization Chamber and Hybridization oven (all from Agilent) for 17 hours at 65°C.

scan_protocol: After washing using Gene Expression Wash Buffer Set (Agilent) the slides were immediately scanned using Axon GenePix 4000B scanner (Molecular Devices, USA) at 5μm and 100% laser power. PMT gain was set to around 600 and 750 for 532 nm and 635 nm excitation respectively with minor adjustments to normalize images. Feature extraction was done using GenePix Pro 6.1 (Molecular Devices, USA).

data_processing: GPR files were analyzed further with Acuity 4.0 software starting with lowess normalization. Normalized Log2 Ratio data from technical replicates (dye swap) were averaged.

organism: Lactococcus lactis

source_name: cells from batch culture

label_protocol: Samples of total RNA (5μg) were labeled with QuickAmp Labeling Kit, Two-Color (Agilent) with Cy3- and Cy5-UTP according to the manufacturer’s protocol.

growth_protocol: IL594 and IL1403 cells were grown in an M17 medium supplemented with desired sugar: cellobiose, galactose, or glucose. Cells were harvested at four distinct growth phases: early exponential [E] at OD600 0.1-0.2, mid-exponential [M] at OD600 0.6-0.7, transition [phase between the exponential and stationary growth; T] at OD600 0.8-0.9, and stationary [S] after further 12 h of incubation.

extract_protocol: Total RNA was prepared using GeneMATRIX Universal RNA Purification Kit (EURx, Poland), according to the manufacturer protocol.

tag: carbon source

value: glucose

tag: growth phase

value: stationary [S]


title: L1_F_DMSO_2


title: 33LungILC2

value: BALB/c

tag: genotype

value: wild type

value: lung ILC2s from IL-33-treated mice


title: P0 Mouse Cortex - Control 2

description: cDNA from rRNA-depleted RNA


title: L1_F_ML355_1


title: H3K9_M5_D4_Soft (H3K9M rep3)

city: Boulder

first: Eduard

last: Casas

state: Colorado

address: Porter Biosciences, CU Campus

department: MCDB

institute: CU Boulder

description:
H3K9 methylation suppressed (H3K9M)
DESEQ-K9M-vs-WT.xls
gseGO.xls
GeneCountsRaw.xls

data_processing:
Alignment with hisat2
Read summarization with featureCounts
Read normalization and differential expression using DESeq2
Gene Set Enrichment Analysis using ClusterProfiler and GO pathways
Genome_build: mm10
Supplementary_files_format_and_content: Raw counts of reads per gene
Supplementary_files_format_and_content: Differential expression using DESeq2
Supplementary_files_format_and_content: Pathway enrichment analysis

molecule: polyA RNA

source_name: Cardiac tissue

growth_protocol: H3K9M and H3WT cardiac cells were cultured (at 37°C and 5% CO2) on prepared 13 kPa PDMS substrates in DMEM-F12 Advanced (Gibco) containing 10% fetal bovine serum (Gibco), 1% penicillin-streptomycin (Gibco) and 25 mM HEPES (Gibco) at a density of 50,000 cells/cm2 for 4 days and collected for analysis.

extract_protocol:
After 4 days in culture, cardiac cells were lyzed with Quiazol. RNA was isolated using Zymo Research Direct-zol RNA Miniprep Kit (Cat No. R2050).
Libraries were prepared using Tecan Universal Plus mRNA –SEQ with NuQuant Library Kit (Cat No. 0520)

treatment_protocol: On Day 0, 1, and 2, the transgene expression was induced with 2µg/ml doxycycline (Sigma).

value: Embryonic cardiac cells

value: induced with 2ug/ml doxycycline on Day 0, 1, 2

value: C57BL/6 x 129S4/SvJae

value: Embryonic (day 18.5)

value: H3K9 methylation suppressed (H3K9M)


title: Skin_AD_F4_80+PaCre-_02

city: Osaka

first: Yu-Tung

last: Li

address: 2-2 Yamada-oka, Suita

country: Japan

institute: Osaka University

data_processing:
Sequencing outputs were demultiplexed using bcl2fastq2 (https://jp.support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html)
Fastq files were aligned to Mus musculus GRCm38 reference using STAR aligner (2.7.1a; https://github.com/alexdobin/STAR)
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: Processed data files are zipped STAR output directory (Solo.out).

source_name: Mouse Skin Macrophage

extract_protocol:
Excised skin samples were digested by collagenase A, dispase II and Dnase I to obtain single cell suspension. MHCII+ cells were positively selected by magnetic beads followed by flow cytometric sorting of target cells.
RNA-seq library was constructed using a modified smart-seq2 protocol. Cells were sorted into 384-well plates with barcoded oligo dT primer for each well (1 cell / well). After reverse transcription in each well, cDNA was pre-amplified using the Accel-NGS 1S Plus DNA Library Kit (Swift Biosciences, Ann Arbor, MI, USA). Purified cDNAs were tagmentationed with Amplicon Tagment enzyme (Illumina) and PCR for library construction was done by using NEBNext High-Fidelity 2× PCR Master Mix (NEB).

value: Skin

value: PDGFRalpha-Cre;ROSAtdTomato


title: L1_F_DMSO_1


title: HepatocyteIL33

value: primary hepatocyte from IL-33-treated mice


title: MHCC97H-shHNRNPC rep2

city: Wuhan

first: Danfei

last: Liu

state: China

address: Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Institute of Liver and Gastrointestinal Diseases, Department of Gastroenterology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology

department: Department of Gastroenterology

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
STAR is used to align clean reads to reference genome. STAR outperforms other aligners by a factor of >50 in mapping speed, while at the same time improving alignment sensitivity and precision. In addition to unbiased de novo detection of canonical junctions, STAR can discover non-canonical splices and chimeric (fusion) transcripts, and is also capable of mapping full-length RNA sequences.
HTSeq v0.6.0 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
We applied DESeq2 algorithm to filter the differentially expressed genes, after the significant analysis and FDR analysis under the following criteria: i) |log2FC| > 1 ; ii) Pvalue < 0.05
GO Analysis: Gene ontology (GO) analysis was performed to facilitate elucidating the biological implications of unique genes in the significant or representative profiles of the differentially expressed gene in the experiment.
Pathway analysis was used to find out the significant pathway of the differential genes according to KEGG database.
Genome_build: STAR
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
RNA was isolated using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA)

value: human highly metastatic HCC cell

value: HNRNPC knockdown by specific shRNA(HNRNPC-shRNA)


title: MHCC97H-shHNRNPC rep3

institute: Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Institute of Liver and Gastrointestinal Diseases


title: H3K9_M3_D4 (H3K9M rep2)


title: IL1403_vs_IL594_Glu_T

value: transition [T]


title: IL1403_vs_IL594_Glu_E

value: early exponential [E]


title: MHCC97H-shHNRNPC rep1


title: Skin_AD_F4_80+PaCre-_01


title: IL1403_vs_IL594_Gal_M

value: galactose

value: mid-exponential [M]


title: IL1403_vs_IL594_Gal_S

value: stationary [S]


title: IL1403_vs_IL594_Gal_T


title: IL1403_vs_IL594_Glu_M

value: glucose


title: H3K9_M1_Soft (H3K9M rep1)


title: MHCC97H-shcontrol rep3

value: control


title: 33LiverILC2

value: BALB/c

value: wild type

value: liver ILC2s from IL-33-treated mice


title: H3_WT_M5_D4_Soft (WT rep3)

description:
Control WT (H3WT)
DESEQ-K9M-vs-WT.xls
gseGO.xls
GeneCountsRaw.xls

value: Embryonic cardiac cells

value: induced with 2ug/ml doxycycline on Day 0, 1, 2

value: C57BL/6 x 129S4/SvJae

value: Embryonic (day 18.5)

value: Control WT (H3WT)


title: Skin_AD_F4_80+PaCre+_02

value: Skin

value: PDGFRalpha-Cre;ROSAtdTomato


title: MHCC97H-shcontrol rep2

value: human highly metastatic HCC cell


title: P0 Mouse Cortex - Control 1

description: cDNA from rRNA-depleted RNA

value: cortex


title: H3_WT_M2_D4 (WT rep2)


title: Skin_AD_F4_80+PaCre+_01


title: IL1403_vs_IL594_Cel_S

value: cellobiose


title: MHCC97H-shcontrol rep1


title: IL1403_vs_IL594_Cel_T

value: transition [T]


title: Skin_AD_F4_80+PaCre+_03


title: CRISPRi_perturb_seq,gex

status: Public on Jul 26 2022

city: San Francisco

first: Sara

last: Sunshine

address: 1700 4th Street

institute: University of California, San Francisco

description: 10x genomics

data_processing:
Alignment using Cell Ranger 10X Genomics CellRanger v3.1
Assembly: custom, based on GRCh38, SARS-CoV-2 and lentiviral sequences; viral_references.tar.gz
Supplementary files format and content: tar.gz containing Cellranger output files and cell identities
Supplementary files format and content: tar.gz containing viral fasta and gtf files
Library strategy: Perturb-seq

organism:
Homo sapiens
Severe acute respiratory syndrome coronavirus 2

growth_protocol: Calu-3 CRISPRi cells were cultured in DMEM/F12 supplemented with 10% FCS, penicillin, streptomycin, glutamine and  non-essential amino acids. These CRISPRi cells were lentivirally transduced with the Perturb-seq library in the presence of polybrene, and puromycin selected.

extract_protocol:
After 24 hours, infected Calu-3 cells were washed with 1X PBS, dissociated with 10X TrypLE Select Enzyme (Thermofisher Scientific), washed, and resuspended in 1X PBS with 0.04% BSA.
Library prep was performed following manufacturer's instructions (10x Genomics Chromium NextGEM Single Cell V(D)J Reagents Kit v1.1); modifications to the manufacturer's single-cell sequencing protocol were made for direct guide capturing and library preparation as previously described (Replogle et al., 2020)

treatment_protocol: Cells were infected with an isolate of SARS-CoV-2.

value: viral infection


title: HEK293T, 0 CpGs, Rep2

city: London

first: Daniel

last: Goncalves-Carneiro

address: Sir Alexander Fleming Building, Imperial College Rd

country: United Kingdom

institute: Imperial College London

data_processing:
Adapter Sequence removed by cutadapt in FASTX-toolkit
Reads sorted by barcoded using fastx_collapser in FASTX-toolkit
9 nucleotides trimed using fastx_trimmer in FASTX-toolkit
Bowtie and Samtools alignement
Reads per nucleotide determined using mpileup and mpileup_To_counts
Assembly: HIV-1 NHG Genome (GenBank: MF944225.1)
Supplementary files format and content: .txt file, reads per nucleotide in HIV-1 genome

organism:
Homo sapiens
synthetic HIV-1

growth_protocol: Cells were culture in DMEM supplemented with 10%FBS and gentamicin, at 37˚C with 5% CO2.

extract_protocol:
ZAP:RNA complexes were crossedlinked by exposure to UV radiation for 2min. Cells were lysed and ZAP was purified by immunoprecipitation. RNA bound to ZAP was released by proteinase K digestion and phenol:chloroform:isoamyl alcohol extraction.
A fluorescently labelled 3’ adapter was ligated to the RNA, gel purified and subsequently ligated to a 5'adapter. Resulting nucleic acids were reversed transcribed and amplified using Illumina primers.

treatment_protocol: At 24h after plasmid DNA transfections, 4-thiouridine was added to the culture mediam and incubated for 18h at 37˚C with 5% CO2.

value: Kindey cell

tag: sample type

value: ZAP:RNA complexes

value: Transfected with plasmids encoding ZAP-L and recoded mutant HIV-1 viruses


title: HEK293T, 15CpGs 11nt and 15CpGs 32nt, Rep1


title: HEK293T, 15CpGs 11nt and 15CpGs 32nt, Rep2


title: IL1403_vs_IL594_Cel_M

value: mid-exponential [M]


title: IL1403_vs_IL594_Gal_E

value: galactose

value: early exponential [E]


title: IL1403_vs_IL594_Cel_E


title: H3_WT_M1_Soft (WT rep1)

value: Embryonic cardiac cells

value: induced with 2ug/ml doxycycline on Day 0, 1, 2


title: D.magna whole body, PIPE-Crystal-Lake-0 ng/L pyriproxyfen-Late Summer-Rep2 G2Z_S133

city: Seattle

first: Mark

last: Jankowski

state: WA

address: 1200 6th Ave

institute: USEPA

description:
D.magna whole body, PIPE-Crystal-Lake-0 ng/L pyriproxyfen-Late Summer-Rep2
Organism Source: Carolina Biological Supply, 2014

data_processing:
Raw sequences were evaluated via FastQC (Andrews, 2010) to determine the baseline quality of the sequencing results. To improve these overall statistics, reads were trimmed to remove Illumina‐specific adapter sequences and low‐quality sequences or sequence tails using the Trimmomatic software (Bolger et al., 2014). FastQC was run again to verify that only high‐quality sequences were retained.
High‐quality sequences were then mapped to D. magna reference transcripts using Kallisto (Bray et al., 2016), a kmer‐based mapper. Kallisto produces a matrix of read counts with transcripts along one axis and samples along the other. To produce a data set for direct differential expression analysis, each cell of this matrix was rounded to the nearest integer value to be compatible with the DESeq. 2 algorithm (Love et al., 2014; an R Package available through Bioconductor). To produce a data set to identify minimal gene signatures separating conditions, each read count was divided by the total reads counted for that sample, producing a fractional matrix. All genes that showed no variance in any one data set were removed from analysis for all data sets to ensure cross‐data set comparability. Initial comparisons indicated a modest batch effect between the wetland and storm‐water samples. A linear model was therefore used to identify and remove batch variance that may have been a result of employing two different genetic backgrounds for each study.
Assembly: RNA-seq reads from this study were aligned to a transcriptome created from the RNA sequencing of 12 Daphnia magna colonies under different stress conditions. Orsini, L., D. Gilbert, R. Podicheti, M. Jansen, J. B. Brown, O. S. Solari, K. I. Spanier, J. K. Colbourne, D. B. Rusch, and E. Decaestecker. 2016. Daphnia magna transcriptome by RNA-Seq across 12 environmental stressors. Scientific Data 3:1-16.
Supplementary files format and content: Kallisto.counts is a matrix of raw counts. Kallisto produces a matrix of read counts with transcripts along one axis and samples along the other. Matrix of read counts with transcripts along one axis and samples along the other.
Supplementary files format and content: Kallisto.tpm is a matrix processed as described herein. Kallisto produces a matrix of read counts with transcripts along one axis and samples along the other. Matrix of read counts with transcripts along one axis and samples along the other. Each cell of this matrix was rounded to the nearest integer value to be compatible with the DESeq2 algorighim. Each read count was then divided by the total reads counted for that sample, producing a fractional matrix. All genes that showed no variance in any one dataset were removed from analysis for all datasets to ensure cross-dataset comparability.

organism: Daphnia magna

source_name: D.magna whole body

growth_protocol: Live D. magna (purchased from Carolina Biological Supply) were placed into aerated St. Cloud State University well water and maintained as an experimental culture under a 16:8‐h light:dark photoperiod. All test water conditions were within Organisation for Economic Co‐operation and Development (OECD) Test No. 211 (OECD, 2012) guidelines.

extract_protocol:
Total RNA extration via PureLink RNA Mini Kit (catalog no. 12183018 A; Thermo Fisher Scientific)
Strand‐specific messenger RNA libraries were created for each total RNA sample of pooled daphnia (n = 5 individual neonates per replicate sample; five groups per treatment).

treatment_protocol: At the end of the 96‐h exposure period, to obtain sufficient RNA quantity for sequencing, the 30 treated (less 0%–7% mortality) neonates were randomly divided into five groups of five individuals, then stored in 100 µl of RNAlater (catalog no. R0901; Sigma‐Aldrich) at −80 °C until RNA extraction. RNA was extracted by sonication (30 s)

value: D.magna whole body


title: D.magna whole body, PIPE-Cedar-Lake-0 ng/L pyriproxyfen-Spring-Rep5 H6X_S40

description:
D.magna whole body, PIPE-Cedar-Lake-0 ng/L pyriproxyfen-Spring-Rep5
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, PIPE-Cedar-Lake-0 ng/L pyriproxyfen-Late Summer-Rep2 H2Z_S138

description:
D.magna whole body, PIPE-Cedar-Lake-0 ng/L pyriproxyfen-Late Summer-Rep2
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, PIPE-Crystal-Lake-0 ng/L pyriproxyfen-Late Summer-Rep3 G3Z_S134

description:
D.magna whole body, PIPE-Crystal-Lake-0 ng/L pyriproxyfen-Late Summer-Rep3
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, PIPE-Crystal-Lake-0 ng/L pyriproxyfen-Spring-Rep3 G3X_S33

description:
D.magna whole body, PIPE-Crystal-Lake-0 ng/L pyriproxyfen-Spring-Rep3
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, PIPE-Cedar-Lake-0 ng/L pyriproxyfen-Spring-Rep4 H5X_S39

description:
D.magna whole body, PIPE-Cedar-Lake-0 ng/L pyriproxyfen-Spring-Rep4
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, PIPE-Cedar-Lake-0 ng/L pyriproxyfen-Early Summer-Rep5 H6Y_S96

description:
D.magna whole body, PIPE-Cedar-Lake-0 ng/L pyriproxyfen-Early Summer-Rep5
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, PIPE-Cedar-Lake-0 ng/L pyriproxyfen-Spring-Rep3 H4X_S38

description:
D.magna whole body, PIPE-Cedar-Lake-0 ng/L pyriproxyfen-Spring-Rep3
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, PIPE-Cedar-Lake-0 ng/L pyriproxyfen-Late Summer-Rep5 H5Z_S141

description:
D.magna whole body, PIPE-Cedar-Lake-0 ng/L pyriproxyfen-Late Summer-Rep5
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, PIPE-Cedar-Lake-0 ng/L pyriproxyfen-Early Summer-Rep3 H4Y_S94

description:
D.magna whole body, PIPE-Cedar-Lake-0 ng/L pyriproxyfen-Early Summer-Rep3
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, PIPE-Cedar-Lake-0 ng/L pyriproxyfen-Late Summer-Rep3 H3Z_S139

description:
D.magna whole body, PIPE-Cedar-Lake-0 ng/L pyriproxyfen-Late Summer-Rep3
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, PIPE-Crystal-Lake-0 ng/L pyriproxyfen-Early Summer-Rep2 G3Y_S87

description:
D.magna whole body, PIPE-Crystal-Lake-0 ng/L pyriproxyfen-Early Summer-Rep2
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, PIPE-Cedar-Lake-0 ng/L pyriproxyfen-Spring-Rep2 H3X_S37

description:
D.magna whole body, PIPE-Cedar-Lake-0 ng/L pyriproxyfen-Spring-Rep2
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, PIPE-Cedar-Lake-0 ng/L pyriproxyfen-Early Summer-Rep4 H5Y_S95

description:
D.magna whole body, PIPE-Cedar-Lake-0 ng/L pyriproxyfen-Early Summer-Rep4
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, PIPE-Crystal-Lake-0 ng/L pyriproxyfen-Late Summer-Rep1 G1Z_S132

description:
D.magna whole body, PIPE-Crystal-Lake-0 ng/L pyriproxyfen-Late Summer-Rep1
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, PIPE-Crystal-Lake-0 ng/L pyriproxyfen-Spring-Rep1 G1X_S31

description:
D.magna whole body, PIPE-Crystal-Lake-0 ng/L pyriproxyfen-Spring-Rep1
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, PIPE-Cedar-Lake-0 ng/L pyriproxyfen-Late Summer-Rep4 H4Z_S140

description:
D.magna whole body, PIPE-Cedar-Lake-0 ng/L pyriproxyfen-Late Summer-Rep4
Organism Source: Carolina Biological Supply, 2014


title: HEK293T, 0 CpGs, Rep1


title: D.magna whole body, PIPE-Cedar-Lake-0 ng/L pyriproxyfen-Spring-Rep1 H2X_S36

description:
D.magna whole body, PIPE-Cedar-Lake-0 ng/L pyriproxyfen-Spring-Rep1
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, PIPE-Cedar-Lake-0 ng/L pyriproxyfen-Early Summer-Rep2 H2Y_S93

description:
D.magna whole body, PIPE-Cedar-Lake-0 ng/L pyriproxyfen-Early Summer-Rep2
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, PIPE-Cedar-Lake-0 ng/L pyriproxyfen-Late Summer-Rep1 H1Z_S137

description:
D.magna whole body, PIPE-Cedar-Lake-0 ng/L pyriproxyfen-Late Summer-Rep1
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, PIPE-Crystal-Lake-0 ng/L pyriproxyfen-Early Summer-Rep1 G2Y_S86

description:
D.magna whole body, PIPE-Crystal-Lake-0 ng/L pyriproxyfen-Early Summer-Rep1
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, LeSouer Wetland-119 ng/L pyriproxyfen-Summer-Rep5 84_S15

description:
D.magna whole body, LeSouer Wetland-119 ng/L pyriproxyfen-Summer-Rep5
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, PIPE-Crystal-Lake-0 ng/L pyriproxyfen-Spring-Rep2 G2X_S32

description:
D.magna whole body, PIPE-Crystal-Lake-0 ng/L pyriproxyfen-Spring-Rep2
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, PIPE-Cedar-Lake-0 ng/L pyriproxyfen-Early Summer-Rep1 H1Y_S92

description:
D.magna whole body, PIPE-Cedar-Lake-0 ng/L pyriproxyfen-Early Summer-Rep1
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, LeSouer Wetland-119 ng/L pyriproxyfen-Summer-Rep3 75_S61

description:
D.magna whole body, LeSouer Wetland-119 ng/L pyriproxyfen-Summer-Rep3
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, LeSouer Wetland-119 ng/L pyriproxyfen-Summer-Rep2 3_S8

description:
D.magna whole body, LeSouer Wetland-119 ng/L pyriproxyfen-Summer-Rep2
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, LeSouer Wetland-119 ng/L pyriproxyfen-Summer-Rep1 38_S10

description:
D.magna whole body, LeSouer Wetland-119 ng/L pyriproxyfen-Summer-Rep1
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, LeSouer Wetland-119 ng/L pyriproxyfen-Summer-Rep4 77_S13

description:
D.magna whole body, LeSouer Wetland-119 ng/L pyriproxyfen-Summer-Rep4
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, LeSouer Wetland-0 ng/L pyriproxyfen-Summer-Rep5 95_S62

description:
D.magna whole body, LeSouer Wetland-0 ng/L pyriproxyfen-Summer-Rep5
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, LeSouer Wetland-0 ng/L pyriproxyfen-Summer-Rep4 78_S14

description:
D.magna whole body, LeSouer Wetland-0 ng/L pyriproxyfen-Summer-Rep4
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, LeSouer Wetland-0 ng/L pyriproxyfen-Summer-Rep2 55_S11

description:
D.magna whole body, LeSouer Wetland-0 ng/L pyriproxyfen-Summer-Rep2
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, LeSouer Wetland-0 ng/L pyriproxyfen-Summer-Rep1 37_S9

description:
D.magna whole body, LeSouer Wetland-0 ng/L pyriproxyfen-Summer-Rep1
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, Lab Water-239 ng/L pyriproxyfen-Summer-Rep5 93_S63

description:
D.magna whole body, Lab Water-239 ng/L pyriproxyfen-Summer-Rep5
Organism Source: Carolina Biological Supply, 2014

value: Lab Water-239 ng/L pyriproxyfen-Summer


title: D.magna whole body, Lab Water-239 ng/L pyriproxyfen-Summer-Rep4 60_S37

description:
D.magna whole body, Lab Water-239 ng/L pyriproxyfen-Summer-Rep4
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, Lab Water-239 ng/L pyriproxyfen-Summer-Rep2 41_S34

description:
D.magna whole body, Lab Water-239 ng/L pyriproxyfen-Summer-Rep2
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, Lab Water-119 ng/L pyriproxyfen-Summer-Rep4 72_S39

description:
D.magna whole body, Lab Water-119 ng/L pyriproxyfen-Summer-Rep4
Organism Source: Carolina Biological Supply, 2014

value: Lab Water-119 ng/L pyriproxyfen-Summer


title: D.magna whole body, LeSouer Wetland-0 ng/L pyriproxyfen-Summer-Rep3 67_S12

description:
D.magna whole body, LeSouer Wetland-0 ng/L pyriproxyfen-Summer-Rep3
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, Lab Water-119 ng/L pyriproxyfen-Summer-Rep5 86_S41

description:
D.magna whole body, Lab Water-119 ng/L pyriproxyfen-Summer-Rep5
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, Lab Water-119 ng/L pyriproxyfen-Summer-Rep2 40_S33

description:
D.magna whole body, Lab Water-119 ng/L pyriproxyfen-Summer-Rep2
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, Lab Water-0 ng/L pyriproxyfen-Summer-Rep3 68_S38

description:
D.magna whole body, Lab Water-0 ng/L pyriproxyfen-Summer-Rep3
Organism Source: Carolina Biological Supply, 2014

value: Lab Water-0 ng/L pyriproxyfen-Summer


title: D.magna whole body, Lab Water-239 ng/L pyriproxyfen-Summer-Rep1 26_S32

description:
D.magna whole body, Lab Water-239 ng/L pyriproxyfen-Summer-Rep1
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, Lab Water-119 ng/L pyriproxyfen-Summer-Rep3 51_S36

description:
D.magna whole body, Lab Water-119 ng/L pyriproxyfen-Summer-Rep3
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, Lab Water-239 ng/L pyriproxyfen-Summer-Rep3 5_S31

description:
D.magna whole body, Lab Water-239 ng/L pyriproxyfen-Summer-Rep3
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, Lab Water-0 ng/L pyriproxyfen-Summer-Rep2 58_S35

description:
D.magna whole body, Lab Water-0 ng/L pyriproxyfen-Summer-Rep2
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, Kerk Wetland-119 ng/L pyriproxyfen-Summer-Rep4 70_S48

description:
D.magna whole body, Kerk Wetland-119 ng/L pyriproxyfen-Summer-Rep4
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, Lab Water-0 ng/L pyriproxyfen-Summer-Rep1 2_S30

description:
D.magna whole body, Lab Water-0 ng/L pyriproxyfen-Summer-Rep1
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, Kerk Wetland-119 ng/L pyriproxyfen-Summer-Rep3 43_S45

description:
D.magna whole body, Kerk Wetland-119 ng/L pyriproxyfen-Summer-Rep3
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, Lab Water-0 ng/L pyriproxyfen-Summer-Rep5 94_S65

description:
D.magna whole body, Lab Water-0 ng/L pyriproxyfen-Summer-Rep5
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, Kerk Wetland-119 ng/L pyriproxyfen-Summer-Rep2 28_S43

description:
D.magna whole body, Kerk Wetland-119 ng/L pyriproxyfen-Summer-Rep2
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, Kerk Wetland-0 ng/L pyriproxyfen-Summer-Rep2 42_S44

description:
D.magna whole body, Kerk Wetland-0 ng/L pyriproxyfen-Summer-Rep2
Organism Source: Carolina Biological Supply, 2014

value: Kerk Wetland-0 ng/L pyriproxyfen-Summer


title: D.magna whole body, Kerk Wetland-0 ng/L pyriproxyfen-Summer-Rep4 74_S47

description:
D.magna whole body, Kerk Wetland-0 ng/L pyriproxyfen-Summer-Rep4
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, Kerk Wetland-0 ng/L pyriproxyfen-Summer-Rep5 97_S69

description:
D.magna whole body, Kerk Wetland-0 ng/L pyriproxyfen-Summer-Rep5
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, Kerk Wetland-0 ng/L pyriproxyfen-Summer-Rep3 66_S46

description:
D.magna whole body, Kerk Wetland-0 ng/L pyriproxyfen-Summer-Rep3
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, Lab Water-119 ng/L pyriproxyfen-Summer-Rep1 105_S64

description:
D.magna whole body, Lab Water-119 ng/L pyriproxyfen-Summer-Rep1
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, Lab Water-0 ng/L pyriproxyfen-Summer-Rep4 76_S40

description:
D.magna whole body, Lab Water-0 ng/L pyriproxyfen-Summer-Rep4
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, Kandiyohi Wetland-119 ng/L pyriproxyfen-Summer-Rep2 104_S66

description:
D.magna whole body, Kandiyohi Wetland-119 ng/L pyriproxyfen-Summer-Rep2
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, Kandiyohi Wetland-119 ng/L pyriproxyfen-Summer-Rep1 101_S22

description:
D.magna whole body, Kandiyohi Wetland-119 ng/L pyriproxyfen-Summer-Rep1
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, Kandiyohi Wetland-119 ng/L pyriproxyfen-Summer-Rep3 30_S17

description:
D.magna whole body, Kandiyohi Wetland-119 ng/L pyriproxyfen-Summer-Rep3
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, Kandiyohi Wetland-0 ng/L pyriproxyfen-Summer-Rep3 82_S19

description:
D.magna whole body, Kandiyohi Wetland-0 ng/L pyriproxyfen-Summer-Rep3
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, Kandiyohi Wetland-0 ng/L pyriproxyfen-Summer-Rep4 89_S21

description:
D.magna whole body, Kandiyohi Wetland-0 ng/L pyriproxyfen-Summer-Rep4
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, Kandiyohi Wetland-0 ng/L pyriproxyfen-Summer-Rep2 54_S18

description:
D.magna whole body, Kandiyohi Wetland-0 ng/L pyriproxyfen-Summer-Rep2
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, Douglas Wetland-0 ng/L pyriproxyfen-Summer-Rep4 64_S3

description:
D.magna whole body, Douglas Wetland-0 ng/L pyriproxyfen-Summer-Rep4
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, Kandiyohi Wetland-0 ng/L pyriproxyfen-Summer-Rep1 29_S16

description:
D.magna whole body, Kandiyohi Wetland-0 ng/L pyriproxyfen-Summer-Rep1
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, Douglas Wetland-119 ng/L pyriproxyfen-Summer-Rep1 57_S5

description:
D.magna whole body, Douglas Wetland-119 ng/L pyriproxyfen-Summer-Rep1
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, Douglas Wetland-119 ng/L pyriproxyfen-Summer-Rep3 90_S60

description:
D.magna whole body, Douglas Wetland-119 ng/L pyriproxyfen-Summer-Rep3
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, Douglas Wetland-119 ng/L pyriproxyfen-Summer-Rep2 73_S7

description:
D.magna whole body, Douglas Wetland-119 ng/L pyriproxyfen-Summer-Rep2
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, Douglas Wetland-0 ng/L pyriproxyfen-Summer-Rep3 50_S4

description:
D.magna whole body, Douglas Wetland-0 ng/L pyriproxyfen-Summer-Rep3
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, Kerk Wetland-119 ng/L pyriproxyfen-Summer-Rep1 103_S68

description:
D.magna whole body, Kerk Wetland-119 ng/L pyriproxyfen-Summer-Rep1
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, Douglas Wetland-0 ng/L pyriproxyfen-Summer-Rep1 1_S1

description:
D.magna whole body, Douglas Wetland-0 ng/L pyriproxyfen-Summer-Rep1
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, Douglas Wetland-0 ng/L pyriproxyfen-Summer-Rep2 35_S2

description:
D.magna whole body, Douglas Wetland-0 ng/L pyriproxyfen-Summer-Rep2
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, Breen Wetland-119 ng/L pyriproxyfen-Summer-Rep3 69_S29

description:
D.magna whole body, Breen Wetland-119 ng/L pyriproxyfen-Summer-Rep3
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, Breen Wetland-119 ng/L pyriproxyfen-Summer-Rep2 49_S27

description:
D.magna whole body, Breen Wetland-119 ng/L pyriproxyfen-Summer-Rep2
Organism Source: Carolina Biological Supply, 2014


title: InputDNA_ChIP1_Dox_Treated_rep1-2 [722]

city: VILLEJUIF

first: Christel

last: GUILLOUF

address: 114 rue Edouard vaillant

country: France

institute: Gustave Roussy

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
ChIP-seq reads were aligned to the mm10 genome assembly using mem algorithm from Burrow Wheeler Aligner (BWA) with the following configurations: option -t equal to 7 paired-end mode used when necessary.
Reads were filtered by applying a threshold of 20 on the MAPQ field of bam files. PCR duplicates were removed.
Normalization between density files of different conditions (bigWig) for each experiment was performed using CHIPIN.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bigWig files generated using HMCan and normalized using CHIPIN.

source_name: Bone marrow leukemic cells

growth_protocol: Cells were maintained in culture with EPO, in exponential growth before treatment with Dox.

extract_protocol:
ChIP assays were performed using the ChIP assay kit (Millipore) following the manufacturer’s protocol as previously described (Ridinger-Saison et al., NAR, 2012). ChIP samples were sonicated for 17min using the Covaris S220 sonicator (peak power 220, duty factor 20 and cycle Burst 200) was used for sonication.
ChIP samples were purified using Agencourt AMPure XP beads (Beckman Coulter). ChIP-seq libraries were prepared from 5ng of double-stranded purified DNA using the MicroPlex Library Preparation kit v2 (C05010014, Diagenode s.a.).

treatment_protocol: Cells have been treated or not with doxycycline for 48h to induce the expression of an shRNA against Spi1.

value: Leukemic erythroid cells

tag: chip antibody


title: D.magna whole body, Breen Wetland-119 ng/L pyriproxyfen-Summer-Rep1 32_S25

description:
D.magna whole body, Breen Wetland-119 ng/L pyriproxyfen-Summer-Rep1
Organism Source: Carolina Biological Supply, 2014

tag: treatment


title: InputDNA_ChIP1_Dox_Untreated_rep1-2 [722]


title: D.magna whole body, Kandiyohi Wetland-119 ng/L pyriproxyfen-Summer-Rep4 85_S20

description:
D.magna whole body, Kandiyohi Wetland-119 ng/L pyriproxyfen-Summer-Rep4
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, Kerk Wetland-0 ng/L pyriproxyfen-Summer-Rep1 27_S42

description:
D.magna whole body, Kerk Wetland-0 ng/L pyriproxyfen-Summer-Rep1
Organism Source: Carolina Biological Supply, 2014


title: H3K4me1_ChIP1_Dox_Treated_rep1 [722]


title: D.magna whole body, Kandiyohi Wetland-0 ng/L pyriproxyfen-Summer-Rep5 92_S67

description:
D.magna whole body, Kandiyohi Wetland-0 ng/L pyriproxyfen-Summer-Rep5
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, Breen Wetland-0 ng/L pyriproxyfen-Summer-Rep5 9_S23

description:
D.magna whole body, Breen Wetland-0 ng/L pyriproxyfen-Summer-Rep5
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, Breen Wetland-0 ng/L pyriproxyfen-Summer-Rep4 98_S58

description:
D.magna whole body, Breen Wetland-0 ng/L pyriproxyfen-Summer-Rep4
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, Breen Wetland-0 ng/L pyriproxyfen-Summer-Rep3 71_S28

description:
D.magna whole body, Breen Wetland-0 ng/L pyriproxyfen-Summer-Rep3
Organism Source: Carolina Biological Supply, 2014


title: H3K27ac_ChIP1_Dox_Treated_rep2 [722]


title: H3K27ac_ChIP1_Dox_Untreated_rep2 [722]


title: D.magna whole body, Breen Wetland-0 ng/L pyriproxyfen-Summer-Rep1 31_S24

description:
D.magna whole body, Breen Wetland-0 ng/L pyriproxyfen-Summer-Rep1
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, BMP-TBNS2-Outfall-0 ng/L pyriproxyfen-Early Summer-Rep5 C7Y_S68

description:
D.magna whole body, BMP-TBNS2-Outfall-0 ng/L pyriproxyfen-Early Summer-Rep5
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, Breen Wetland-0 ng/L pyriproxyfen-Summer-Rep2 65_S26

description:
D.magna whole body, Breen Wetland-0 ng/L pyriproxyfen-Summer-Rep2
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, Douglas Wetland-0 ng/L pyriproxyfen-Summer-Rep5 83_S6

description:
D.magna whole body, Douglas Wetland-0 ng/L pyriproxyfen-Summer-Rep5
Organism Source: Carolina Biological Supply, 2014


title: H3K27ac_ChIP1_Dox_Treated_rep1 [722]


title: D.magna whole body, BMP-TBNS2-Outfall-0 ng/L pyriproxyfen-Spring-Rep4 C6X_S14

description:
D.magna whole body, BMP-TBNS2-Outfall-0 ng/L pyriproxyfen-Spring-Rep4
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, BMP-TBNS2-Outfall-0 ng/L pyriproxyfen-Late Summer-Rep5 C6Z_S116

description:
D.magna whole body, BMP-TBNS2-Outfall-0 ng/L pyriproxyfen-Late Summer-Rep5
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, BMP-TBNS2-Outfall-0 ng/L pyriproxyfen-Spring-Rep5 C7X_S15

description:
D.magna whole body, BMP-TBNS2-Outfall-0 ng/L pyriproxyfen-Spring-Rep5
Organism Source: Carolina Biological Supply, 2014


title: CPEB3 Elu [1902 2018]

city: Barcelona

first: Oscar

last: Reina Garcia

state: Barcelona

address: C/Baldiri Reixac 10

department: Biostatistics and Bioinformatics

institute: IRB Barcelona

description:
Replicate#00, HA-CPEB3 microinjected
2030_29688_TAGCTT

data_processing:
FastQ files were aligned against the Xenopus laevis genome (UCSC version 9.2, excluding chrUn chromosomes), with Bowtie2 2.2.2, 1 mismatch and reporting best alignment site per read.
Gene regions were extracted from the Xenbase Xenopus laevis 9.2 annotation GFF, using the makeTxDbFromGFF function from the GenomicFeatures 1.34.8 and R 3.5.1.
Gene level counts were generated with the featureCounts function from the Rsubread package 1.32.4 in R3.5.1, using  options allowMultiOverlap=TRUE, ignoreDup=FALSE, countMultimappingReads=FALSE,minMQS=1.
Genome_build: Xenopus laevis genome (UCSC version 9.2, excluding chrUn chromosomes)
Supplementary_files_format_and_content: Excel XLSX file with per-sample Xenbase Xenopus laevis 9.2 gene-level counts.

organism: Xenopus laevis

source_name: SVI oocyte

growth_protocol: Defolliculated isolated oocytes were kept in Modified Bath Saline media (MBS: 88 mM NaCl, 1 mM KCl, 1 mM MgSO4, 2.5 mM NaHCO3, 0.7 mM CaCl2, pH 7.8) at 18ºC.

extract_protocol:
16-hours post microinjection, live oocytes were lysed by pipetting in 9 μL/oocyte cold IP lysis buffer (20 mM Tris-HCl pH 8, 100 mM NaCl, 0.4% NP40, 1 mM EDTA, 1 mM MgCl2, 1x Complete EDTA-free protease inhibitors (Roche)). Homogenates were clarified by centrifugation for 10 minutes at 12000 g 4ºC. 1 μL of 10x H1K phosphatase inhibitors (80 mM sodium β-glycerophosphate, 0.5 mM sodium orthovanadate) was added per 9 μL of recovered aqueous phase and a second clarification step was performed. 50 μL of clarified lysate were put aside for protein input, 50 μL for RNA input and 600-800 μL were used for immunoprecipitation. HA-conjugated magnetic beads (Pierce Anti-HA Magnetic Beads, 88837, Thermo Fisher Scientific) were washed twice in PBS and twice in lysis buffer prior to use. A proportion of 150 μL bead-slurry per 1 mL clarified lysate was used. The clarified lysates were supplemented with 0.5 U/μL of Ribolock (Thermo Fisher Scientific) and incubated with the HA-beads for 2 hours on a wheel at 4ºC. The beads were washed thrice with one volume of Ribolock-supplemented cold lysis buffer. 1/10 of the lysate-bead-slurry was devoted to protein extraction and 9/10 to RNA extraction. Following the third wash, the RNA was eluted from the beads by Proteinase K digestion. Briefly, the beads slurry or inputs, both in 50 μL of Ribolock-supplemented IP lysis buffer, were incubated in 400 μL of Proteinase K buffer (200 mM Tris-HCl pH 7.5, 100 mM NaCl, 10 mM EDTA, 1% SDS, 40 U/μL Ribolock) with 200 μg/mL Proteinase K (3115887001, Proteinase K, recombinant, PCR grade, Roche) for 30 minutes at 37ºC. Subsequently, the RNA in the supernatant was purified by organic phase extraction using Trizol Reagent (Thermo Fisher Scientific) and chloroform followed by ethanol precipitation. The pellet resulting from precipitation was reconstituted in 40 μL (inputs) or 15 μL (eluates) of TURBO DNase premix (1x TURBO buffer, AM1907, Invitrogen, supplemented with 1 U/μL Ribolock) and treated with 1 μL TURBO DNase for 30 minutes at 37ºC. The enzyme was inactivated following manufacturer’s instructions.
mRNA-purification from 0.75 and 1.7 µg of RNA was applied to input samples using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs). No mRNA purification was performed on the IP samples. NGS libraries for RNA-seq were prepared using the kit NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs) and 8-10 cycles of library amplification.

treatment_protocol: 140 – 120 fully-grown oocytes were microinjected with 46nL of 50 ng/mL in vitro transcribed polyadenylated RNAs per condition.

value: Oocyte

value: HA-CPEB3 microinjected

tag: rip antibody

value: Anti-HA (3F10) High Affinity (ROAHAHA)


title: H3K27ac_ChIP1_Dox_Untreated_rep1 [722]


title: D.magna whole body, BMP-TBNS2-Outfall-0 ng/L pyriproxyfen-Late Summer-Rep4 C5Z_S115

description:
D.magna whole body, BMP-TBNS2-Outfall-0 ng/L pyriproxyfen-Late Summer-Rep4
Organism Source: Carolina Biological Supply, 2014


title: NI Input [1894 2018]

description:
Replicate#00, not-injected input
2030_29688_ATCACG

value: not-injected input


title: 4.IN [397 2019]

description:
Replicate#04, not-injected input
0450_32672_TTAGGC


title: D.magna whole body, BMP-TBNS2-Outfall-0 ng/L pyriproxyfen-Early Summer-Rep4 C4Y_S67

description:
D.magna whole body, BMP-TBNS2-Outfall-0 ng/L pyriproxyfen-Early Summer-Rep4
Organism Source: Carolina Biological Supply, 2014


title: H3K4me1_ChIP1_Dox_Untreated_rep1 [722]


title: CPEB1 Elu [1901 2018]

description:
Replicate#00, HA-CPEB1 microinjected
2030_29688_ACTTGA

value: HA-CPEB1 microinjected


title: 1 [398 2019]

description:
Replicate#01, not-injected
0450_32672_TGACCA

value: not-injected


title: D.magna whole body, BMP-TBNS2-Outfall-0 ng/L pyriproxyfen-Late Summer-Rep3 C4Z_S114

description:
D.magna whole body, BMP-TBNS2-Outfall-0 ng/L pyriproxyfen-Late Summer-Rep3
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, BMP-TBNS2-Outfall-0 ng/L pyriproxyfen-Spring-Rep3 C4X_S13

description:
D.magna whole body, BMP-TBNS2-Outfall-0 ng/L pyriproxyfen-Spring-Rep3
Organism Source: Carolina Biological Supply, 2014


title: 3.3 [404 2019]

description:
Replicate#03, HA-CPEB3 microinjected
0450_32672_TAGCTT


title: 4.3 [409 2019]

description:
Replicate#04, HA-CPEB3 microinjected
0450_32672_GTTTCG


title: D.magna whole body, BMP-TBNS2-Outfall-0 ng/L pyriproxyfen-Early Summer-Rep3 C3Y_S66

description:
D.magna whole body, BMP-TBNS2-Outfall-0 ng/L pyriproxyfen-Early Summer-Rep3
Organism Source: Carolina Biological Supply, 2014


title: 3.4 [405 2019]

description:
Replicate#03, HA-CPEB4 microinjected
0450_32672_GGCTAC

value: HA-CPEB4 microinjected


title: D.magna whole body, BMP-TBNS2-Outfall-0 ng/L pyriproxyfen-Late Summer-Rep2 C3Z_S113

description:
D.magna whole body, BMP-TBNS2-Outfall-0 ng/L pyriproxyfen-Late Summer-Rep2
Organism Source: Carolina Biological Supply, 2014


title: 1.4 [400 2019]

description:
Replicate#01, HA-CPEB4 microinjected
0450_32672_GCCAAT


title: D.magna whole body, BMP-TBNS2-Outfall-0 ng/L pyriproxyfen-Spring-Rep2 C3X_S12

description:
D.magna whole body, BMP-TBNS2-Outfall-0 ng/L pyriproxyfen-Spring-Rep2
Organism Source: Carolina Biological Supply, 2014


title: 4 [406 2019]

description:
Replicate#04, not-injected
0450_32672_CTTGTA


title: D.magna whole body, BMP-TBNS2-Outfall-0 ng/L pyriproxyfen-Early Summer-Rep2 C2Y_S65

description:
D.magna whole body, BMP-TBNS2-Outfall-0 ng/L pyriproxyfen-Early Summer-Rep2
Organism Source: Carolina Biological Supply, 2014


title: 3.2 [403 2019]

description:
Replicate#03, HA-CPEB2 microinjected
0450_32672_GATCAG

value: HA-CPEB2 microinjected


title: 3.IN [396 2019]

description:
Replicate#03, not-injected input
0450_32672_CGATGT


title: D.magna whole body, BMP-TBNS2-Outfall-0 ng/L pyriproxyfen-Late Summer-Rep1 C1Z_S112

description:
D.magna whole body, BMP-TBNS2-Outfall-0 ng/L pyriproxyfen-Late Summer-Rep1
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, BMP-TBNS2-Outfall-0 ng/L pyriproxyfen-Early Summer-Rep1 C1Y_S64

description:
D.magna whole body, BMP-TBNS2-Outfall-0 ng/L pyriproxyfen-Early Summer-Rep1
Organism Source: Carolina Biological Supply, 2014


title: NI Elu [1899 2018]

description:
Replicate#00, not-injected
2030_29688_GCCAAT


title: 4.2 [408 2019]

description:
Replicate#04, HA-CPEB2 microinjected
0450_32672_CCGTCC


title: D.magna whole body, BMP-TBNS2-Outfall-0 ng/L pyriproxyfen-Spring-Rep1 C2X_S11

description:
D.magna whole body, BMP-TBNS2-Outfall-0 ng/L pyriproxyfen-Spring-Rep1
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, BMP-TBNS2-Inflow-0 ng/L pyriproxyfen-Early Summer-Rep5 d7Y_S73

description:
D.magna whole body, BMP-TBNS2-Inflow-0 ng/L pyriproxyfen-Early Summer-Rep5
Organism Source: Carolina Biological Supply, 2014


title: 3 [401 2019]

description:
Replicate#03, not-injected
0450_32672_CAGATC


title: D.magna whole body, BMP-TBNS2-Inflow-0 ng/L pyriproxyfen-Late Summer-Rep5 d6Z_S121

description:
D.magna whole body, BMP-TBNS2-Inflow-0 ng/L pyriproxyfen-Late Summer-Rep5
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, BMP-TBNS2-Inflow-0 ng/L pyriproxyfen-Spring-Rep5 d7X_S20

description:
D.magna whole body, BMP-TBNS2-Inflow-0 ng/L pyriproxyfen-Spring-Rep5
Organism Source: Carolina Biological Supply, 2014


title: 4.4 [410 2019]

description:
Replicate#04, HA-CPEB4 microinjected
0450_32672_ATTCCT


title: 1.IN [395 2019]

description:
Replicate#01, not-injected input
0450_32672_ATCACG


title: 4.1 [407 2019]

description:
Replicate#04, HA-CPEB1 microinjected
0450_32672_AGTCAA


title: D.magna whole body, BMP-TBNS2-Inflow-0 ng/L pyriproxyfen-Early Summer-Rep4 d5Y_S72

description:
D.magna whole body, BMP-TBNS2-Inflow-0 ng/L pyriproxyfen-Early Summer-Rep4
Organism Source: Carolina Biological Supply, 2014


title: 3.1 [402 2019]

description:
Replicate#03, HA-CPEB1 microinjected
0450_32672_ACTTGA


title: D.magna whole body, BMP-TBNS2-Inflow-0 ng/L pyriproxyfen-Spring-Rep4 d5X_S19

description:
D.magna whole body, BMP-TBNS2-Inflow-0 ng/L pyriproxyfen-Spring-Rep4
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, BMP-TBNS2-Inflow-0 ng/L pyriproxyfen-Late Summer-Rep4 d4Z_S120

description:
D.magna whole body, BMP-TBNS2-Inflow-0 ng/L pyriproxyfen-Late Summer-Rep4
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, BMP-TBNS2-Inflow-0 ng/L pyriproxyfen-Early Summer-Rep3 d4Y_S71

description:
D.magna whole body, BMP-TBNS2-Inflow-0 ng/L pyriproxyfen-Early Summer-Rep3
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, BMP-TBNS2-Inflow-0 ng/L pyriproxyfen-Late Summer-Rep3 d3Z_S119

description:
D.magna whole body, BMP-TBNS2-Inflow-0 ng/L pyriproxyfen-Late Summer-Rep3
Organism Source: Carolina Biological Supply, 2014


title: shHOTAIR, Day14, rep3

city: Oxford

first: Katherine

middle: E

last: Pinnick

state: Oxon

address: OCDEM, Churchill Hospital

institute: University of Oxford

data_processing:
gene.counts:  Raw sequencing reads were mapped to the human genome hg19 using STAR version 2.5.1
gene.counts:  GENCODE v19 GTF was applied to guide the spliced alignment. Duplicated alignments were marked with the MarkDuplicates script from the Picard tools v2.1.1 suite
gene.counts:  Gene expression was quantified with featureCounts (Liao et al., 2014) using the GENCODE v19 GTF file.
Isoform.Counts:  Quality of raw data evaluated using FastQC 0.11.8 (Andrews, 2010) and MultiQC v1.7 (Ewels et al., 2016)
Isoform.Counts:  Transcript isoforms were quantified using Salmon v.1.2.1 (-l A --seqBias --gcBias --posBias -p 12), against the Human GENCODE reference transcriptome (GRCh37) indexed with Salmon using default parameters.
Isoform.Counts:  Transcript-level alternative splicing analysis conducted using 3D-RNA-Seq GUI (accessed 21/04/2021; Guo et al., 2021). Event-level alternative splicing analysis carried out using SUPPA2 v2.3 (Trincado et al., 2018; --method empirical -nan 0 --tpm-threshold 0 --lower-bound 0.1 --alpha 0.05)
Assembly: hg19/GRCh37
Supplementary files format and content: tsv file containing gene counts for each sample
Supplementary files format and content: csv file containing gene counts for each sample

source_name: Immortalized gluteal preadipocytes

extract_protocol:
Total RNA was harvested according to the Tri-Reagent protocol (Ambion) followed by DNAase treatment
TruSeq paired-end RNA-seq libraries were prepared according to manufacturers instructions (Illumina)

treatment_protocol: Adipogenic differentiation was induced by treatment of fully confluent cells (designated day 0, D0) with 100 nM human insulin, 10 nM triiodo-L-thyronine and 1 μM dexamethasone. Troglitazone (4 μM) and 3-isobutyl-1-methylxanthine (0.25 mM) were added to the adipogenic medium for the first 4 days only

tag: cell line

value: Immortalized gluteal preadipocytes

value: shRNA HOTAIR

tag: time

value: Adipogenesis Day 14


title: 1.2 [399 2019]

description:
Replicate#01, HA-CPEB2 microinjected
0450_32672_ACAGTG


title: shHOTAIR, Day14, rep2


title: D.magna whole body, BMP-TBNS2-Inflow-0 ng/L pyriproxyfen-Spring-Rep3 d4X_S18

description:
D.magna whole body, BMP-TBNS2-Inflow-0 ng/L pyriproxyfen-Spring-Rep3
Organism Source: Carolina Biological Supply, 2014

value: D.magna whole body


title: shHOTAIR, Day14, rep1


title: shHOTAIR, Day4, rep3

value: Adipogenesis Day 4


title: D.magna whole body, BMP-TBNS2-Inflow-0 ng/L pyriproxyfen-Early Summer-Rep2 d3Y_S70

description:
D.magna whole body, BMP-TBNS2-Inflow-0 ng/L pyriproxyfen-Early Summer-Rep2
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, BMP-TBNS2-Inflow-0 ng/L pyriproxyfen-Spring-Rep2 d2X_S17

description:
D.magna whole body, BMP-TBNS2-Inflow-0 ng/L pyriproxyfen-Spring-Rep2
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, BMP-TBNS2-Inflow-0 ng/L pyriproxyfen-Late Summer-Rep2 d2Z_S118

description:
D.magna whole body, BMP-TBNS2-Inflow-0 ng/L pyriproxyfen-Late Summer-Rep2
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, BMP-TBNS2-Inflow-0 ng/L pyriproxyfen-Late Summer-Rep1 d1Z_S117

description:
D.magna whole body, BMP-TBNS2-Inflow-0 ng/L pyriproxyfen-Late Summer-Rep1
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, BMP-TBNS2-Inflow-0 ng/L pyriproxyfen-Early Summer-Rep1 d2Y_S69

description:
D.magna whole body, BMP-TBNS2-Inflow-0 ng/L pyriproxyfen-Early Summer-Rep1
Organism Source: Carolina Biological Supply, 2014


title: shHOTAIR, Day4, rep2


title: shHOTAIR, Day0, rep2

value: Adipogenesis Day 0


title: D.magna whole body, BMP-TBNS1-Outfall-0 ng/L pyriproxyfen-Late Summer-Rep5 A7Z_S106

description:
D.magna whole body, BMP-TBNS1-Outfall-0 ng/L pyriproxyfen-Late Summer-Rep5
Organism Source: Carolina Biological Supply, 2014


title: shHOTAIR, Day4, rep1


title: shHOTAIR, Day0, rep1


title: D.magna whole body, BMP-TBNS2-Inflow-0 ng/L pyriproxyfen-Spring-Rep1 d1X_S16

description:
D.magna whole body, BMP-TBNS2-Inflow-0 ng/L pyriproxyfen-Spring-Rep1
Organism Source: Carolina Biological Supply, 2014


title: shControl, Day14, rep2

value: shRNA control


title: shControl, Day14, rep1


title: D.magna whole body, BMP-TBNS1-Outfall-0 ng/L pyriproxyfen-Early Summer-Rep5 A6Y_S56

description:
D.magna whole body, BMP-TBNS1-Outfall-0 ng/L pyriproxyfen-Early Summer-Rep5
Organism Source: Carolina Biological Supply, 2014


title: shControl, Day14, rep3


title: D.magna whole body, BMP-TBNS1-Outfall-0 ng/L pyriproxyfen-Early Summer-Rep4 A5Y_S55

description:
D.magna whole body, BMP-TBNS1-Outfall-0 ng/L pyriproxyfen-Early Summer-Rep4
Organism Source: Carolina Biological Supply, 2014


title: shControl, Day4, rep2


title: shControl, Day4, rep3


title: D.magna whole body, BMP-TBNS1-Outfall-0 ng/L pyriproxyfen-Spring-Rep4 A5X_S4

description:
D.magna whole body, BMP-TBNS1-Outfall-0 ng/L pyriproxyfen-Spring-Rep4
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, BMP-TBNS1-Outfall-0 ng/L pyriproxyfen-Late Summer-Rep4 A5Z_S105

description:
D.magna whole body, BMP-TBNS1-Outfall-0 ng/L pyriproxyfen-Late Summer-Rep4
Organism Source: Carolina Biological Supply, 2014


title: shControl, Day4, rep1


title: D.magna whole body, BMP-TBNS1-Outfall-0 ng/L pyriproxyfen-Early Summer-Rep3 A4Y_S54

description:
D.magna whole body, BMP-TBNS1-Outfall-0 ng/L pyriproxyfen-Early Summer-Rep3
Organism Source: Carolina Biological Supply, 2014


title: shControl, Day0, rep3


title: shControl, Day0, rep1


title: shControl, Day0, rep2


title: D.magna whole body, BMP-TBNS1-Outfall-0 ng/L pyriproxyfen-Late Summer-Rep3 A3Z_S104

description:
D.magna whole body, BMP-TBNS1-Outfall-0 ng/L pyriproxyfen-Late Summer-Rep3
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, BMP-TBNS1-Outfall-0 ng/L pyriproxyfen-Spring-Rep3 A3X_S3

description:
D.magna whole body, BMP-TBNS1-Outfall-0 ng/L pyriproxyfen-Spring-Rep3
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, BMP-TBNS1-Outfall-0 ng/L pyriproxyfen-Early Summer-Rep2 A3Y_S53

description:
D.magna whole body, BMP-TBNS1-Outfall-0 ng/L pyriproxyfen-Early Summer-Rep2
Organism Source: Carolina Biological Supply, 2014


title: shHOTAIR, Day0, rep3


title: RC_154_6w_IFX_R_RNA

city: Kiel

first: Neha

last: Mishra

address: Rosalind-Franklin-Str. 12

country: Germany

institute: Institute of Clinical Molecular Biology

data_processing:
Fastq files were mapped and aligned using nf-core ((https://github.com/nf-core/rnaseq)) rnaseq pipeline.
Adapters and low-quality bases from the RNA-seq reads were removed using Trim Galore (version 0.4.4), which is a wrapper tool for Cutadapt and FastQC. Reads that were shorter than 35 bp after trimming were discarded.
The filtered reads were mapped to the human genome (GRCh38, gencode version 25) using STAR aligner (version 2.5.2b).
featureCounts (version 1.5.2) was used to estimate the expression counts of the genes.
Genome_build: (GRCh38, gencode version 25)
Supplementary_files_format_and_content: tab-delimited text files include feature counts

source_name: Peripheral Whole-Blood

extract_protocol:
Patient peripheral blood was collected in 2.5mL tubes PAXgene Blood RNA Tubes, RNA was automated isolated in QIAGEN’s QIAcube using the PAXgene Blood miRNA Kit from QIAGEN PreAnalytiX.
RNA Sequencing libraries were prepared from Paxgene™ Blood RNA Tubes (Qiagen) according to the Illumina TruSeq® messenger RNA (mRNA) sequencing protocol (TruSeq® RNA Seq Library Prep Kit v2)
Paired-end sequencing (2x75bp) was performed on Illumina HiSeq 4000

tag: patient

tag: cohort

value: Replication

value: Infliximab

tag: remission at week 14

value: Remission

tag: time point

tag: diagnosis

value: UC


title: D.magna whole body, BMP-TBNS1-Outfall-0 ng/L pyriproxyfen-Early Summer-Rep1 A2Y_S52

description:
D.magna whole body, BMP-TBNS1-Outfall-0 ng/L pyriproxyfen-Early Summer-Rep1
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, BMP-TBNS1-Outfall-0 ng/L pyriproxyfen-Spring-Rep2 A2X_S2

description:
D.magna whole body, BMP-TBNS1-Outfall-0 ng/L pyriproxyfen-Spring-Rep2
Organism Source: Carolina Biological Supply, 2014


title: RC_016_2w_IFX_NR_RNA

value: Non-remission


title: RC_036_6w_IFX_R_RNA

value: CD


title: RC_154_2w_IFX_R_RNA


title: D.magna whole body, BMP-TBNS1-Outfall-0 ng/L pyriproxyfen-Spring-Rep5 A7X_S5

description:
D.magna whole body, BMP-TBNS1-Outfall-0 ng/L pyriproxyfen-Spring-Rep5
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, BMP-TBNS1-Outfall-0 ng/L pyriproxyfen-Late Summer-Rep1 A1Z_S102

description:
D.magna whole body, BMP-TBNS1-Outfall-0 ng/L pyriproxyfen-Late Summer-Rep1
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, BMP-TBNS1-Outfall-0 ng/L pyriproxyfen-Spring-Rep1 A1X_S1

description:
D.magna whole body, BMP-TBNS1-Outfall-0 ng/L pyriproxyfen-Spring-Rep1
Organism Source: Carolina Biological Supply, 2014


title: RC_031_baseline_ADA_NR_RNA

value: Adalimumab

value: baseline


title: RC_007_baseline_IFX_NR_RNA


title: RC_112_2w_IFX_R_RNA


title: D.magna whole body, BMP-TBNS1-Inflow-0 ng/L pyriproxyfen-Late Summer-Rep5 B7Z_S111

description:
D.magna whole body, BMP-TBNS1-Inflow-0 ng/L pyriproxyfen-Late Summer-Rep5
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, BMP-TBNS1-Inflow-0 ng/L pyriproxyfen-Spring-Rep5 B7X_S10

description:
D.magna whole body, BMP-TBNS1-Inflow-0 ng/L pyriproxyfen-Spring-Rep5
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, BMP-TBNS1-Inflow-0 ng/L pyriproxyfen-Early Summer-Rep5 B7Y_S62

description:
D.magna whole body, BMP-TBNS1-Inflow-0 ng/L pyriproxyfen-Early Summer-Rep5
Organism Source: Carolina Biological Supply, 2014


title: RC_161_2w_IFX_NR_RNA


title: D.magna whole body, BMP-TBNS1-Inflow-0 ng/L pyriproxyfen-Early Summer-Rep4 B6Y_S61

description:
D.magna whole body, BMP-TBNS1-Inflow-0 ng/L pyriproxyfen-Early Summer-Rep4
Organism Source: Carolina Biological Supply, 2014


title: RC_112_baseline_IFX_R_RNA


title: D.magna whole body, BMP-TBNS1-Inflow-0 ng/L pyriproxyfen-Spring-Rep4 B6X_S9

description:
D.magna whole body, BMP-TBNS1-Inflow-0 ng/L pyriproxyfen-Spring-Rep4
Organism Source: Carolina Biological Supply, 2014


title: RC_004_2w_IFX_NR_RNA


title: RC_070_baseline_IFX_R_RNA


title: D.magna whole body, BMP-TBNS1-Inflow-0 ng/L pyriproxyfen-Early Summer-Rep3 B5Y_S60

description:
D.magna whole body, BMP-TBNS1-Inflow-0 ng/L pyriproxyfen-Early Summer-Rep3
Organism Source: Carolina Biological Supply, 2014


title: RC_036_baseline_IFX_R_RNA


title: D.magna whole body, BMP-TBNS1-Inflow-0 ng/L pyriproxyfen-Late Summer-Rep4 B4Z_S110

description:
D.magna whole body, BMP-TBNS1-Inflow-0 ng/L pyriproxyfen-Late Summer-Rep4
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, BMP-TBNS1-Outfall-0 ng/L pyriproxyfen-Late Summer-Rep2 A2Z_S103

description:
D.magna whole body, BMP-TBNS1-Outfall-0 ng/L pyriproxyfen-Late Summer-Rep2
Organism Source: Carolina Biological Supply, 2014


title: RC_140_baseline_IFX_R_RNA


title: RC_063_2w_IFX_NR_RNA


title: RC_012_baseline_IFX_R_RNA


title: D.magna whole body, BMP-TBNS1-Inflow-0 ng/L pyriproxyfen-Late Summer-Rep3 B3Z_S109

description:
D.magna whole body, BMP-TBNS1-Inflow-0 ng/L pyriproxyfen-Late Summer-Rep3
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, BMP-TBNS1-Inflow-0 ng/L pyriproxyfen-Early Summer-Rep2 B4Y_S59

description:
D.magna whole body, BMP-TBNS1-Inflow-0 ng/L pyriproxyfen-Early Summer-Rep2
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, BMP-TBNS1-Inflow-0 ng/L pyriproxyfen-Spring-Rep3 B4X_S8

description:
D.magna whole body, BMP-TBNS1-Inflow-0 ng/L pyriproxyfen-Spring-Rep3
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, BMP-TBNS1-Inflow-0 ng/L pyriproxyfen-Late Summer-Rep1 B1Z_S107

description:
D.magna whole body, BMP-TBNS1-Inflow-0 ng/L pyriproxyfen-Late Summer-Rep1
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, BMP-TBNS1-Inflow-0 ng/L pyriproxyfen-Spring-Rep2 B2X_S7

description:
D.magna whole body, BMP-TBNS1-Inflow-0 ng/L pyriproxyfen-Spring-Rep2
Organism Source: Carolina Biological Supply, 2014


title: RC_042_6w_IFX_NR_RNA


title: RC_004_baseline_IFX_NR_RNA


title: RC_016_baseline_IFX_NR_RNA


title: D.magna whole body, BMP-TBNS1-Inflow-0 ng/L pyriproxyfen-Early Summer-Rep1 B3Y_S58

description:
D.magna whole body, BMP-TBNS1-Inflow-0 ng/L pyriproxyfen-Early Summer-Rep1
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, BMP-TBNS1-Inflow-0 ng/L pyriproxyfen-Late Summer-Rep2 B2Z_S108

description:
D.magna whole body, BMP-TBNS1-Inflow-0 ng/L pyriproxyfen-Late Summer-Rep2
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, BMP-TBNS1-Inflow-0 ng/L pyriproxyfen-Spring-Rep1 B1X_S6

description:
D.magna whole body, BMP-TBNS1-Inflow-0 ng/L pyriproxyfen-Spring-Rep1
Organism Source: Carolina Biological Supply, 2014


title: RC_161_baseline_IFX_NR_RNA


title: D.magna whole body, BMP-37ST-Outfall-0 ng/L pyriproxyfen-Early Summer-Rep5 E7Y_S79

description:
D.magna whole body, BMP-37ST-Outfall-0 ng/L pyriproxyfen-Early Summer-Rep5
Organism Source: Carolina Biological Supply, 2014


title: RC_142_baseline_IFX_R_RNA


title: RC_162_2w_IFX_NR_RNA


title: D.magna whole body, BMP-37ST-Outfall-0 ng/L pyriproxyfen-Late Summer-Rep5 E5Z_S126

description:
D.magna whole body, BMP-37ST-Outfall-0 ng/L pyriproxyfen-Late Summer-Rep5
Organism Source: Carolina Biological Supply, 2014


title: RC_111_6w_IFX_NR_RNA


title: RC_022_6w_IFX_R_RNA


title: RC_162_6w_IFX_NR_RNA


title: RC_162_baseline_IFX_NR_RNA


title: RC_144_2w_IFX_R_RNA


title: D.magna whole body, BMP-37ST-Outfall-0 ng/L pyriproxyfen-Spring-Rep4 E4X_S24

description:
D.magna whole body, BMP-37ST-Outfall-0 ng/L pyriproxyfen-Spring-Rep4
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, BMP-37ST-Outfall-0 ng/L pyriproxyfen-Early Summer-Rep3 E4Y_S77

description:
D.magna whole body, BMP-37ST-Outfall-0 ng/L pyriproxyfen-Early Summer-Rep3
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, BMP-37ST-Outfall-0 ng/L pyriproxyfen-Late Summer-Rep4 E4Z_S125

description:
D.magna whole body, BMP-37ST-Outfall-0 ng/L pyriproxyfen-Late Summer-Rep4
Organism Source: Carolina Biological Supply, 2014


title: RC_111_2w_IFX_NR_RNA


title: RC_161_6w_IFX_NR_RNA


title: D.magna whole body, BMP-37ST-Outfall-0 ng/L pyriproxyfen-Early Summer-Rep2 E3Y_S76

description:
D.magna whole body, BMP-37ST-Outfall-0 ng/L pyriproxyfen-Early Summer-Rep2
Organism Source: Carolina Biological Supply, 2014


title: RC_012_2w_IFX_R_RNA


title: RC_016_6w_IFX_NR_RNA


title: D.magna whole body, BMP-37ST-Outfall-0 ng/L pyriproxyfen-Late Summer-Rep3 E3Z_S124

description:
D.magna whole body, BMP-37ST-Outfall-0 ng/L pyriproxyfen-Late Summer-Rep3
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, BMP-37ST-Outfall-0 ng/L pyriproxyfen-Spring-Rep3 E3X_S23

description:
D.magna whole body, BMP-37ST-Outfall-0 ng/L pyriproxyfen-Spring-Rep3
Organism Source: Carolina Biological Supply, 2014


title: RC_031_6w_ADA_NR_RNA


title: D.magna whole body, BMP-37ST-Outfall-0 ng/L pyriproxyfen-Spring-Rep5 E5X_S25

description:
D.magna whole body, BMP-37ST-Outfall-0 ng/L pyriproxyfen-Spring-Rep5
Organism Source: Carolina Biological Supply, 2014


title: RC_140_2w_IFX_R_RNA


title: D.magna whole body, BMP-37ST-Outfall-0 ng/L pyriproxyfen-Late Summer-Rep2 E2Z_S123

description:
D.magna whole body, BMP-37ST-Outfall-0 ng/L pyriproxyfen-Late Summer-Rep2
Organism Source: Carolina Biological Supply, 2014


title: RC_063_6w_IFX_NR_RNA


title: D.magna whole body, BMP-37ST-Outfall-0 ng/L pyriproxyfen-Spring-Rep2 E2X_S22

description:
D.magna whole body, BMP-37ST-Outfall-0 ng/L pyriproxyfen-Spring-Rep2
Organism Source: Carolina Biological Supply, 2014


title: MPNST_SEL_R_3

city: Shanghai

first: Zhichao

last: Wang

address: 639 Zhizaoju Road, Shanghai 200011, P.R. China

department: Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine

institute: Department of Plastic and Reconstructive Surgery

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters.
Reads Oer Kilobase of exon per Megabase of libarary size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimitied text files include RPKM values for each Sample.

source_name: MPNST cell lines

growth_protocol: All cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM, Gibco), supplemented with 10% fetal bovine serum (FBS, Gibco), glutamine and 1 x penicillin/streptomycin (Gibco) at 37℃ in a ddH2O humidified atmosphere with 5% CO2.

extract_protocol:
Cells were flash frozen on dry ice, 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.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: To generate MEKi-resistant cell lines, the parental NF1-MPNST cell line S462 was induced by conventional continuous exposure to trametinib, TAK-733 and selumetinib in a dose-stepwise increment for five months (with a change in medium three times per week).

value: Malignant peripheral nerve sheath tumors (MPNSTs)

value: selumetinib resistant


title: RC_060_2w_IFX_NR_RNA


title: MPNST_TAK_R_3

value: TAK-733 resistant


title: D.magna whole body, BMP-37ST-Outfall-0 ng/L pyriproxyfen-Early Summer-Rep4 E5Y_S78

description:
D.magna whole body, BMP-37ST-Outfall-0 ng/L pyriproxyfen-Early Summer-Rep4
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, BMP-37ST-Outfall-0 ng/L pyriproxyfen-Early Summer-Rep1 E1Y_S75

description:
D.magna whole body, BMP-37ST-Outfall-0 ng/L pyriproxyfen-Early Summer-Rep1
Organism Source: Carolina Biological Supply, 2014


title: MPNST_TAK_R_2


title: D.magna whole body, BMP-37ST-Outfall-0 ng/L pyriproxyfen-Late Summer-Rep1 E1Z_S122

description:
D.magna whole body, BMP-37ST-Outfall-0 ng/L pyriproxyfen-Late Summer-Rep1
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, BMP-37ST-Inflow-0 ng/L pyriproxyfen-Late Summer-Rep6 F7Y_S85

description:
D.magna whole body, BMP-37ST-Inflow-0 ng/L pyriproxyfen-Late Summer-Rep6
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, BMP-37ST-Outfall-0 ng/L pyriproxyfen-Spring-Rep1 E1X_S21

description:
D.magna whole body, BMP-37ST-Outfall-0 ng/L pyriproxyfen-Spring-Rep1
Organism Source: Carolina Biological Supply, 2014


title: RC_054_baseline_IFX_NR_RNA


title: RC_010_2w_IFX_NR_RNA


title: MPNST_TAK_R_1


title: MPNST_TRA_R_2

value: trametinib resistant


title: RC_112_6w_IFX_R_RNA


title: MPNST_TRA_R_1


title: D.magna whole body, BMP-37ST-Inflow-0 ng/L pyriproxyfen-Early Summer-Rep4 F6Y_S84

description:
D.magna whole body, BMP-37ST-Inflow-0 ng/L pyriproxyfen-Early Summer-Rep4
Organism Source: Carolina Biological Supply, 2014


title: MPNST_TRA_R_3


title: RC_060_6w_IFX_NR_RNA


title: D.magna whole body, BMP-37ST-Inflow-0 ng/L pyriproxyfen-Late Summer-Rep5 F5Z_S131

description:
D.magna whole body, BMP-37ST-Inflow-0 ng/L pyriproxyfen-Late Summer-Rep5
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, BMP-37ST-Inflow-0 ng/L pyriproxyfen-Spring-Rep5 F6X_S30

description:
D.magna whole body, BMP-37ST-Inflow-0 ng/L pyriproxyfen-Spring-Rep5
Organism Source: Carolina Biological Supply, 2014


title: MPNST_SEL_R_2


title: MPNST_SEL_R_1


title: MPNST_S462_P_2

value: control 2


title: RC_142_2w_IFX_R_RNA


title: D.magna whole body, BMP-37ST-Inflow-0 ng/L pyriproxyfen-Early Summer-Rep3 F5Y_S83

description:
D.magna whole body, BMP-37ST-Inflow-0 ng/L pyriproxyfen-Early Summer-Rep3
Organism Source: Carolina Biological Supply, 2014

value: D.magna whole body


title: RC_042_2w_IFX_NR_RNA


title: MPNST_S462_P_1

value: control 1