title: WT rep1_mRNAseq

description:
MRNA_CONT_01
mRNA_normalized_counts.txt.gz


title: B.fo.Sp#1.12

status: Public on Nov 16 2018

type: SRA

city: Boston

first: Liang

last: Yang

state: MA

address: 77 Avenue Louis Pasteur

department: Pathology

country: USA

institute: Harvard Medical School

description:
Follicular B Cell
Gene_count_table.csv

library_source: transcriptomic

data_processing:
Reads were mapped to the mouse reference genome (mm10) with STAR 2.5.4a
Non-uniquely mapped reads were discarded.
The uniquely mapped reads were assigned to genes using featureCounts with GENCODE annotation (vM16)
Genome_build: mm10
Supplementary_files_format_and_content: raw read counts

molecule: total RNA

organism: Mus musculus

source_name: Spleen

growth_protocol: 5 week old C57BL/6J mice from the Jackson Laboratory (Bar Harbor, ME) housed in facility at least one week before harvesting cells

extract_protocol:
Extractions follow ImmGen standard operating protocol (available on https://www.immgen.org/). Briefly, organs are harvested aorund 9am on day of sort, perterbed as little as possible during preparation, and 1000 cells are double sorted into TCL buffer (Qiagen, Hilden, Germany) containing 1% BME.
Libraries are constructed according to the standard protocol for Smart-seq2 (Picelli et al, 2013) at the Broad Techology Labs in Cambridge, MA

tag: strain

tag: age

value: 6 weeks old

tag: tissue

value: Spleen

tag: sorting markers

tag: cell type

value: B Cell


title: kidney sample 19

city: Seattle

first: Chengxiang

last: Qiu

state: WA

address: William H. Foege Hall, 3720 15th Ave NE

department: Genome Sciences

institute: University of Washington

data_processing:
Illumina's CASAVA 1.8.2 was used for basecalling.
After first assessing sequence quality using FastQC and then trimming the adaptor and lower-quality bases using Trim-galore, RNA-seq reads were aligned to the human genome (hg19/GRCh37) using STAR (v2.4.1d) based on GENCODE v19 annotations.
Genome_build: hg19/GRCh37
Supplementary_files_format_and_content: tab-delimited text files include log2 (RPKM) for each Sample

organism: Homo sapiens

source_name: Kidney

extract_protocol:
Collected tissue was immersed in RNAlater solution at 4°C for several hours prior to being stored at -80°C in RNAlater. Tissue was thawed on ice, placed in RNAlater, and manually microdissected for glomerulus and tubule compartments.
RNA quality was assessed with the Agilent Bioanalyzer 2100. Only samples with RIN scores above 7 and a minimum total RNA of 100 ng were used for cDNA production. Non-strand specific, polyA+ selected RNA-seq libraries were generated using the Illumina TruSeq protocol. Libraries were sequenced to a median depth of 35 million 100-bp single end reads.

value: Kidney (glomerular and tubular portions)

tag: disease state

value: Healthy


title: P10 Pkd1V/V cystic kidney-3

type: RNA

city: Baltimore

first: Feng

last: Qian

address: 655 W. Baltimore Street

department: School of medicine, Department of medicine

institute: University of Maryland

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

label: biotin

source_name: kidney

label_protocol: standard

extract_protocol: Total RNAs were extracted from the kidneys using the RNeasy mini kit (Qiagen) and the quality of total RNA samples were verified by a 260/280 ratio in NanoDrop and agarose gel electrophoresis.

value: Kidney

tag: genotype

value: Pkd1V/V cystic


title: E and P replicate 5

city: St. Louis

first: Maxim

last: Artyomov

state: Missouri

address: 425 S Euclid Ave

department: Pathology & Immunology

institute: WASHINGTON UNIVERSITY IN ST LOUIS

data_processing:
quality control: RSeQC version 2.3.
alignment: STAR version 2.0.4b.
quantification: Subread: featureCount version 1.4.5.
Genome_build: GRCm38 (Ensembl release 76)
Supplementary_files_format_and_content: Gene counts tables

source_name: estrogen and progesterone

extract_protocol:
Vaginas were extracted and placed in RNAlater. Then RNA was extracted using a Zymo RNA extraction kit
mRNA poly-A purified library prep

value: vagina


title: E and P replicate 4


title: klp10a-KD rep3_smRNAseq

first: Charlotte

middle: Park

last: Choi

state: MD

address: 3400 North Charles Street

department: Department of Biology

institute: Johns Hopkins University

description:
antisense_piRNA_normalized_counts.txt
sense_piRNA_normalized_counts.txt

data_processing:
Basecalling was performed using Illumina's default Real Time Analysis (RTA) basecalling and quality scoring software application.
Conversion from qseq files to fastq files and demultiplexing was performed using custom Awk and Python scripts.
Small RNAs were clipped from 3’ adapter sequences using Trimmomatic 0.27  (Bolger et al., 2014).
Reads were aligned to the D. melanogaster transcriptome (Dm3) with at most 1 mismatch allowed using Bowtie2 v2.2.3. Abundance estimation was done at annotated genes, piRNA clusters, and TEs using the eXpress pipeline within the piPipes suite (Han et al., 2015; Roberts and Pachter, 2013).
For piRNA analysis, we selected reads that were 23-29 nucleotides in length to ensure other endo-siRNA species did not influence downstream analysis. miRNA hairpin reads were used to normalize between libraries.
Genome_build: dm3
Supplementary_files_format_and_content: Processed data files contains a matrix of transposons (rows) and normalized piRNA counts in each library (columns).

organism: Drosophila melanogaster

source_name: Testis

extract_protocol: 300 pairs of testes  were removed and Total RNAs were extracted by the Trizol method. For small RNA sequencing, 2.5 µg of total RNAs were treated with DNase I (Amplification Grade, ThermoFisher) and recovered by RNA Clean & Concentrator-5 columns (Zymo). Libraries were generated using reagents from the TruSeq Small RNA Library Prep Kit (Illumina), while following a previously published protocol from (Wickersheim & Blumenstiel 2013) that uses a terminator oligo to deplete Drosophila 2S rRNA from the final sequencing libraries.

value: testis

value: 0-2 days


title: B.fo.Sp#1.11

description:
Follicular B Cell
Gene_count_table.csv


title: E and P replicate 3


title: E and P replicate 2


title: klp10a-KD rep2_smRNAseq


title: kidney sample 18


title: E and P replicate 1


title: klp10a-KD rep1_smRNAseq


title: kidney sample 16


title: B.fo.Sp#1.1

description:
Follicular B Cell
Gene_count_table.csv


title: 7565_7355

city: Los Angeles

first: Tiffany

last: Armenta

state: CA

address: 610 Charles E. Young Dr. East

department: Ecology & Evolutionary Biology

institute: UCLA

data_processing:
Filtering and quality:  Raw sequences were processed using Trim Galore! 0.3.1 to remove Illumina adapters and filter out sequences that did not meet the quality thresholds (q > 20, length > 20 bp).
Alignment : Alignment of reads was performed on TOPHAT2 2.1.0  using the thirteen-lined ground squirrel (Ictidomys tridecemlineatus) as a reference genome (Ensembl release 84; ftp://ftp.ensembl.org/pub/release-84/fasta/ictidomys_tridecemlineatus/dna/Ictidomys_tridecemlineatus.spetri2.dna.toplevel.fa.gz) . To maximize the number of unique reads mapped to the reference genome, we used the following parameters: read mismatches 8, bp gap length 10, read-edit-dist 20.
Counts: Aligned reads were converted to raw counts using HTSEQ (Anders  et al., 2014) with the “union” mode, resulting in alignment to 22,389 genes.
Normalization: After removal of nine globin-related genes (ENSSTOG00000006499, ENSSTOG00000020876, ENSSTOG00000010650, ENSSTOG00000024317, ENSSTOG00000025073, ENSSTOG00000020904, ENSSTOG00000022777, ENSSTOG00000010645) with high expression levels prior to normalization, values for the remaining 22,389 genes were normalized using the trimmed mean of M-values (TMM) method and adjusted for gene length and GC content using the package VOOM in R (Law et al. 2014).
Differential expression: We performed principal components analysis to identify and remove technical factors from the expression data (sequencing platform, sequencing lane, extraction date, number of uniquely mapped reads, RIN score, neutrophil count). Linear mixed models were used to identify differentially expressed genes in dispersing marmots using the limma package in R (Ritchie et al., 2015). We adjusted our significance values to account for multiple hypothesis testing using the false discovery rate (FDR) method as implemented in the qvalue package in R (Storey  et al., 2015) and selected genes falling below q < 0.1
Genome_build: Ictidomys tridecemlineatus (Ensembl release 84), GenBank Assembly ID GCA_000236235.1
Supplementary_files_format_and_content: Comma separated file (csv) including the regressed normalized counts on 11,381 genes
Supplementary_files_format_and_content: regressed_normalized_counts.txt: VOOM count output after technical variation was regressed out
Supplementary_files_format_and_content: normalized_counts.txt: HTSEQ count output normalized using VOOM
Supplementary_files_format_and_content: raw_counts_genelength_gccontent.txt: raw expression counts quantified using HTSEQ

organism: Marmota flaviventris

source_name: Blood sample

extract_protocol:
Total RNA was extracted from 1.0 mL whole blood preserved in 2.5 mL PAXGene blood RNA solution using the PAXGene Blood RNA extraction kit, followed by globin removal using the Ambion GLOBINClear Mouse kit (Life Technologies, Inc). RNA was quantified on the Agilent Bioanalyzer (Agilent Technologies, USA).
cDNA libraries were created using a TruSeq Library Prep Kit v2 (Illumina, Madison, WI) and quantified with the KAPA SYBR® Fast qPCR library quantification kit (Kapa Biosystems Inc., Wilmington, MA).  Individual sample libraries were pooled in equimolar ratios with 8 to 10 samples per pool. Each pool was sequenced on a single lane of an Illumina HiSeq 2000 or HiSeq 4000 sequencing platform.

value: Blood

tag: dispersal (0=resident;1=disperser)


title: 7623_7612


title: 7652_7619


title: 7810_7238


title: kidney sample 17


title: kidney sample 15


title: Estrogen replicate 4

source_name: estrogen


title: WT rep2_smRNAseq

value: wild type


title: 7560_7868


title: Estrogen replicate 5


title: WT rep3_smRNAseq


title: Estrogen replicate 3


title: WT rep1_smRNAseq


title: kidney sample 14


title: kidney sample 13


title: Estrogen replicate 2


title: 7405_7444


title: kidney sample 12


title: 7376_7578


title: Estrogen replicate 1


title: 7973_7978


title: kidney sample 11


title: Progesterone replicate 5

source_name: progesterone


title: kidney sample 9


title: kidney sample 10


title: Progesterone replicate 3


title: Progesterone replicate 4


title: 7310_7303


title: Progesterone replicate 2


title: 7289_6695


title: 7365_7368


title: 7292_7293


title: 7442_7655


title: 7284_7109


title: Progesterone replicate 1


title: kidney sample 6


title: kidney sample 5


title: kidney sample 7


title: Vehicle replicate 4

source_name: vehicle


title: Vehicle replicate 5


title: 7205_7492


title: Vehicle replicate 3


title: kidney sample 3


title: 7190_7286


title: Vehicle replicate 2


title: kidney sample 4


title: kidney sample 2


title: Vehicle replicate 1


title: 7113_6680


title: 6697_7124


title: kidney sample 8


title: kidney sample 1


title: 6647_6634


title: 6643_6605


title: 7227_7239


title: day3-PC-cell-RNA.rep3

city: Beijing

first: Zhuqiang

last: Zhang

address: 15 Datun Road, Chaoyang District.

country: China

institute: Institute of Biophysics, CAS

data_processing:
Basecalls performed by Annoroad Co. Ltd. (naïve B and Day2 B) / BerryGenomics Co. Ltd. (Day3 B and day3 PCs)
RNA-Seq data were mapped by STAR aligner v2.5.2b and quantitified by Cufflinks and Cuffdiff.
Genome_build: GENCODE M12 (mm10)
Supplementary_files_format_and_content: The transcription levels (RPKM) were quantified with Cufflinks (v2.0.2) software.

molecule: polyA RNA

source_name: antigen stimulated day3 PCs

extract_protocol:
Total RNA from at least 50,000 isolated mouse B cells was extracted by Trizol (Life Technology) and precipitated by RNase-free glycogen(Life technology). Immediately, we isolated mRNA from total RNA with NEBNext® Poly(A) mRNA Magnetic isolation Module(E7490S).
high throughput sequencing library was constructed with NEBNext® Ultra™ II RNA Library Prep Kit for Illumina®(E7770S).

tag: strain background

value: primary lymphocytes

tag: stimulation

value: antigen stimulated day3 PCs

tag: genotype/variation

value: spleen

tag: developmental stage

value: 8 weeks


title: day3-PC-cell-RNA.rep2


title: day3-PC-cell-RNA.rep1


title: ZS.3_4505

city: HOUSTON

first: Jidong

last: Liu

state: TX

address: One Baylor Plaza

institute: Baylor College of Medicine

data_processing:
raw sequence reads from each biological replicate of total RNA were first aligned to the UCSC mm10 genome with Tophat v2.1.0 using default parameters.
HTSeq was used to obtain read counts from the aligned reads.
DESeq2 (version 1.8.2) was used to normalized the read counts and perform differential gene analysis.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table include p value and fold change between the groups

source_name: Gastrocnemius Muscle

growth_protocol: C57BL/6 male mice were purchased from the Jackson Laboratory and were raised under specific-pathogen free conditions, with 22-25 oC environmental temperature and 40-70% humidity.

extract_protocol:
Gastrocnemius muscle were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Total RNA was extracted from the mouse gastrocnemius muscle samples using the RNA extraction kit (RNeasy Mini Kit, Qiagen) and 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Sample 4-6: 2.5 ppm iAs treatment in the drinking water was started from around 8 weeks old. Sodium (meta)arsenite (Sigma-Aldrich, Germany) was dissolved in deionized water as storage solution and further diluted to working solution Sodium arsenite supplemented drinking water were freshly prepared and were changed weekly.

tag: gender

value: Male

value: Gastrocnemius Muscle

tag: treatment

value: normal drinking water


title: ZS.6_4080

value: 2.5 ppm iAs in drinking water for 24 weeks


title: ZS.5_4079


title: ZS.2_4482


title: day3-B-cell-RNA.rep3

source_name: antigen stimulated day3 B

value: antigen stimulated day3 B cells


title: day3-B-cell-RNA.rep2


title: 7991_7974


title: day3-B-cell-RNA.rep1


title: 7996_7004


title: Hungry rep7

city: Gainesville

first: Sean

middle: Michael

last: Crosson

state: FL

department: Opthalmology

institute: University of Florida

data_processing:
Library was sequenced on an Illumina HiSeq 2000
Sequenced reads were demultiplexed, trimmed for adaptor sequences using trimmomatic, then analyzed for quality using FastQC.
Trimmed reads were aligned to the GRCm38.p4 mouse reference genome using Tophat running the bowtie2 alignment algorithm.
Transcript assembly was completed using Cufflinks
A merged GTF file was created using Cuffmerge
Differential expression analysis was performed using Cuffdiff
Genome_build: GRCm38.p4
Supplementary_files_format_and_content: merged.gtf file includes a tab-delimited file of FPKM values as well as fold change FPKM values between samples. The additional files are tab-delimited text files which contain standard output information from cuffdiff which is used in further analysis with the R package cummeRbund. For simple FPKM abundance counts, the file genes.fpkm_tracking contains this info for each sample.
Supplementary_files_format_and_content: merged.gtf: merged isoform, gene, tss, and cds abundance/tracking info for all samples
Supplementary_files_format_and_content: gene_exp.diff: Gene abundance measurements
Supplementary_files_format_and_content: genes.count_tracking: Gene abundance measurements
Supplementary_files_format_and_content: genes.fpkm_tracking: Gene abundance measurements
Supplementary_files_format_and_content: genes.read_group_tracking: Gene abundance measurements
Supplementary_files_format_and_content: isoform_exp.diff: Isoform abundance measurements
Supplementary_files_format_and_content: isoforms.count_tracking: Isoform abundance measurements
Supplementary_files_format_and_content: isoforms.fpkm_tracking: Isoform abundance measurements
Supplementary_files_format_and_content: isoforms.read_group_tracking: Isoform abundance measurements
Supplementary_files_format_and_content: splicing.diff: splicing abundance
Supplementary_files_format_and_content: tss_group_exp.diff: transcription start site abundance and tracking
Supplementary_files_format_and_content: tss_groups.count_tracking: transcription start site abundance and tracking
Supplementary_files_format_and_content: tss_groups.fpkm_tracking: transcription start site abundance and tracking
Supplementary_files_format_and_content: tss_groups.read_group_tracking: transcription start site abundance and tracking
Supplementary_files_format_and_content: var_model.info: variance model

source_name: Circumvallate Taste Bud

extract_protocol:
Tongues were removed and circumvallate papillae were dissected in Tyrode’s buffer. Total RNA was extracted using the Absolutely RNA Nanoprep kit.
cDNA library was generated using oligo(dT) primers and SuperScript III Reverse Transcriptase. The library was prepared for Illumina sequencing using the RNA-seq Library Preparation Kit.

value: Circumvallate Taste Bud

value: Adult 20-24 weeks

tag: group

value: Hungry


title: 7964_7955


title: 7976_7089


title: 7956_7953


title: 21_22_25_15%

city: HaiKou

last: Li

state: HaiNan

address: No. 99, longkun south road

department: Hainan normal university

institute: College of Life Science

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then use Trinity(version:trinityrnaseq_r20140413) software for de novo assembly.
The clean reads obtained by sequencing are mapped to the assembled transcriptome by using the software Bowtie.
RSEM uses bowtie's alignment results to perform expression statistics. Get the number of read counts that per sample compared to each gene, and then FPKM conversion is performed to obtain the gene expression level.
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

organism: Trachemys scripta elegans

source_name: liver

growth_protocol: nine healthy T. s. elegans (BW: 424-478g, 2 years old) were divided into 3 groups in pools (190 cm × 65 cm × 32 cm) of differing salinity: one in freshwater serving as the control (0 practical salinity units, psu), and the other two challenged with 5 ‰ (5 psu) or 15 ‰ (15 psu) saltwater. Turtles were fed a commercial diet each Monday and Thursday and 24 h after feeding, unused feed was siphoned out followed by replacement of one-third of the water in each tank volume. Water salinity was measured every day and then adjusted to the proper salinity as needed.

extract_protocol:
Extraction of total RNA from liver samples used TRIzol® Reagent, following manufacturer’s instructions. Total RNA purity and concentration were determined using a NanoDrop 2000.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: liver

value: two years

tag: practical salinity units


title: 7536_7534


title: Hungry rep5


title: ZS.4_4078


title: Hungry rep4


title: 7326_6571


title: Hungry rep3


title: 7198_6820


title: Y5-2

city: Chengdu

first: Xu

last: Zhongxian

address: NO. 211, Huiming Road, Wenjiang District

institute: Sichuan Agricultural University

description: 21 brain_mRNA_log2_fpkm+1_0.1.txt/21 brain_lncRNA_log2_fpkm+1.txt

data_processing:
The quality control of raw data were completed by removing low-quality reads, adaptor sequences, empty reads, reads with N sequences over 10% and rRNA reads.
Processed reads from each sample were mapped to the reference genome of chicken using Hisat, The mapped reads were assembled with Stringtie v1.3.3; and then the assembled transcripts were merged into consensus transcripts using custom Python scripts,the known transcripts were removed by blastx and HMMER
The Coding Potential Calculator (CPC) was applied to estimate the coding ability of the remaining transcripts, and transcripts with CPC score > 0 were filtered. Subsequently, transcripts with FPKM > 0 at least in one biological replicate were identified as lncRNAs. LncRNAs were initially classified as 2 major categories according to the lncRNA location with respect to mRNA (Protein Coding Genes) by FEELnc
The expression levels of the transcripts were expressed as FPKM (fragments per kilobase of transcript per million mapped reads) values of mRNA and lncRNA using the Cufflinks v2.2.1 and Stringtie v1.3.3, noting that a value of 1 was added to the FPKM value of each gene before log2 transformation to avoid infinite values. FPKM > 0.1 was used to filter the expressed mRNA. Pearson correlations were estimated across 8 developmental stages, hierarchical clustering was performed using MultiExperimentViewer (MeV version 4.9.0)
Differentially expressed mRNAs and lncRNAs were calculated by DESeq2 based on the reads count that produced from FPKM calculated by Stringtie v1.3.3. We used the analysis of variance (ANOVA) to do pair-wise comparisons between 2 adjacent time points. Genes and transcripts with the FC ≥ 2 or ≤ 0.5 plus the P-value ≤ 0.05 were identified to age-dependent genes.
We constructed a co-expression network using the Weighted Gene Co-expression Network Analysis (WGCNA) in the R package
Genome_build: Gallus_gallus-5.0
Supplementary_files_format_and_content: tab-delimited text files include log2 (FPKM+1) values for each Sample

organism: Gallus gallus

source_name: Brain

growth_protocol: Fertile eggs were incubated at 37.8 ℃ with 70-80% humidity, a 24-h lighting program and intermittent rotations were employed. Young chickens aged from 1 to 300 days after hatching were raised in Ya’an poultry farm under the same environment which belongs to Sichuan Agriclutural University. Meanwhile, hens at the age of 1, 3, 5 years old were collected from Lhasa, Tibet.

extract_protocol:
Brains were collected and snap-frozen in liquid nitrogen immediately, and TRIzol Regent was used to isolate total RNA.
Sequencing libraries were constructed using Illumina HiSeq X Ten platform with paired-end sequencing length of 150 bp (PE150).
rRNA deleted RNA-Seq

treatment_protocol: Sex determination of embryos were fulfilled by PCR according to amplify CDH1-Z/W sequence.

value: Brain

value: 5 years old

value: Adult and aged stage


title: Y5-1


title: 7140_7136

value: Blood


title: 7960_7982


title: Hungry rep1

value: wild type


title: 7131_7126


title: Hungry rep2


title: Y3-2

value: 3 years old


title: Y3-1


title: Satiated rep6

value: Satiated


title: Satiated rep7


title: ZS.1_4380

value: Male


title: Y1-3

value: 1 year old


title: Hungry rep6


title: 7097_7064


title: 7081_7095


title: Satiated rep5


title: 11_13_16_5%


title: 7069_7999


title: Y1-2


title: 01_03_06_control group


title: Y1-1


title: Satiated rep4


title: 7027_6570


title: D300-3

value: 300 days old

value: Rapid growth stage


title: Satiated rep3


title: D300-2


title: 6803_6884


title: 6687_6677


title: D300-1


title: D100-3

value: 100 days old


title: 6560_7061


title: Satiated rep1

value: Circumvallate Taste Bud


title: Ad lib rep7

value: Adult 20-24 weeks

value: Ad lib


title: Satiated rep2


title: 6532_6580


title: 6127_7339


title: D100-1


title: D100-2


title: Ad lib rep6


title: Ad lib rep5


title: 6089_7015


title: E20-2

value: Embryonic day 20

value: Embryonic stage


title: Ad lib rep4


title: 2607_7075


title: Cells 6 hours pgg- biological rep2

city: Kaohsiung City

first: Yi-Ming

middle: Arthur

last: Chen

state: Taiwan

address: No. 100, Shih-Chuan Ist Rd

country: Taiwan

institute: Kaohsiung Medical University

description: Gene expression data from Huh7 cells treated with PGG after 6 hour of treatment

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on Human U133 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the standard Affymetrix protocol by GeneChip® Scanner 3000 7G

data_processing: The data was pre-processed using the rma method from the Affymetrix Expression Console software.

source_name: Human liver cancer cell lines Huh7

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, Affymetrix).

growth_protocol: Huh7 Human liver cancer were cultured in DMEM in a humidified incubator with 5% CO2 at 37°C.

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

treatment_protocol: Cells were treated with PGG (0.1 mg/ml)  dissolved in PBS for 0, 6, and 48 hours.

tag: cancer cell line

value: Liver cancer cell lines Huh7


title: E16-3

value: Brain

value: Embryonic day 16


title: Cells 48 hours pgg- biological rep1

description: Gene expression data from Huh7 cells treated with PGG after 48 hour of treatment


title: Cells 6 hours pgg- biological rep3


title: Cells 48 hours pgg- biological rep3


title: Cells 48 hours pgg- biological rep2


title: Cells 48 hours PBS- biological rep3

description: Gene expression data from Huh7 cells treated with PGG after 0 hour of treatment


title: SrfM2 deletion mutant 3

city: Chicago

first: Hyunwoo

last: Lee

state: IL

address: 900 S. Ashland Ave., MBRB #3020

department: Center for Biomolecular Sciences

institute: University of Illinois at Chicago

description: mRNA

data_processing:
Illumina Casava1.8 software was used for basecalling.
Raw sequencing reads were preprocessed to remove adapter sequences and bases with low sequencing quality, and the preprocessed reads were mapped to the genome of Salmonella enterica Typhimurium 14028S (CP001363.1) using bowtie 2 (v. 2.3.3) with default parameters for adapter sequences and those with low sequencing quality were removed.
Using featureCounts from subread (v. 1.5.1), expression levels of the annotated genes (CP001363.gff3) were quantified with uniquely mapped reads.
To identify genes differentially expressed, DESeq2 package (version 1.10.1) in R was used.
Genes with adjusted p-values ≤0.001 and with fold changes ≥2 were considered significant and differentially expressed.
Genome_build: CP001363.1
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for the annotated genes.

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

source_name: Bacteria

growth_protocol: Overnight cultures of respective strains grown in LB was diluted 100-fold and grown for 2.5 h, at which cells were harvested for total RNA isolation.

extract_protocol:
Total RNA was isolated using Ribopure microbial RNA isolation kit (Ambion). After treatment with RNase-free DNase I supplied with the Ribopure RNA isolation kit, RNA was purified by phenol/chloroform extraction and ethanol/sodium acetate (pH 5.2) precipitation.
Illiumina sequencing library was prepared with Illumina's ScriptSeq kit with bacterial ribosomal RNA depletion.

value: SrfM2 mutant


title: Cells 6 hours pgg- biological rep1


title: Ad lib rep3

tag: strain

value: wild type


title: Cells 48 hours PBS- biological rep1


title: Ad lib rep2

tag: age


title: SrfM2 deletion mutant 2

description: mRNA


title: Ad lib rep1

tag: tissue


title: SrfM2 deletion mutant 1

description: mRNA


title: Wild type 3

description: mRNA

value: Wild type


title: E16-2


title: E16-1


title: E12-3

value: Embryonic day 12


title: Wild type 2

description: mRNA


title: QC: replicate_1

city: Fujisawa

first: Kentaro

last: Otake

state: Kanagawa

address: 26-1, Muraoka-Higashi 2-Chome

department: Neuroscience Drug Discovery Unit

country: Japan

institute: Takeda Pharmaceutical Company Limited

data_processing:
Base Calls were performed in MiSeq suquencing system.
Mapping to genome and counting the reads were performed by RNA-seq pipeline implemented in Omicsoft Array Studio (QIAGEN).
Count per million mapped reads (CPM) was calculated.
Genome_build: B37.3
Supplementary_files_format_and_content: Tab-delimited files representing raw counts.

source_name: CSF purchased fom Proteogenex

extract_protocol:
Up to 1 mL of human CSF was centrifuged at 2,000 x g for 5 min and 10,000 x g for 20 min. Supernatant from final centrifugation was applied to exoRNeasy spin column and RNA was extracted.
Whole cDNA amplification was performed with SMART-seq v4 Ultra Low Input RNA Kit. Illumina library was constructed with Nextera XT DNA Library Prep Kit.

value: CSF purchased fom Proteogenex


title: QC: replicate_2


title: Cells 48 hours PBS- biological rep2


title: Wild type 1

description: mRNA


title: E12-1


title: E88-/- #2 RNAseq

status: Public on Nov 15 2018

city: La Jolla

first: Padma

last: Natarajan

address: 10550 N.Torrey Pines Road

department: CCBB

institute: The Scripps Research Institute

data_processing:
Illumina bcl2fastq software used for basecalling.
The reads were adapter trimmed and aligned to reference genome using STAR.
Genome coverages for chromosomes 6 and 12 on both positive and negative strands were generated from STAR alignments (BAM files) using bedtools untility  (resulting in bedgraph files provided) .
Genome_build: NCBI Build 37; UCSC version mm9
Supplementary_files_format_and_content: bedGraph

source_name: E88-/- .RAG1-/-pro-B cells

growth_protocol: 445.3 cells were cultured in RPMI suplemented with 10% Fetal Bovine Serum (FBS), 0.055 uM 2-mercaptoethanol, and 1% Penicillin-streptomycin-glutamine (PSG)

extract_protocol:
Bone marrow pro-B cells were isolated from 6 to 10 wk old female and male B6.RAG1-/- or E88-/-.RAG1-/- mice using CD19 MicroBeads for positive selection using MACS column separation.   Total RNA was prepared with an RNeasy plus kit (Qiagen).
Ribo Zero rRNA removal kit (Human/Mouse/Rat)-Epicentre. Libraries generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina.

treatment_protocol: 445.3 cells were treated with STI571 (Gleevec) (5 ug / mL) for 48 hours at 37 degrees celsius

value: Bone marrow pro-B cells


title: 445.3 WT#1 RNAseq

source_name: 445.3 cells

tag: cell lie

value: Abelson virus (v-Abl) transformed pro-B cell line


title: E88-/- #1 RNAseq

tag: cell type


title: E20-1


title: 3_01EX_005YNCCU_Keap1_dbminus_NRF2

city: Camden

first: Xiaoxin

middle: Luke

state: NJ

address: 403 Haddon Ave

institute: Coriell Institute for Medical Research

library_source: genomic

data_processing:
Basecalls performed using Real-Time Analysis (RTA), RTA v2
The 75-nt sequence reads generated by Illumina sequencing (using NextSeq 500) are mapped to the genome using the BWA algorithm with default settings.
Only reads that pass Illumina’s purity filter, align with no more than 2 mismatches, and map uniquely to the mm10 genome are used in the subsequent analysis.
Peaks were called using the MACS 2.1.0.
Genome_build: mm10

molecule: genomic DNA

source_name: Esophagus, Keap1KO

extract_protocol:
Esophagus were havested, flash frozen on dry ice, and genomic DNA was extracted.
Libraries were prepared for sequencing using standard Illumina protocols
Nrf2 ChIP-seq was conducted by Active Motif (Carlsbad, CA) using a ChIP-seq validated antibody

value: Esophagus

tag: chip antibody

value: Nrf2 (Santa Cruz, sc-13032)


title: 1_01EV_005YNCCU_WT_NRF2

source_name: Esophagus, Wild-type

tag: genotype

value: Wild-type


title: 445.3 WT-cre

source_name: 445.3-cre cells

value: WT-cre


title: 445.3 E88-/- #3


title: 2_01F5_005YNCCU_Nrf2_dbminus_NRF2

source_name: Esophagus, Nrf2KO


title: 4_01F2_005YNCCU_Pooled_Input

source_name: Esophagus, Input DNA

value: pooled

value: none (input)


title: E12-2

value: Embryonic stage


title: B6#1 RNAseq

source_name: B6.RAG1-/-  pro-B cells


title: B6#2 RNAseq


title: ngn3 islets 1

city: Nashville

first: Ken

last: Lau

state: TN

address: 2215 Garland Ave. MRBIV10475

department: Cell and Developmental Biology

institute: Vanderbilt University

data_processing:
After sequencing, reads were filtered, sorted by their barcode of origin and aligned to the reference transcriptome using inDrops pipeline (https://github.com/indrops/indrops). Mapped reads were quantified into UMI-filtered counts per gene, and barcodes that correspond to cells were retrieved based on previously established methods
Barcodes with number of unique UMIs greater than a threshold (Klein et al., 2015) were selected, resulting in the processed data table.
Technical read: read2 - UMI/cell barcode - the oligo barcodes are inDrop Version 2 which is positioned exactly as in (Klein et al. 2015)
Biological read: read1 - 3' end
Genome_build: Mouse: GRCm38.85
Supplementary_files_format_and_content: Delimited tables, with cells and genes, as columns and rows

source_name: pancreas

growth_protocol: primary cells

extract_protocol:
Mouse islets were isolated and endocrine cells were enriched by flow sorting for Ngn3eGFP low and high (please refer to paper). Cells were > 95% viable so did not enrich with MACs. Cells were encapsulated using the inDrop platform (1CellBio), and RNA was extracted according to the protocol of Klein et al., 2015.
CEL-Seq linear amplification of RNA/cDNA followed by index primer-based amplification

value: pancreas

value: Ngn3 negative

value: endocrine enrichment


title: ngn3 islets 2


title: 445.3 WT#3 RNAseq


title: 445.3 WT#2 RNAseq


title: CamkIIa_cortex_MeCP2_ChIP_rep2

first: Will

last: Renthal

address: 60 Fenwood Rd.

institute: Brigham and Women's Hospital

data_processing:
Raw reads were mapped to the mm10 genome using Bowtie2 (version 2.2.4) with default parameters.
PCR duplicates were removed using samtools rmdup (version 0.1.19)
Mapped ChIP and input reads were randomly down-sampled to the same read depth. Reads were extended to fragment length of 250bp using UCSC-tools bedExtendRanges.
Mapped ChIP and input reads were counted in mm10 gene body locations using Bedtools map (version 2.23.0)
Genome_build: mm10
Supplementary_files_format_and_content: reads mapped to gene bodies

source_name: CamkIIa-positive nuclei from cortex

extract_protocol:
Nuclei were isolated from cortex of mice expressing the SUN1-sfGFP-MYC nuclear membrane protein in CamkIIa-positive neurons as described in Mo A et al Neuron 2015. CamkIIa-positive nuclei were immunoprecipitated with a GFP antibody (Fisher G10362) and Protein G Dynabeads (Invitrogen). Nuclei were cross-linked in 1% formaldehyde in PBS for 10 min at room temperature, quenched with 125mM glycine for 5 min, and washed twice with PBS. Nuclei were resuspended in LB3 buffer (10 mM Tris pH 8, 100 mM NaCl, 1mM EDTA, 0.5 mM EGTA, 0.1% Na-Deoxycholate, 0.5% N-Lauroylsarcosine, protease inhibitors), and sonicated in a Diagenode Bioruptor. Insoluble material and beads were removed by spinning at 16,000g for 10 min at 4ºC, and Triton X-100 was added to soluble chromatin at a final concentration of 1%. Chromatin was pre-cleared for two hours with Protein A Dynabeads, then incubated with Protein A Dynabeads conjugated to an MeCP2 antibody overnight at 4ºC. Beads were washed twice with Low Salt Buffer (20 mM Tris pH 8, 150 mM NaCl, 2mM EDTA, 1% Triton X-100, 0.1% SDS), twice with High Salt Buffer (20 mM Tris pH 8, 500 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS), twice with LiCl Wash Buffer (10 mM Tris pH 8, 1 mM EDTA, 1% NP-40, 250 mM LiCl, 1% sodium deoxycholate) and once with TE Buffer (50 mM Tris pH 8, 10 mM EDTA) at 4ºC. Chromatin was eluted off beads by incubating in TE Buffer with 1% SDS at 65ºC for one hour, and crosslinks were reversed by incubating overnight at 65ºC. Chromatin was treated with RNase A for 30 min at 37ºC and Proteinase K for 2 hours at 55ºC. DNA was phenol-chloroform extracted and purified with the Qiagen PCR purification kit.
Libraries were generated using the NuGEN Ovation Ultralow System V2 following manufacturer instructions.

value: 8 weeks

value: CamkIIa-positive nuclei from cortex

value: MeCP2 (Chen WG et al. Science 2003)


title: CamkIIa_cortex_input_rep1


title: nextseq8: female mecp2 mouse

data_processing:
The raw fastq files uploaded here were prepared from Illumina bcl files in a format compatible with the inDrops.py pipeline. In brief, each NextSeq run results in 16 fastq files (4 lanes x 4 reads per lane). The read files have the following content, also as described in the documentation for inDrops.py (github/indrops):
*_R1_001.fastq.gz   : contains the 3' UTR cDNA read
*_R2_001.fastq.gz   : contains the first half of the cell barcode
*_R3_001.fastq.gz   : contains the library index for demultiplexing libraries
*_R4_001.fastq.gz   : contains the second half of the barcode and the UMI.
All  subsequent processing steps from fastq files to count matrixes were performed using a custom pipeline for inDrops data analysis (github.com/indrops), using the default version 3 parameters.
inDrops.py first filters reads based on information present in read files 2,3, and 4, for presence of i) two cell barcode sequences, ii) unique molecular identifier, iii) Illumina libray index. inDrops.py demultiplexes by Illumina library index (read 3).
For read 3, the library indices provided to the indrop.py custom pipeline are given in the yaml files. Libraries called "not_included_in_study_*" were not included in the study, but their indexes should be specified when using the indrop.py pipeline for demultiplexing.
inDrops.py then trims Read 1 using Trimmomatic (version 0.32; parameters: LEADING:28 SLIDINGWINDOW:4:20  MINLEN:30).
inDrops.py then matches cell barcodes (revealed by Read 2 and 4) against a list of the pre-determined barcodes. The reads were then split into barcode-specific files for mapping and UMI filtering.
inDrops.py then aligns the reads using Bowtie (version 1.1.1, parameters: -n 1 -l 15 -e 70 -m 200 -best -strata -a) to the mouse transcriptome. The reference transcriptome was built using annotations from ENSEMBL (GRCm38.81 or GRCh38.85) including all annotations with ""Transcript Support Levels"" of 1, 2, or NA (only accepted for protein coding genes). The reference index is assembled using inDrops.py as described in the manual.
inDrops.py performs UMI correction and returns gene expression counts of UMI-filtered transcripts per gene. Resulting raw count files are provided and called  *.counts.tsv.gz.
Supplementary_files_format_and_content: Raw counts tables from each sample were then combined by their respective experiment into the *counts.csv.gz files available in GEO and analyzed in the Seurat single-cell analysis pipeline as describe din the manuscript (Renthal et al.)
Genome_build: GRCm38, GRCh38

source_name: female mecp2 mouse

extract_protocol:
For single cell extractions, mouse cortical neurons were dissociated into a single cell suspension as described in Hrvatin et al. Nat. Neurosci 2017 and Renthal et al. For single nuclei extractions, human tissue was dissociated by dounce homgenization and clarified by ultracentrifugation through a Optiprep gradient based on a protocol (Mo et al. Neuron 2015) and modified in Renthal et al.
Cells were encapsulated using the inDrops platform, into droplets on ice and lysed in the 3 nL microfluidic droplets using a final concentration of 0.4% w/v Igepal-CA630. Single cell lysates were subject to reverse transcription at 50°C without purification of RNA (as previously described in Klein et al., Cell 2015 and Zilionis et al., Nat. Protoc. 2017). Libraries were prepared as in Zilionis et al., Nat. Protoc. 2017, with modifications summarized in the associated mansucript (Renthal et al.)

value: female

value: visual cortex

value: mixed sample (non-demultiplexed)


title: nextseq6: female mecp2 mouse


title: nextseq5: female mecp2 mouse


title: M5562: E14.5 ureters, Tbx2/Tbx3cDKO vs control, rep1

city: Hannover

first: Andreas

last: Kispert

address: Carl-Neuberg-Str. 1

department: Molekularbiologie

country: Germany

institute: Medizinische Hochschule Hannover

hyb_protocol: cRNA fragmentation, hybridization and washing steps were carried-out exactly as recommended in the 'Two-Color Microarray-Based Gene Expression Analysis Protocol V5.7' (Agilent Technologies), except that 2500ng of each labeled cRNA population were used for hybridization.

scan_protocol: Slides were scanned on the Agilent Micro Array Scanner G2565CA (pixel resolution 5 µm, bit depth 20).

data_processing:
Data extraction, processing and intra-array normalization of raw fluorescence intensity values were performed with the ‘Feature Extraction Software V10.7.3.1’ by using the recommended default extraction protocol file ‘GE2_107_Sep09.xml’.
Measurements of on-chip replicates were averaged using the geometric mean of ProcessedSignal (PS) values (for each channel independently) to retrieve one resulting value per probe, sample, and channel. Single Features were excluded from averaging, if they i) were manually flagged, ii) were identified as Outliers by the Feature Extraction Software, iii) lay outside the interval of ‘1.42 x interquartile range‘ regarding the PS distribution of the respective on-chip replicate population, or, iv) showed a coefficient of variation of pixel intensities per feature that exceeded 0.5.
For inter-array normalization, averaged processed intensity values, ‘gProcessedSignal’ (gPS) and ‘rProcessedSignal’ (rPS), were further transformed as follows: All PS values (gPS and rPS) of one particular microarray (‘Array i’ in the formula shown below) were multiplied with a microarray-specific scaling factor. This factor was calculated by dividing a ‘reference 75th Percentile value’ (set as 1500) by the 75th Percentile of the microarray dataset to be normalized. Accordingly, normalized PS values for all samples (microarray data sets) were calculated by the following formula:
normalized PSArray i = PSArray i  x (1500 / 75th Percentile gPSArray i)
Finally, a lower intensity threshold (surrogate value) was defined based on intensity distribution of negative control features. This value was fixed at 15 normalized PS units. All of those measurements that fell below this intensity cutoff were substituted by the respective surrogate value of 15.

source_name: control

label_protocol: Synthesis of AlexaFluor555- or AlexaFluor647- (Invitrogen) labeled cRNA was performed with the 'Amino Allyl MessageAmp™ II aRNA Amplification Kit' (#AM1753, Life Technologies) according to the manufacturer's recommendations, except that the proportion of aminoallyl-UTP/UTP was adjusted to 1+11 (instead of 1+1) and that reaction volumes were halved.

extract_protocol: Total RNA was extracted using peqGOLD RNAPure™ (VWR) according to the manufacturer's recommendations

value: NMRI

value: Ureter


title: nextseq7: female mecp2 mouse

city: Boston


title: CamkIIa_cortex_input_rep2


title: M5563: E14.5 ureters, Tbx2/Tbx3cDKO vs control, rep2

value: male


title: 445.3 E88-/- #1

value: Abelson virus (v-Abl) transformed pro-B cell line


title: nextseq4: male mecp2 mouse

source_name: male mecp2 mouse


title: 445.3 E88-/- #2


title: CamkIIa_cortex_MeCP2_ChIP_rep1


title: nextseq3: male mecp2 mouse


title: nextseq2: male mecp2 mouse


title: TNFa 120 mins

city: Pasadena

first: Luke

last: Frankiw

state: California

address: 1200 E California Blvd

institute: Caltech

description:
16529_TC63_ScrTnf120_TAGGCATG-CTAAGCCT_L999
processed data file:

data_processing:
Single-end 50-mer reads were aligned using Tophat v2.1.1.
Gene expression was determined using Cufflinks v2.2.1 and the FPKM (Fragments Per Kilobase Million) metric.
Intron retention analysis performed with custom Python script.
igvtools count function with -z 10 and -w 5 was used to generate tdf files.
Genome_build: mm9
Supplementary_files_format_and_content: FPKM values for each sample; intron retention analysis including delta SR at each junction; splicing in tdf files

growth_protocol: C56BL6/J mice were sacrificed via CO2 euthanasia and sterilized with 70% ethanol. Femur and tibia bones harvested and stripped of muscle tissue. Bone marrow cells were resuspended in 20mL of fresh DMEM. 2.5 *10^6 bone-marrow cells plated in a 150mm dish in 20mL of BMDM Media (DMEM, 20% FBS, 30% L929 condition media, and 1% Pen/Strep) and grown at 5% CO2 and 37°C. BMDM media was completely replaced on day 3 as well as a supplemental addition of 5mL L929 condition media on day 5.

extract_protocol:
Total RNA was purified from BMDMs using TRIzol reagent (Ambion) as per the manufacturer’s instructions.  For fractionation experiments, confluent 10-cm dish of mature BMDMs were scraped into 400µL cold NP-40 lysis buffer, APJ1 (10mM Tris-HCl (pH 7.5), 0.08% NP-40, 150mM NaCl). Lysed cells layered onto 1mL cold sucrose 322 cushion, APJ2 (10mM Tris-HCl (pH 7.5), 150mM NaCl, 24% w/v sucrose) and centrifuged for 10min at 4°C and 13000 rpm. The supernatant from this spin represents the cytoplasmic RNA fraction, which is immediately added to 3 volumes of 100% ethanol and 2 volumes of buffer RLT (4M GuSCN, 325 0.1M β-mercaptoethanol, 0.5% N-lauroyl sarcosine, 25mM Na-citrate, pH7.2) and stored at -80°C until ready to purify RNA. Pellet, containing intact nuclei, is resuspended in 500µL TRIzol reagent.
Full length cDNA libraries were barcoded using the Nextera XT Tagmentation protocol (Illumina).

treatment_protocol: Stimulation involved with either 20ng/mL of TNFα, 5ug/mL Poly(I:C) (Sigma), or 5µM ODN 1585 (InvivoGen).

value: Bone Marrow Derived Macrophage (BMDM)

value: TNFa 120 mins


title: Bud13 KD - Poly(I:C) 480 mins - Cyto

description:
16594_TC66_Bud-Cyto-8_S26_L999
processed data file:
Cuff_Gene_Exp_Data.xlsx, SR_Data_Fractionation.xlsx

source_name: BMDM_Bud13 KD - Poly(I:C)

tag: shRNA

value: Poly(I:C) 480 mins


title: Control - Poly(I:C) Exp #2 720 mins

description:
19483_TC72-Scr12_S11_L001
processed data file:
Cuff_Gene_Exp_Data.xlsx, SR_Data_Rbmx2Snip1.xlsx

source_name: BMDM_Control - Poly(I:C)

tag: strain background

value: Scramble

value: Poly(I:C) Exp #2 720 mins


title: Snip1 KD - Poly(I:C) Exp #2 1440 mins

description:
19483_TC72-Snip24_S4_L001
processed data file:
Cuff_Gene_Exp_Data.xlsx, SR_Data_Rbmx2Snip1.xlsx

source_name: BMDM_Snip1 KD - Poly(I:C)

value: Poly(I:C) Exp #2 1440 mins


title: Rbmx2 KD - Poly(I:C) Exp #2 720 mins

description:
19483_TC72-RN12_S7_L001
processed data file:
Cuff_Gene_Exp_Data.xlsx, SR_Data_Rbmx2Snip1.xlsx

source_name: BMDM_Rbmx2 KD - Poly(I:C)


title: TNFa 60 mins

description:
16529_TC63_ScrTnf60_GGACTCCT-CTAAGCCT_L999
processed data file:

value: TNFa 60 mins


title: Snip1 KD - Poly(I:C) Exp #2 720 mins

description:
19483_TC72-Snip12_S3_L001
processed data file:
Cuff_Gene_Exp_Data.xlsx, SR_Data_Rbmx2Snip1.xlsx


title: TNFa 30 mins

description:
16529_TC63_ScrTnf30_AGGCAGAA-CTAAGCCT_L999
processed data file:

value: TNFa 30 mins


title: TNFa 0 mins

description:
16529_TC63_ScrTnf0_TAAGGCGA-CTAAGCCT_L999
processed data file:

value: TNFa 0 mins


title: Rbmx2 KD - Poly(I:C) Exp #2 360 mins

description:
19483_TC72-RN6_S6_L001
processed data file:
Cuff_Gene_Exp_Data.xlsx, SR_Data_Rbmx2Snip1.xlsx

value: Poly(I:C) Exp #2 360 mins


title: Bud13 KD - Poly(I:C) 0 mins - Cyto

description:
16594_TC66_Bud-Cyto-0_S22_L999
processed data file:
Cuff_Gene_Exp_Data.xlsx, SR_Data_Fractionation.xlsx

value: Poly(I:C) 0 mins


title: Rbmx2 KD - Poly(I:C) Exp #2 0 mins

description:
19483_TC72-RN0_S5_L001
processed data file:
Cuff_Gene_Exp_Data.xlsx, SR_Data_Rbmx2Snip1.xlsx

value: Poly(I:C) Exp #2 0 mins


title: Bud13 KD - Poly(I:C) 720 mins - Cyto

description:
16594_TC66_Bud-Cyto-12_S27_L999
processed data file:
Cuff_Gene_Exp_Data.xlsx, SR_Data_Fractionation.xlsx

value: Poly(I:C) 720 mins


title: Control - Poly(I:C) Exp #2 0 mins

description:
19483_TC72-Scr0_S9_L001
processed data file:
Cuff_Gene_Exp_Data.xlsx, SR_Data_Rbmx2Snip1.xlsx


title: Control - Poly(I:C) Exp #2 1440 mins

description:
19483_TC72-Scr24_S12_L001
processed data file:
Cuff_Gene_Exp_Data.xlsx, SR_Data_Rbmx2Snip1.xlsx


title: Snip1 KD - Poly(I:C) Exp #2 0 mins

description:
19483_TC72-Snip0_S1_L001
processed data file:
Cuff_Gene_Exp_Data.xlsx, SR_Data_Rbmx2Snip1.xlsx


title: Control - Poly(I:C) 720 mins - Cyto

description:
16594_TC66_Scr-Cyto-12_S41_L999
processed data file:
Cuff_Gene_Exp_Data.xlsx, SR_Data_Fractionation.xlsx


title: IFNa 120 mins

description:
19483_TC72-Scr120ifnno_S38_L001
processed data file:

value: IFNa 120 mins


title: Control - Poly(I:C) 480 mins - Cyto

description:
16594_TC66_Scr-Cyto-8_S40_L999
processed data file:
Cuff_Gene_Exp_Data.xlsx, SR_Data_Fractionation.xlsx


title: Control - Poly(I:C) 240 mins - Cyto

description:
16594_TC66_Scr-Cyto-4_S39_L999
processed data file:
Cuff_Gene_Exp_Data.xlsx, SR_Data_Fractionation.xlsx

value: Poly(I:C) 240 mins


title: Control - Poly(I:C) Exp #2 360 mins

description:
19483_TC72-Scr6_S10_L001
processed data file:
Cuff_Gene_Exp_Data.xlsx, SR_Data_Rbmx2Snip1.xlsx


title: nextseq1: male mecp2 mouse

value: male

value: visual cortex

value: mixed sample (non-demultiplexed)


title: IFNa 60 mins

description:
19483_TC72-Scr60ifnno_S36_L001
processed data file:

value: Bone Marrow Derived Macrophage (BMDM)

value: IFNa 60 mins


title: Snip1 KD - Poly(I:C) Exp #2 360 mins

description:
19483_TC72-Snip6_S2_L001
processed data file:
Cuff_Gene_Exp_Data.xlsx, SR_Data_Rbmx2Snip1.xlsx


title: Control - Poly(I:C) 60 mins - Cyto

description:
16594_TC66_Scr-Cyto-1_S38_L999
processed data file:
Cuff_Gene_Exp_Data.xlsx, SR_Data_Fractionation.xlsx

value: Scramble

value: Poly(I:C) 60 mins


title: Control - Poly(I:C) 0 mins - Cyto

description:
16594_TC66_Scr-Cyto-0_S36_L999
processed data file:
Cuff_Gene_Exp_Data.xlsx, SR_Data_Fractionation.xlsx


title: Bud13 KD - Poly(I:C) 720 mins - Nuc

description:
16594_TC66_Bud-Nuc-12_S20_L999
processed data file:
Cuff_Gene_Exp_Data.xlsx, SR_Data_Fractionation.xlsx


title: Bud13 KD - Poly(I:C) 60 mins - Cyto

description:
16594_TC66_Bud-Cyto-1_S24_L999
processed data file:
Cuff_Gene_Exp_Data.xlsx, SR_Data_Fractionation.xlsx


title: Rbmx2 KD - Poly(I:C) Exp #2 1440 mins

description:
19483_TC72-RN24_S8_L001
processed data file:
Cuff_Gene_Exp_Data.xlsx, SR_Data_Rbmx2Snip1.xlsx

value: Poly(I:C) Exp #2 1440 mins


title: Bud13 KD - Poly(I:C) 240 mins - Cyto

description:
16594_TC66_Bud-Cyto-4_S25_L999
processed data file:
Cuff_Gene_Exp_Data.xlsx, SR_Data_Fractionation.xlsx


title: Bud13 KD - Poly(I:C) 0 mins - Nuc

description:
16594_TC66_Bud-Nuc-0_S15_L999
processed data file:
Cuff_Gene_Exp_Data.xlsx, SR_Data_Fractionation.xlsx


title: Bud13 KD - Poly(I:C) 240 mins - Nuc

description:
16594_TC66_Bud-Nuc-4_S18_L999
processed data file:
Cuff_Gene_Exp_Data.xlsx, SR_Data_Fractionation.xlsx


title: Bud13 KD - Poly(I:C) 60 mins - Nuc

description:
16594_TC66_Bud-Nuc-1_S17_L999
processed data file:
Cuff_Gene_Exp_Data.xlsx, SR_Data_Fractionation.xlsx


title: Bud13 KD - Poly(I:C) 480 mins - Nuc

description:
16594_TC66_Bud-Nuc-8_S19_L999
processed data file:
Cuff_Gene_Exp_Data.xlsx, SR_Data_Fractionation.xlsx

value: Poly(I:C) 480 mins


title: Control - Poly(I:C) 720 mins - Nuc

description:
16594_TC66_Scr-Nuc-12_S34_L999
processed data file:
Cuff_Gene_Exp_Data.xlsx, SR_Data_Fractionation.xlsx


title: Control - Poly(I:C) 480 mins - Nuc

description:
16594_TC66_Scr-Nuc-8_S33_L999
processed data file:
Cuff_Gene_Exp_Data.xlsx, SR_Data_Fractionation.xlsx


title: Control - CpG 0 mins

description:
19483_TC72-Scr0no_S30_L001
processed data file:
Cuff_Gene_Exp_Data.xlsx, SR_Data_CPG.xlsx

source_name: BMDM_Control - CpG

value: CpG 0 mins


title: Bud13 KD - CpG 1440 mins

description:
19483_TC72-Budcpg24_S28_L001
processed data file:
Cuff_Gene_Exp_Data.xlsx, SR_Data_CPG.xlsx

source_name: BMDM_Bud13 KD - CpG

value: CpG 1440 mins


title: Control - CpG 720 mins

description:
19483_TC72-Scrcpg12_S39_L001
processed data file:
Cuff_Gene_Exp_Data.xlsx, SR_Data_CPG.xlsx

value: CpG 720 mins


title: Bud13 KD - CpG 0 mins

description:
19483_TC72-Bud0no_S18_L001
processed data file:
Cuff_Gene_Exp_Data.xlsx, SR_Data_CPG.xlsx


title: Control - Poly(I:C) 240 mins - Nuc

description:
16594_TC66_Scr-Nuc-4_S32_L999
processed data file:
Cuff_Gene_Exp_Data.xlsx, SR_Data_Fractionation.xlsx


title: Control - CpG 1440 mins

description:
19483_TC72-Scrcpg24_S40_L001
processed data file:
Cuff_Gene_Exp_Data.xlsx, SR_Data_CPG.xlsx


title: Control - Poly(I:C) 720 mins

description:
16529_TC63_Scr720_TCCTGAGC-ACTGCATA_L999
processed data file:
Cuff_Gene_Exp_Data.xlsx, SR_Data_PIC.xlsx


title: Bud13 KD - Poly(I:C) 0 mins

description:
16529_TC63_Bud0_TAAGGCGA-CTCTCTAT_L999
processed data file:
Cuff_Gene_Exp_Data.xlsx, SR_Data_PIC.xlsx

value: Poly(I:C) 0 mins


title: Bud13 KD - Poly(I:C) 240 mins

description:
16529_TC63_Bud240_GGACTCCT-GTAAGGAG_L999
processed data file:
Cuff_Gene_Exp_Data.xlsx, SR_Data_PIC.xlsx


title: Control - Poly(I:C) 1440 mins

description:
16529_TC63_Scr1440_TAGGCATG-ACTGCATA_L999
processed data file:
Cuff_Gene_Exp_Data.xlsx, SR_Data_PIC.xlsx

value: Poly(I:C) 1440 mins


title: Bud13 KD - Poly(I:C) 720 mins

description:
16529_TC63_Bud720_AGGCAGAA-ACTGCATA_L999
processed data file:
Cuff_Gene_Exp_Data.xlsx, SR_Data_PIC.xlsx

value: Poly(I:C) 720 mins


title: Bud13 KD - Poly(I:C) 60 mins

description:
16529_TC63_Bud60_TAAGGCGA-GTAAGGAG_L999
processed data file:
Cuff_Gene_Exp_Data.xlsx, SR_Data_PIC.xlsx


title: Bud13 KD - CpG 720 mins

description:
19483_TC72-Budcpg12_S27_L001
processed data file:
Cuff_Gene_Exp_Data.xlsx, SR_Data_CPG.xlsx


title: Bud13 KD - Poly(I:C) 15 mins

description:
16529_TC63_Bud15_GGACTCCT-CTCTCTAT_L999
processed data file:
Cuff_Gene_Exp_Data.xlsx, SR_Data_PIC.xlsx

value: Poly(I:C) 15 mins


title: Control - Poly(I:C) 240 mins

description:
16529_TC63_Scr240_TAGGCATG-GTAAGGAG_L999
processed data file:
Cuff_Gene_Exp_Data.xlsx, SR_Data_PIC.xlsx

value: Poly(I:C) 240 mins


title: Control - Poly(I:C) 60 mins

description:
16529_TC63_Scr60_CGTACTAG-GTAAGGAG_L999
processed data file:
Cuff_Gene_Exp_Data.xlsx, SR_Data_PIC.xlsx


title: Control - Poly(I:C) 15 mins

description:
16529_TC63_Scr15_TAGGCATG-CTCTCTAT_L999
processed data file:
Cuff_Gene_Exp_Data.xlsx, SR_Data_PIC.xlsx


title: Control - Poly(I:C) 0 mins

description:
16529_TC63_Scr0_CGTACTAG-CTCTCTAT_L999
processed data file:
Cuff_Gene_Exp_Data.xlsx, SR_Data_PIC.xlsx


title: Bud13 KD - TNFa 60 mins

description:
13680_TC56_Bud-60_GGACTCCT-TATCCTCT_L999
processed data file:
Cuff_Gene_Exp_Data.xlsx, SR_Data_TNF.xlsx

source_name: BMDM_Bud13 KD - TNFa

value: TNFa 60 mins


title: Control - Poly(I:C) 60 mins - Nuc

description:
16594_TC66_Scr-Nuc-1_S31_L999
processed data file:
Cuff_Gene_Exp_Data.xlsx, SR_Data_Fractionation.xlsx


title: Bud13 KD - TNFa 120 mins

description:
13680_TC56_Bud-120_TAGGCATG-TATCCTCT_L999
processed data file:
Cuff_Gene_Exp_Data.xlsx, SR_Data_TNF.xlsx

value: TNFa 120 mins


title: Bud13 KD - Poly(I:C) 1440 mins

description:
16529_TC63_Bud1440_GGACTCCT-ACTGCATA_L999
processed data file:
Cuff_Gene_Exp_Data.xlsx, SR_Data_PIC.xlsx


title: Control - Poly(I:C) 0 mins - Nuc

description:
16594_TC66_Scr-Nuc-0_S29_L999
processed data file:
Cuff_Gene_Exp_Data.xlsx, SR_Data_Fractionation.xlsx


title: Bud13 KD - TNFa 30 mins

description:
13680_TC56_Bud-30_AGGCAGAA-TATCCTCT_L999
processed data file:
Cuff_Gene_Exp_Data.xlsx, SR_Data_TNF.xlsx

value: TNFa 30 mins


title: Control - TNFa 0 mins

description:
13680_TC56_Scramble-0_TAAGGCGA-CTCTCTAT_L999
processed data file:
Cuff_Gene_Exp_Data.xlsx, SR_Data_TNF.xlsx

source_name: BMDM_Control - TNFa

value: Bone Marrow Derived Macrophage (BMDM)

value: TNFa 0 mins


title: Bud13 KD - TNFa 0 mins

description:
13680_TC56_Bud-0_TAAGGCGA-TATCCTCT_L999
processed data file:
Cuff_Gene_Exp_Data.xlsx, SR_Data_TNF.xlsx


title: Control - TNFa 120 mins

description:
13680_TC56_Scramble-120_TAGGCATG-CTCTCTAT_L999
processed data file:
Cuff_Gene_Exp_Data.xlsx, SR_Data_TNF.xlsx

value: Scramble


title: Control - TNFa 30 mins

description:
13680_TC56_Scramble-30_AGGCAGAA-CTCTCTAT_L999
processed data file:
Cuff_Gene_Exp_Data.xlsx, SR_Data_TNF.xlsx


title: Wan-012 WT, 6hr after differentiation

city: Chapel Hill

first: Di

last: Wu

state: North Carolina

address: 385 S. Columbia Street

department: Periodontics

institute: University of North Carolina, Chapel Hill

description:
mRNA gene expression
Data.txi.csv
Data.voom.csv

data_processing:
Reads (32-45 Million reads per sample) were analyzed with Salmon [version 0.9.1] (Patro et al., 2017) software to align and quantify the transcript expression.
R packages in Bioconductor, tximport and tximportData (Soneson et al., 2015) were used to aggregate transcript-level quantifications to the estimated counts at the gene level, with the R package biomaRt for gene and transcripts mapping. The option "lengthScaledTPM" for countsFromAbundance in tximport was used.
R function voom (Law et al., 2014) in limma package was further used to transform the estimated count data into log2 scale weighted by the mean-variance relationship. Ready to be used in a linear model.
Genome_build: mm10
Supplementary_files_format_and_content: Two precessed datasets in Excel. One (y1) is for the estimated counts; the other (y2) is after voom transformation in log2 scale.

source_name: activated pathogenic Th17 cells

growth_protocol: CD4 T cells were purified from indicated genotype of mice. WT and RASA3 KO CD4 T cells were differentiation under IL-1b+IL-6+IL-23 for 6hr in X-VIVO medium.

extract_protocol:
6hr after culture under pathogenic- Th17 condtion, RNA was harvested using RNA-easy mini kit (Qiagen). Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing following Illumina's protocols

value: T cells

tag: time point

value: 6hr after differentiation

value: wild type


title: Wan-013 RASA3 KO rep2, 6hr after differentiation


title: Wan-004 RASA3 knockout,6hr after differentiation


title: Wan-003 WT, 6hr after differentiation


title: RNADIP_siLUC (rep2)

city: Oxford

first: Nicholas

last: Proudfoot

address: South Parks Road

country: United Kingdom

institute: Sir William Dunn School of Pathology,  University of Oxford

description: chromatin RNA

data_processing:
Library strategy: RNA-DIP-seq
RNADIP-seq reads were trimmed using Cutadapt and then mapped to the human reference genome with Bowtie2.
Aligned reads were processed to only include  uniquely mapped reads with no more than 2 mismatches using SAMtools. RNA-DIP-seq peaks were called using MACS2 algorithm with default options
Data were scaled to library size (genomeCoverageBed) using Bedtools.
Genome_build: hg19
Supplementary_files_format_and_content: RNADIP-seq peak file

source_name: cervix

growth_protocol: HeLa cells were maintained in DMEM supplemented with 10%FBS

extract_protocol:
Lysates were clarified from sonicated nuclei and RNA:DNA hybrids were isolated with antibody for RNA-DIP-seq
For the RNA DIP-seq, the RNA component of the R-loop was used to prepare the library using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina, v1.0 (E7420) according to manufacturer's guidelines. For the ChhrRNA-seq, chromatin associated RNA was used for library prepration as for RNA DIP-seq

treatment_protocol: RNAi  was performed with Lipofectamine RNAiMax using siSpt6 and siLuciferase delivered at 30nM final concentration.

tag: cell line

value: HeLa

value: cervical cancer cells

value: siLUC


title: AAV-GFP_RNA-Seq

first: yongqing

last: liu

address: 38 Xue Yuan Road

department: Department of Biochemistry and Molecular Biology

institute: Peking University Health Science Center

description: CDYL-Processed data.txt

data_processing:
Illumina HiSeq sequencer and software used for sequencing and basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to reference genome of mm10 using HISTA.
Transcript assembly were performed using Cufflink. DEG analyses were performed using Cuffdiff.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw counts, p-value, q-value for each Sample.

source_name: AAV-GFP virus overexpressed mice

growth_protocol: PL tissues from 8-week old C57BL/6 mice

extract_protocol:
PL tissues were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. NEBNext Ultra RNA Library Prep Kit for Illumina (Cat#E7530S) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Prelimbic cortex

value: 8 weeks

value: AAV-GFP virus overexpression


title: AAV-CDYL_RNA-Seq

description: CDYL-Processed data.txt

source_name: AAV-CDYL virus overexpressed mice

value: AAV-CDYL virus overexpression


title: RNADIP_siSPT6 (rep2)

description: chromatin RNA


title: Susceptible_RNA-Seq

description: CSDS-Processed data.txt

source_name: susceptible mice after chronic social defeat stress

tag: phenotype

value: stress-susceptible

tag: stress

value: chronic social defeat stress


title: RNADIP_siSPT6 (rep1)

description: chromatin RNA

tag: treatment


title: Control_RNA-Seq

description: CSDS-Processed data.txt

source_name: control mice after chronic social defeat stress

value: control


title: Rett3_MeCP2_high_nuclear_RNA

description: nuclear RNA

data_processing:
Raw reads were mapped to the hg38 genome with Tophat2 (version 2.1.0) using default parameters.
Genome_build: hg38

source_name: Sorted nuclei from occipital cortex

extract_protocol:
Nuclei were isolated from occipital cortex tissue and incubated with an MeCP2 antibody (Chen WG et al 2003) followed by a goat anti-rabbit 647 secondary antibody (Invitrogen). Nuclei were sorted into MeCP2 high and low populations on a Sony SH800Z Cell Sorter. Nuclei were sorted into TRIzol LS (Invitrogen) and total RNA was chloroform extracted and purified with the Qiagen RNeasy Micro Kit with on-column DNase treatment.
Total RNA-seq libraries were generated with the NEBNext Ultra Directional Library Prep Kit with rRNA depletion.

value: Occipital cortex

tag: sorted population

value: MeCP2 high

tag: diagnosis

value: Rett syndrome


title: Control - TNFa 60 mins

description:
13680_TC56_Scramble-60_GGACTCCT-CTCTCTAT_L999
processed data file:
Cuff_Gene_Exp_Data.xlsx, SR_Data_TNF.xlsx

value: Scramble

value: Bone Marrow Derived Macrophage (BMDM)

value: TNFa 60 mins


title: Rett3_MeCP2_low_nuclear_RNA

description: nuclear RNA

value: MeCP2 low


title: RNADIP_siLUC (rep1)

description: chromatin RNA

value: HeLa


title: Rett2_MeCP2_high_nuclear_RNA

description: nuclear RNA


title: Rett2_MeCP2_low_nuclear_RNA

description: nuclear RNA


title: nextseq10: female rett brain donor (human)

source_name: female rett brain donor

tag: gender

value: female

value: occipital cortex

tag: donor

value: mixed sample (non-demultiplexed)


title: nextseq9: female rett brain donor (human)

tag: age


title: Low growth (LG) Anterior Pituitary, Week 5, Rep 4 vs. Pituitary Reference Pool (High and Low Growth, Weeks 1, 3, 5, 7)

city: Athens

first: Laura

last: Ellestad

state: GA

address: 110 Cedar Street

department: Department of Poultry Science

institute: Unviversity of Georgia

hyb_protocol: The microarray was hybridized overnight at 42oC with Cy3-labeled experimental sample cDNA and an aliquot of the Cy5-labeled reference pool cDNA using microarray hybridization buffer (Amersham Biosciences).  Slides were washed in increasing stringency using salt sodium citrate.

scan_protocol: Microarray slides were scanned using a 418 confocal laser scanner (Affymetrix) at 550 nM for Cy3 and 649 nM for Cy5 to generate two TIFF images for each slide.

data_processing: The two images from each slide were processed with Spotfinder version 2.2.4 (The Institute for Genomic Research, Rockville, MD) using the following settings:  Otsu thresholding algorithm (minimum spot size 3 and maximum spot size 25); keep flagged values; keep raw data; and quality control filter set so 50% cutoff equals background plus 1 standard deviation.  Data were normalized using Microarray Data Analysis System (MIDAS) version 2.18 (The Institute for Genomic Research).  In MIDAS, channel A and B flags and channel A and B background checking were used, and the signal-to-noise threshold was set at 3.0.  Data from the Cy3 channel were first Lowess (LocFit) normalized by pin (block) using a smoothing parameter of 0.33, with Cy5 as the reference, and then subjected to standard deviation regularization first by pin (block) then by slide, with Cy5 as the reference.  Data from each spot on each slide were expressed as log2-ratio, or log2(normalized Cy3/raw Cy5), which is given in the data table below. Log2-ratios for the spots were statistically analyzed by two-way ANOVA using a linear mixed model procedure (PROC MIXED; SAS institute Inc., Cary, NC) to identify differentially expressed genes that were significantly different (n=4; P<0.05) by line or the line-by-age interaction and where there was a >160% difference between the highest expression in one line and the lowest expression in the other.

source_name: LG, pituitary, week 5

label_protocol: One microgram aRNA (equivalent to one microgram mRNA) of each individual sample or the reference pool was converted to cDNA using random primers with the Amino Allyl cDNA Labeling Kit (Ambion), following which Cy3- or Cy5-monoreactive NHS esters (Amersham Biosciences, Piscataway, NJ) were coupled to the cDNA.  Labeled cDNA was purified from unicorporated dye using CyScribe GFX Purification Kit (Amersham Biosciences). For the Cy5-labeled reference sample, a pool was made of all Cy5-labeled cDNA and split among the 32 slides in the experiment.

growth_protocol: Birds were grown using standard broiler chicken production parameters.

extract_protocol: Total RNA was extracted with the RNeasy Mini Kit according to the manufacturer's protocol (Qiagen, Valencia, CA) and amplified using a modification of the Eberwine Procedure (Phillips J, Eberwine JH 1996 METHODS: A Companion to Methods in Enzymology 10: 283-288). Briefly, 500 ng was reverse-transcribed using SuperScript II (Invitrogen, Carlsbad, CA) and an oligo(dT) primer containing a T7 promoter site (5'-GGCCAGTGAATTGTAATATCGACTCACTATAGGGAGGCGGT24-3'; Affymetrix, Santa Clara, CA).  Following second strand synthesis and purification, double-stranded cDNA was used as a template for in vitro transcription using the T7 MEGAscript kit (Ambion, Austin, TX) and the resulting amplified antisense RNA (aRNA) was quantified with the Ribogreen RNA Quantitation Kit (Invitrogen, Carlsbad, CA).

treatment_protocol: Birds were divergently selected for body weight at 8 weeks of age and are maintained at SRA-INRA (France). Anterior pituitary glands were collected at 1, 3, 5, and 7 weeks of age, snap frozen in liquid nitrogen, and stored at -80oC until RNA extraction.

tag: tissue

value: anterior pituitary gland

value: low growth

tag: Sex

value: male

value: posthatch week 5

source_name: Anterior Pituitary Reference Pool (High and Low Growth lines, posthatch weeks 1, 3, 5, and 7)

tag: sample type

value: pool of High Growth and Low Growth aRNA from all 32 samples

value: posthatch weeks 1, 3, 5, and 7


title: Low growth (LG) Anterior Pituitary, Week 7, Rep 3 vs. Pituitary Reference Pool (High and Low Growth, Weeks 1, 3, 5, 7)

source_name: LG, pituitary, week 7

value: posthatch week 7


title: Low growth (LG) Anterior Pituitary, Week 5, Rep 3 vs. Pituitary Reference Pool (High and Low Growth, Weeks 1, 3, 5, 7)


title: Low growth (LG) Anterior Pituitary, Week 7, Rep 1 vs. Pituitary Reference Pool (High and Low Growth, Weeks 1, 3, 5, 7)


title: t_vs_t0_sog1-1_rep1_24h

first: Julie

middle: Ann

last: Law

address: 10010 North Torrey Pines Rd

department: PLANT MOLECULAR AND CELLULAR BIOLOGY LABORATORY

institute: The Salk Institute for Biological Studies

data_processing:
Illumina Casava software used for basecalling and demultiplexing.
Read Filtering and Mapping: mRNA-seq reads were mapped to TAIR10 reference genome using STAR (v2.5.0c) allowing 2 mismatches.
UCSC browser tracks (bedGraph files) were generated using the Homer suite of NGS tools and normalized to a million (1e7) reads.
Genome_build: TAIR10
Supplementary_files_format_and_content: bedGraph file, including header and chr#, start position, end position and normalized value (rp10M).

organism: Arabidopsis thaliana

source_name: 6 day-old Seedlings

growth_protocol: Arabidopsis seedlings used in this study were in the Columbia-0 (Col) ecotype for the wt and in a mixed Landsberg erecta (Ler)/Col background containing a CYCB1;1promoter::GUS fusion for the sog1-1 mutant. Seedlings were grown under constqnt light at 23°C in a Percival growth cabinet.

extract_protocol:
10 seedlings were collected and total RNA was isolated using the Quick-RNA MiniPrep kit (Zymo Research, Cat# R1055).
2.0μg of total RNA from each genotype was used to generate mRNA-seq libraries using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB E7490) for mRNA purification and NEBNext Ultra RNA Library Prep Kit for Illumina (NEB E7530). Sera-Mag Magnetic SpeedBeads (Thermo scientific, Cat# 65152105050250) were used for all the size selection and clean-up steps. The resulting libraries were equally pooled and sequenced with in SE50 mode using a HiSeq2500 machine.

treatment_protocol: 100 Gy using a Co60 radioactive source at a dose-rate of 10 Gy/min

value: 100 Gy Gamma-IR

tag: time after ir


title: High growth (HG) Anterior Pituitary, Week 7, Rep 2 vs. Pituitary Reference Pool (High and Low Growth, Weeks 1, 3, 5, 7)

source_name: HG, pituitary, week 7

value: high growth


title: High growth (HG) Anterior Pituitary, Week 7, Rep 1 vs. Pituitary Reference Pool (High and Low Growth, Weeks 1, 3, 5, 7)


title: High growth (HG) Anterior Pituitary, Week 7, Rep 4 vs. Pituitary Reference Pool (High and Low Growth, Weeks 1, 3, 5, 7)


title: t_vs_t0_sog1-1_rep2_12h

tag: genotype


title: High growth (HG) Anterior Pituitary, Week 7, Rep 3 vs. Pituitary Reference Pool (High and Low Growth, Weeks 1, 3, 5, 7)


title: Low growth (LG) Anterior Pituitary, Week 7, Rep 2 vs. Pituitary Reference Pool (High and Low Growth, Weeks 1, 3, 5, 7)


title: Rett1_MeCP2_high_nuclear_RNA

description: nuclear RNA

value: Occipital cortex

value: MeCP2 high

value: Rett syndrome


title: t_vs_t0_sog1-1_rep1_12h


title: Rett1_MeCP2_low_nuclear_RNA

description: nuclear RNA

value: MeCP2 low


title: t_vs_t0_sog1-1_rep2_6h


title: Low growth (LG) Anterior Pituitary, Week 7, Rep 4 vs. Pituitary Reference Pool (High and Low Growth, Weeks 1, 3, 5, 7)


title: t_vs_t0_sog1-1_rep2_24h


title: Low growth (LG) Anterior Pituitary, Week 3, Rep 3 vs. Pituitary Reference Pool (High and Low Growth, Weeks 1, 3, 5, 7)

source_name: LG, pituitary, week 3

value: posthatch week 3


title: High growth (HG) Anterior Pituitary, Week 5, Rep 3 vs. Pituitary Reference Pool (High and Low Growth, Weeks 1, 3, 5, 7)

source_name: HG, pituitary, week 5


title: High growth (HG) Anterior Pituitary, Week 5, Rep 4 vs. Pituitary Reference Pool (High and Low Growth, Weeks 1, 3, 5, 7)


title: Low growth (LG) Anterior Pituitary, Week 5, Rep 1 vs. Pituitary Reference Pool (High and Low Growth, Weeks 1, 3, 5, 7)


title: Low growth (LG) Anterior Pituitary, Week 3, Rep 4 vs. Pituitary Reference Pool (High and Low Growth, Weeks 1, 3, 5, 7)


title: High growth (HG) Anterior Pituitary, Week 5, Rep 1 vs. Pituitary Reference Pool (High and Low Growth, Weeks 1, 3, 5, 7)


title: High growth (HG) Anterior Pituitary, Week 5, Rep 2 vs. Pituitary Reference Pool (High and Low Growth, Weeks 1, 3, 5, 7)


title: t_vs_t0_sog1-1_rep1_6h


title: t_vs_t0_sog1-1_rep2_3h


title: t_vs_t0_sog1-1_rep1_3h


title: Low growth (LG) Anterior Pituitary, Week 5, Rep 2 vs. Pituitary Reference Pool (High and Low Growth, Weeks 1, 3, 5, 7)


title: High growth (HG) Anterior Pituitary, Week 3, Rep 4 vs. Pituitary Reference Pool (High and Low Growth, Weeks 1, 3, 5, 7)

source_name: HG, pituitary, week 3


title: t_vs_t0_sog1-1_rep2_1h30min


title: t_vs_t0_sog1-1_rep1_1h30min


title: t_vs_t0_sog1-1_rep2_45min


title: Low growth (LG) Anterior Pituitary, Week 3, Rep 1 vs. Pituitary Reference Pool (High and Low Growth, Weeks 1, 3, 5, 7)


title: Low growth (LG) Anterior Pituitary, Week 3, Rep 2 vs. Pituitary Reference Pool (High and Low Growth, Weeks 1, 3, 5, 7)


title: t_vs_t0_sog1-1_rep2_20min


title: t_vs_t0_sog1-1_rep1_20min


title: t_vs_t0_sog1-1_rep1_45min


title: t_vs_t0_sog1-1_rep2_10min


title: t_vs_t0_sog1-1_rep1_10min


title: t_vs_t0_wt_rep2_24h

value: wild-type


title: High growth (HG) Anterior Pituitary, Week 3, Rep 3 vs. Pituitary Reference Pool (High and Low Growth, Weeks 1, 3, 5, 7)


title: High growth (HG) Anterior Pituitary, Week 3, Rep 1 vs. Pituitary Reference Pool (High and Low Growth, Weeks 1, 3, 5, 7)


title: t_vs_t0_wt_rep1_24h


title: t_vs_t0_sog1-1_rep2_0

value: mock


title: t_vs_t0_wt_rep2_12h


title: t_vs_t0_wt_rep2_6h


title: High growth (HG) Anterior Pituitary, Week 3, Rep 2 vs. Pituitary Reference Pool (High and Low Growth, Weeks 1, 3, 5, 7)


title: High growth (HG) Anterior Pituitary, Week 1, Rep 1 vs. Pituitary Reference Pool (High and Low Growth, Weeks 1, 3, 5, 7)

source_name: HG, pituitary, week 1

value: posthatch week 1


title: t_vs_t0_wt_rep2_3h


title: t_vs_t0_wt_rep1_12h


title: High growth (HG) Anterior Pituitary, Week 1, Rep 2 vs. Pituitary Reference Pool (High and Low Growth, Weeks 1, 3, 5, 7)

value: anterior pituitary gland


title: High growth (HG) Anterior Pituitary, Week 1, Rep 4 vs. Pituitary Reference Pool (High and Low Growth, Weeks 1, 3, 5, 7)


title: Low growth (LG) Anterior Pituitary, Week 1, Rep 1 vs. Pituitary Reference Pool (High and Low Growth, Weeks 1, 3, 5, 7)

source_name: LG, pituitary, week 1

value: low growth


title: Low growth (LG) Anterior Pituitary, Week 1, Rep 4 vs. Pituitary Reference Pool (High and Low Growth, Weeks 1, 3, 5, 7)

value: male


title: Low growth (LG) Anterior Pituitary, Week 1, Rep 3 vs. Pituitary Reference Pool (High and Low Growth, Weeks 1, 3, 5, 7)


title: t_vs_t0_sog1-1_rep1_0


title: Low growth (LG) Anterior Pituitary, Week 1, Rep 2 vs. Pituitary Reference Pool (High and Low Growth, Weeks 1, 3, 5, 7)


title: t_vs_t0_wt_rep1_3h


title: t_vs_t0_wt_rep1_1h30min


title: t_vs_t0_wt_rep1_45min


title: t_vs_t0_wt_rep2_1h30min


title: t_vs_t0_wt_rep2_20min


title: Reference

city: Heidelberg

first: Wolfgang

last: Wick

address: Im Neuenheimer Feld 400

department: Neurooncology

institute: Ruprecht-Karls University Heidelberg

hyb_protocol: cRNA fragmentation, hybridization, and staining with streptavidin-phycoerythrin and biotinylated anti-streptavidin antibody (Molecular Probes, Leiden, Netherlands)

scan_protocol: Affymetrix Gene-Chip Scanner 3000 using default settings for all parameters

data_processing: GCOS software (Affymetrix), using default settings for all parameters. For normalization, 100 housekeeping genes provided by Affymetrix were used. Relative expression values were calculated from the signal log ratios given by the software and the normal kidney sample was arbitrarily set to 1.0.

source_name: NTk

label_protocol: GeneChip IVT Labelling Kit (Affymetrix)

extract_protocol: Double-stranded cDNA was synthesized from 5–8 µg of total RNA, using SuperScript RTII (Invitrogen) and the oligo-dT-T7 primer (MWG Biotech, Ebersberg, Germany) as described in the manual

value: normal kidney


title: Glioblastoma 2050

value: glioblastoma


title: Glioblastoma 2052


title: Glioblastoma 2053


title: Glioblastoma 2054


title: t_vs_t0_wt_rep1_20min


title: t_vs_t0_wt_rep1_10min


title: Glioblastoma 2048


title: t_vs_t0_wt_rep1_6h


title: t_vs_t0_wt_rep2_0


title: t_vs_t0_wt_rep2_45min


title: THP_2

city: Seattle

first: Molly

last: Ohainle

address: 1100 Fairview Ave N, C2-023

institute: Fred Hutchinson Cancer Research Center

data_processing:
Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18 software, followed by generation of  fastq files using Illumina's bcl2fastq Conversion Software v1.8.4 (http://support.illumina.com/downloads) /bcl2fastq_conversion_software_184.html).
Reads of low quality were filtered out prior to demultiplexing  using FASTX-Toolkit v0.0.13
Reads were trimmed and aligned to the PIKA HIV guide library using Bowtie v1.0.0, allowing 0 mismatches in the guide sequence, followed by tabulation of read counts using R
Genome_build: PIKA HIV sgRNA Library
Supplementary_files_format_and_content: tab delimited files with read counts for each guide sequence

source_name: THP-1 monocytic cell line

growth_protocol: THP-1 monocytic cells are grown in RPMI with 10% FBS and Pen/Strep (supplemented to 10mM HEPES, 4.5 g/L D-Glucose, 0.11 g/L Sodium Pyruvate + Glutamax), passaging between 2e5 cells/mL and 1e6 cells/mL.

extract_protocol:
Genomic DNA was extracted using a QIAamp DNA Blood Midi kit (Qiagen)
Genomic DNA or reverse-transcribed viral RNA were amplified by a two-step PCR (PCR1: 12 cycles, PCR2: 20 cycles) to amplify 20bp sgRNA sequences in the HIV-CRISPR vector. All Viral RNA was amplified for each sample where appropriate. For Genomic DNA samples a total of 500-fold coverage of the 15,414 sgRNAs were amplified (10^6 cells were estimated to contain 6.6μg gDNA) with a maximum of 2μg gDNA per PCR reaction. For each sample, PCR1 reactions were pooled, cleaned up over a QIAquick PCR purification Kit (2 columns per sample), pooled again and used as template for PCR2. For viral RNA, all PCR1 was amplified in the second round. For gDNA, 5uL of pooled PCR1 was used as input for PCR2 (PCR2 primers include Illumina barcodes and adaptor sequences). Amplicons from PCR2 were pooled, purified by double-sided SPRI (AMPureXP, Beckman Coulter), quantified with a Qubit HS dsDNA assay and pooled for sequencing.

treatment_protocol: 8e6 cells (>500X coverage) were transduced with the PIKAHIV library (MOI of 0.75) and selected in 1ug/mL puromycin for 10-14 days. For each replicate, 8e6 cells were infected with or without overnight IFNα treatment with HIV. Cells and viral supernatants were harvested 3 days post-infection.

tag: cell type

value: ZAP-KO THP-1 +CCR5

value: ZAP-KO

tag: ifn treatment

value: yes


title: THP_1


title: Glioblastoma 2051


title: t_vs_t0_wt_rep2_10min

value: 100 Gy Gamma-IR


title: Glioblastoma 2049


title: Glioblastoma 2046


title: Glioblastoma 2047


title: MDA-MB231 RAT-seq

city: Palo Alto

first: Jifan

last: Hu

address: 3801 Miranda Ave, Bldg 100, Room E4-200

department: Palo Alto Veterans Institute for Research

institute: Stanford University Medical School

description: FECR1-interacting DNA identified by RAT-Seq

data_processing:
Library strategy: RAT-Seq
Raw data were filtered with Fastx (version: 0.0.13) and approximately 12 million single-end clean reads of 50bp length from RAT-seq were mapped to hg38 reference genome using Bowtie (version 0.12.8) with default parameters [44]. Only reads with at most one mismatch and a Phred quality score greater than or equal to 30 were kept for further analysis. Multiple reads that map to exact same coordinates were further filtered out as PCR duplicates. The remaining high quality mapping reads were extended to 500bp fragments, which were then used to compute genome-wide coverage at 5kb resolution with "bedtools genomecov" function [45]. The resulting coverage tracks (bedgraph file) were visualized in the UCSC genome browser.
Genome_build: hg38
Supplementary_files_format_and_content: bedgraph

growth_protocol: MDA-MB231 breast cancer cells were fixed with 2% formaldehyde and lysed with hypotonic buffer (10 mM Hepes, pH 7.9, 1.5 mM MgCl2, 10 mM KCl, 0.4% NP-40, RNAase inhibitor 100U/ml, 1x protease inhibitors). After crosslinking, FECR1 was reverse transcribed in situ using a circular RNA-specific complementary primer located at the exon 4-exon 2 splicing site, at 65℃ using Maxima Reverse Transcriptase in the presence of biotin-dCTP. The FECR1 biotin-cDNA chromatin complex was pulled down with streptavidin beads for library sequencing.

extract_protocol:
DNA was extracted by phenol-chloroform-isoamyl alcohol
The FECR1-interacting genomic DNAs was digested by Mbo I and ligated with the NEBNext adaptors (NEBNext® ChIP-Seq Library Prep Master Mix Set for Illumina) to construct the library. The library DNAs were subject to Illumina sequencing

value: breast cancer cell

tag: genome-wide binding targets of


title: myb3r135_rep2_3h_+y

growth_protocol: The Arabidopsis seedlings used in this study were in the Columbia-0 (Col) ecotype and were grown under constant light at 23°C in a Percival growth cabinet.

extract_protocol:
6 seedlings were collected and total RNA was isolated using the Quick-RNA MiniPrep kit (Zymo Research, Cat# R1055).
2.0μg of total RNA from each genotype was used to generate mRNA-seq libraries using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB E7490) for mRNA purification and NEBNext UltraII RNA Library Prep Kit for Illumina (NEB E7770). Sera-Mag Magnetic SpeedBeads (Thermo scientific, Cat# 65152105050250) were used for all the size selection and clean-up steps. The resulting libraries were equally pooled and sequenced with in SE50 mode using a HiSeq2500 machine.

treatment_protocol: 100 Gy using a Co60 radioactive source at a dose-rate of 12.8 Gy/min


title: myb3r135_rep2_3h_-y


title: wt_rep2_3h_+y


title: wt_rep1_3h_+y


title: myb3r135_rep1_3h_+y


title: myb3r135_rep1_3h_-y


title: wt_rep2_3h_-y


title: wt_rep1_3h_-y


title: gIR_vs_mock_wt_rep2_20min_-y


title: gIR_vs_mock_wt_rep2_1h30min_-y


title: gIR_vs_mock_wt_rep2_24h_-y


title: gIR_vs_mock_wt_rep1_1h30min_-y


title: gIR_vs_mock_wt_rep1_24h_-y


title: gIR_vs_mock_wt_rep1_20min_-y


title: gIR_vs_mock_wt_rep1_10min_-y


title: gIR_vs_mock_wt_rep2_10min_-y


title: gIR_vs_mock_wt_rep2_1h30min_+y


title: gIR_vs_mock_wt_rep1_24h_+y


title: gIR_vs_mock_wt_rep1_1h30min_+y


title: gIR_vs_mock_wt_rep2_20min_+y


title: Glioblastoma 2044


title: Glioblastoma 2043


title: Glioblastoma 2045


title: gIR_vs_mock_wt_rep2_10min_+y


title: gIR_vs_mock_DREMmodel_sog1-1_rep2_24h_-y

extract_protocol:
8 seedlings were collected and total RNA was isolated using the Quick-RNA MiniPrep kit (Zymo Research, Cat# R1055).
2.0μg of total RNA from each genotype was used to generate mRNA-seq libraries using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB E7490) for mRNA purification and NEBNext Ultra RNA Library Prep Kit for Illumina (NEB E7530). Sera-Mag Magnetic SpeedBeads (Thermo scientific, Cat# 65152105050250) were used for all the size selection and clean-up steps. The resulting libraries were equally pooled and sequenced with in SE50 mode using a HiSeq2500 machine.


title: gIR_vs_mock_DREMmodel_sog1-1_rep1_24h_-y


title: Glioblastoma 2040


title: gIR_vs_mock_DREMmodel_sog1-1_rep2_6h_-y


title: gIR_vs_mock_DREMmodel_sog1-1_rep1_12h_-y


title: gIR_vs_mock_wt_rep2_24h_+y


title: gIR_vs_mock_DREMmodel_sog1-1_rep1_6h_-y


title: gIR_vs_mock_DREMmodel_sog1-1_rep1_3h_-y


title: gIR_vs_mock_DREMmodel_sog1-1_rep2_3h_-y


title: gIR_vs_mock_DREMmodel_sog1-1_rep2_1h30min_-y


title: gIR_vs_mock_DREMmodel_sog1-1_rep1_1h30min_-y


title: UPCISCC152

city: Houston

first: Curtis

last: Pickering

address: 1515 Holcombe Blvd

department: Head and Neck Surgery

institute: The University of Texas MD Anderson Cancer Center

data_processing:
Alignment was performed using tophat2
Aligment quality was accessed by fastqc, samtools and htseq-qa
Counting reads was using htseq-count with parameters: python -m HTSeq.scripts.count -s no -t exon sortByName.sam.mod REFFILE > OUTFILE
The normalization of raw read counts was performed by edgeR package in R. The procedure was described in limma package in R. The features were first filtered out if the total counts less than 50
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include normalized values for each Sample.

extract_protocol:
RNeasy Plus (Qiagen)
TruSeq Stranded Total RNA Sample Prep Kit (Illumina); 75-bp paired-end (Illumina HiSeq3000)

tag: cell line

value: head and neck squamous cell carcinoma (HNSCC) cell line


title: VU147T


title: gIR_vs_mock_DREMmodel_sog1-1_rep2_20min_-y


title: JHU029


title: UMSCC104


title: UMSCC14B


title: Glioblastoma 2042


title: MDA686TU


title: gIR_vs_mock_wt_rep1_20min_+y


title: MDA1986LN


title: gIR_vs_mock_DREMmodel_sog1-1_rep1_20min_-y


title: gIR_vs_mock_wt_rep1_10min_+y


title: Glioblastoma 2039


title: MDA1186


title: gIR_vs_mock_DREMmodel_sog1-1_rep2_12h_-y


title: gIR_vs_mock_DREMmodel_sog1-1_rep2_24h_+y


title: JHU011


title: HELA

value: HELA

value: cervical squamous cell carcinoma (CESC) cell line


title: Glioblastoma 2041


title: HT3


title: CASKI

value: CASKI


title: gIR_vs_mock_DREMmodel_sog1-1_rep1_24h_+y


title: gIR_vs_mock_DREMmodel_sog1-1_rep2_12h_+y


title: UMSCC4


title: gIR_vs_mock_DREMmodel_sog1-1_rep1_12h_+y


title: X1483


title: UMSCC22A


title: UPCISCC090


title: UMSCC47


title: UMSCC11A


title: gIR_vs_mock_DREMmodel_sog1-1_rep2_3h_+y


title: gIR_vs_mock_DREMmodel_sog1-1_rep2_6h_+y


title: SqCC.Y1


title: UMSCC14A


title: gIR_vs_mock_DREMmodel_sog1-1_rep1_6h_+y


title: SW756


title: UMSCC11B


title: SCC25


title: PCI15A


title: MS751


title: ME180


title: gIR_vs_mock_DREMmodel_sog1-1_rep2_1h30min_+y


title: gIR_vs_mock_DREMmodel_sog1-1_rep1_1h30min_+y


title: MDA1586


title: gIR_vs_mock_DREMmodel_sog1-1_rep2_20min_+y


title: HMS001


title: UMSCC3


title: gIR_vs_mock_DREMmodel_sog1-1_rep1_20min_+y


title: C4.II


title: MDA1386LN


title: gIR_vs_mock_DREMmodel_sog1-1_rep1_3h_+y


title: gIR_vs_mock_DREMmodel_wt_rep1_24h_-y

value: wild-type


title: UPCISCC154


title: UMSCC22B


title: UTSCC45


title: C33A


title: UMSCC17B


title: gIR_vs_mock_DREMmodel_wt_rep2_24h_-y

value: mock


title: DETROIT562


title: X183


title: UMSCC17A


title: UMSCC10B


title: gIR_vs_mock_DREMmodel_wt_rep2_12h_-y


title: gIR_vs_mock_DREMmodel_wt_rep2_6h_-y


title: gIR_vs_mock_DREMmodel_wt_rep1_12h_-y


title: UDSCC2


title: JHU022


title: HN31


title: HN30


title: gIR_vs_mock_DREMmodel_wt_rep1_6h_-y


title: gIR_vs_mock_DREMmodel_wt_rep2_3h_-y


title: SIHA

value: SIHA


title: SCC61


title: MDA686LN


title: gIR_vs_mock_DREMmodel_wt_rep1_3h_-y


title: MDA1386TU


title: gIR_vs_mock_DREMmodel_wt_rep2_1h30min_-y


title: X584A2


title: PE.CAPJ34


title: C4.I


title: TR146


title: MDA886LN


title: gIR_vs_mock_DREMmodel_wt_rep1_1h30min_-y


title: LIN-41_IP_3

city: Basel

first: Sarah

last: Carl

address: Maulbeerstrasse 66

department: Epigenetics

country: Switzerland

institute: Friedrich Miescher Institute

description: 671F11-1_151210_D00404_0198_BC8154ANXX_CAGATC-NoIndex_L004

data_processing:
Basecalling was performed using RTA v. 1.13.48.
PCR duplicates were removed by collapsing reads with an identical 5’ end coordinate to a single read using the SAMtools rmdup command.
Reads were aligned to the ce10 (WS220) genome assembly using the qAlign function from the QuasR R package (v. 1.20.0) with the parameter "splicedAlignment = TRUE", which calls the SpliceMap aligner with default parameters.
Gene expression was quantified using WS220 annotations downloaded from WormBase. The qCount function in the QuasR package was used to count reads overlapping all annotated exons for each gene.
Genome_build: ce10 (WS220)
Supplementary_files_format_and_content: Tab-delimited file. First column contains gene names (WormBase identifiers), following columns contain raw counts of reads overlapping each gene for each sample, after removing duplicate reads.

organism: Caenorhabditis elegans

growth_protocol: Embryos were extracted from gravid adults with bleaching solution (30% (v/v) sodium hypochlorite (5% chlorine) reagent, 750 mM KOH) and plated on enriched peptone plates with Escherichia coli NA22 bacteria. The plates were incubated at 25 °C for approximately 30 hours to harvest the resulting semi-synchronous worm populations.

extract_protocol:
Lysis of pellets of about 1 ml with L3/L4 stage worms was performed in extraction buffer (50 mM HEPES/KOH (pH 7.4 at 4 °C), 150 mM KCl, 5 mM MgCl2, 0.1% (v/v) Triton X-100, 10% (w/v) glycerol, 1 mM PMSF, 7 mg/ml cOmplete Protease Inhibitor Tablets (EDTA-free), 200 U/ml SUPERase In RNase Inhibitor), by adding liquid nitrogen and grinding with mortar and pestle. All subsequent steps were performed at 4 °C. Lysates were centrifuged at 12,000g for 10 min and the supernatant used for Anti-FLAG IPs. 3 mg total protein were incubated with 30 µl of anti-FLAG M2 magnetic beads (Sigma–Aldrich; M8823) for 3 h on a rotating wheel. With extraction buffer without protease and RNase inhibitors, the beads were washed 5 times for 5 min. Finally, the bound RNA was extracted by directly adding Tri Reagent to the beads. 5 IPs were performed in parallel for each condition to recover a sufficient amount of RNA. Using an aliquot of remaining input lysate, input RNA was extracted with Tri Reagent.
TruSeq Stranded mRNA HT Sample Prep Kit (Illumina; RS 122 2103)

treatment_protocol: Worms were washed off the plates and subsequently washed 3 additional times with M9 buffer (42 mM Na2HPO4, 22 mM KH2PO4, 86 mM NaCl, 1 mM MgSO4) and worm pellets frozen at -80 °C.

tag: developmental stage

value: L3/L4 stage animals

tag: genotype/variation

value: whole worm

tag: rip anitbody


title: SART-3_input_2

description: 671F4-1_151210_D00404_0198_BC8154ANXX_GCCAAT-NoIndex_L003

value: anti-FLAG M2 magnetic beads (Sigma–Aldrich; M8823)


title: SART-3_IP_3

description: 671F12-1_151210_D00404_0198_BC8154ANXX_CTTGTA-NoIndex_L004


title: SART-3_IP_2

description: 671F10-1_151210_D00404_0198_BC8154ANXX_GCCAAT-NoIndex_L004


title: SART-3_input_3

description: 671F6-1_151210_D00404_0198_BC8154ANXX_CTTGTA-NoIndex_L003


title: LIN-41_input_3

description: 671F5-1_151210_D00404_0198_BC8154ANXX_CAGATC-NoIndex_L003


title: gIR_vs_mock_DREMmodel_wt_rep2_20min_-y

tag: treatment


title: SCC4


title: gIR_vs_mock_DREMmodel_wt_rep1_20min_-y


title: SCC9


title: LIN-41_IP_2

description: 671F9-1_151210_D00404_0198_BC8154ANXX_ACAGTG-NoIndex_L004


title: SCC15


title: gIR_vs_mock_DREMmodel_wt_rep1_24h_+y


title: LIN-41_input_2

description: 671F3-1_151210_D00404_0198_BC8154ANXX_ACAGTG-NoIndex_L003


title: OSC19


title: SART-3_IP_1

description: 671F8-1_151210_D00404_0198_BC8154ANXX_TGACCA-NoIndex_L004


title: UMSCC85


title: UMSCC33


title: PCI13


title: gIR_vs_mock_DREMmodel_wt_rep2_12h_+y


title: SART-3_input_1

description: 671F2-1_151210_D00404_0198_BC8154ANXX_TGACCA-NoIndex_L003


title: gIR_vs_mock_DREMmodel_wt_rep1_12h_+y


title: MSK922


title: HN4


title: UMSCC6


title: CAL27


title: UMSCC19


title: PCI15B


title: gIR_vs_mock_DREMmodel_wt_rep2_24h_+y


title: PCI24


title: HN5


title: UMSCC25


title: LIN-41_input_1

description: 671F1-1_151210_D00404_0198_BC8154ANXX_CGATGT-NoIndex_L003


title: gIR_vs_mock_DREMmodel_wt_rep2_3h_+y


title: FaDu

value: FaDu


title: UMSCC1


title: gIR_vs_mock_DREMmodel_wt_rep2_1h30min_+y