title: ClonTechv4_Xins-cell-35

description:
L23782
ClonTechv4_read_counts.xlsx


title: GP_NF_06_HYP

status: Public on Jun 14 2018

type: SRA

city: Jena

first: Marco

last: Groth

address: Beutenbergstraße 11

department: Core Facility - Next Generation Sequencing

country: Germany

institute: Leibniz Institute on Aging - FLI

library_source: transcriptomic

data_processing:
Extraction of read information in FastQ format was done using the tool bcl2astq v1.8.4 (provided by Illumina).
Reads were mapped using STAR (v2.4.1d) with a maximum mismatch of 6% and a minimum aligned length of 90%. Reads mapped to multiple loci were discarded.
Reads per gene were counted using HTSeq framework (0.6.1p1)
Genome_build: genome (cavpor3) can be download from UCSC (ftp://hgdownload.cse.ucsc.edu/goldenPath/cavPor3/bigZips/)
Supplementary_files_format_and_content: The Excel sheet includes raw counts for all genes and each sample.

molecule: polyA RNA

organism: Cavia porcellus

source_name: hypothalamus

extract_protocol:
Extraction was done as described in Bens et al. 2016. (PMID:26763976)
Library preparation was done using Illumina's TruSeq RNA Library Prep Kit v2 kit following the manufacturer's description.

tag: strain

tag: Sex

value: female

tag: tissue

value: hypothalamus

tag: age

value: 0.96 years

tag: reproductive status

value: non-breeder


title: ClonTechv4_Xins-cell-37

city: Kansas City

first: Hua

last: Li

state: MO

address: 1000 E 50th Street

country: USA

institute: Stowers Institute for Medical Research

description:
L23784
ClonTechv4_read_counts.xlsx

data_processing:
for sample 1 to sample 160: Basecalling and bcl to fastq generation was done using bcl2fastq2 v2.18 from illumina.
for sample 1 to sample 160: RNA-seq was aligned to smed transcriptome smed_20140614 defined in GEO submission GSE72389 using Bowtie 2 version 2.2.9
for sample 1 to sample 160: Read counts for each transcripts are generated using samtools idxstats (version 1.3.1)
for sample 161 to sample 162: Cell Range pipleine (v1.3), mkfastq and count, was used to generate fastq files, perform alignments, filter and generate UMI counts.
Genome_build: Schmidtea mediterranea transcriptome is available from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE72389
Supplementary_files_format_and_content: for sample 1 to sample 160: Read counts in excel files
Supplementary_files_format_and_content: for sample 161 to sample 162: Normalized expression values in csv files

molecule: total RNA

organism: Schmidtea mediterranea

growth_protocol: Asexual S. mediterranea (strain CIW4) and sexual S2F8 animals were maintained at 20 °C as previously described (Newmark and Sanchez Alvarado, 2000). For all experiments, animals were starved for at least 7 days.

extract_protocol:
For plate based single cell RNA-seq assay, cells were harvested into 96-well plate directly, and cDNA libraries were prepared using SMART-Seq v4 Ultra Low Input RNA Kit (Takara) as per manufacturer’s recommendations using 18 cycles of amplification.  Specifically, reactions were run at  the recommended volume.  Libraries were made using the Nextera XT kit (Illumina). After the PCR step, the libraries were individually cleaned with 0.8x AMPure XP SPRI beads (Beckman Coulter), and eluted in Resuspension Buffer. The libraries were quantified using Quant-IT DNA High-Sensitivity Assay Kit (Invitrogen) and examined using a high sensitivity DNA chip (Agilent). All libraries were then combined to one pool at equimolar concentrations for sequencing.  Finally, samples were sequenced deeply using a HiSeq 2500 sequencer.
cDNA libraries were prepared using SMART-Seq v4 Ultra Low Input RNA Kit (Takara) as per manufacturer’s recommendations using 18 cycles of amplification.

treatment_protocol: 1) For regenerating sample, animals were amputated to produce pre-pharyngeal pieces; 2) GammaCell 40 Exactor irradiator exposed animals to 1,250  rad for sublethal irradiations.

tag: genotype

value: Wild-type

tag: treatment

value: 3days after amputation from small fragments


title: ClonTechv4_Xins-cell-33

description:
L23780
ClonTechv4_read_counts.xlsx


title: GP_NF_03_HYP

value: 0.97 years


title: ClonTechv4_Xins-cell-7

description:
L23754
ClonTechv4_read_counts.xlsx


title: ClonTechv4_X1-cell-18

description:
L23715
ClonTechv4_read_counts.xlsx


title: ClonTechv4_Xins-cell-40

description:
L23787
ClonTechv4_read_counts.xlsx


title: GP_BF_15_HYP

value: 0.95 years

value: breeder


title: ClonTechv4_Xins-cell-34

description:
L23781
ClonTechv4_read_counts.xlsx


title: ClonTechv4_Xins-cell-36

description:
L23783
ClonTechv4_read_counts.xlsx


title: ClonTechv4_Xins-cell-39

description:
L23786
ClonTechv4_read_counts.xlsx


title: GP_BF_12_HYP


title: GP_BF_14_HYP


title: GP_BF_05_HYP


title: GP_BF_02_HYP


title: GP_NM_30_HRT

source_name: heart

value: male

value: heart


title: GP_BF_01_HYP


title: GP_NM_29_HRT


title: GP_NM_28_HRT


title: GP_NF_08_HYP


title: GP_NM_18_HRT

value: 0.74 years


title: GP_NM_23_HRT


title: GP_NM_19_HRT


title: GP_BM_24_HRT


title: GP_BM_22_HRT


title: GP_BM_21_HRT


title: GP_BM_25_HRT


title: GP_NF_11_HRT


title: GP_NF_09_HRT


title: GP_BM_16_HRT


title: GP_NF_08_HRT


title: GP_BM_20_HRT


title: ClonTechv4_Xins-cell-38

description:
L23785
ClonTechv4_read_counts.xlsx


title: GP_NF_13_HRT


title: GP_NF_06_HRT


title: GP_NF_03_HRT


title: GP_BF_15_HRT


title: GP_BF_12_HRT


title: GP_BF_14_HRT


title: GP_BF_02_HRT


title: GP_BF_05_HRT


title: GP_NM_28_CER

source_name: cerebellum

value: cerebellum


title: GP_BF_01_HRT


title: GP_NM_29_CER


title: GP_BM_25_CER


title: GP_BM_24_CER


title: GP_BM_22_CER


title: GP_BM_16_CER


title: GP_NF_11_CER


title: GP_NF_13_CER


title: GP_BM_21_CER


title: GP_NF_09_CER


title: GP_BM_20_CER


title: GP_NF_06_CER


title: GP_NF_03_CER


title: GP_BF_15_CER


title: GP_BF_12_CER


title: GP_BF_05_CER


title: GP_BF_14_CER


title: GP_BF_01_CER


title: GP_NM_30_CER


title: GP_NM_23_CER


title: GP_NM_19_CER


title: GP_NM_18_CER


title: GP_NM_23_ADR

source_name: adrenal gland

value: adrenal gland


title: GP_NM_19_ADR


title: GP_NM_28_ADR


title: GP_NM_18_ADR


title: GP_BM_25_ADR


title: GP_BM_24_ADR


title: GP_BM_21_ADR


title: GP_BM_22_ADR


title: GP_BM_16_ADR


title: GP_NF_13_ADR


title: GP_BM_20_ADR


title: GP_NF_08_CER


title: GP_BF_02_CER


title: ClonTechv4_X1-cell-5

description:
L23702
ClonTechv4_read_counts.xlsx


title: GP_BF_05_ADR


title: GP_NF_03_ADR


title: GP_NF_11_ADR


title: GP_BF_14_ADR


title: GP_NF_08_ADR


title: GP_BF_01_ADR


title: GP_BF_02_ADR


title: GP_NM_30_ADR


title: GP_NF_06_ADR


title: GP_NM_29_ADR


title: WT2_S11825

city: Milan

first: Peter

last: De Wulf

address: via Adamello 16

department: Department of Experimental Oncology

country: Italy

institute: European Institute of Oncology

description:
MATa ade2-1 trp1-1 can1-100 his3-11,15 leu2-3,112 ura3-1 RIO1-AID PADH1-OsTIR1.
Total RNA depleted of rRNA.

data_processing:
Sequence reads were filtered by length, the reads less than 74 bp were filtered out.
Sequence reads were mapped to the sacCer3 reference genome using TopHat v2.0.8 with parameters --library-type=fr-unstranded.
Readcounts were obtained using HTSeq-count with parameters -m intersection-strict -s no -a 1 -t exon -i gene_id.
Differential expression was performed using the R package DESeq.
Genome_build: sacCer3
Supplementary_files_format_and_content: Tab delimited file containing raw count of sequencing reads.

organism: Saccharomyces cerevisiae

source_name: RIO1-AID PADH1-OsTIR1 strain not treated with auxin.

growth_protocol: Cells were grown exponentially at 23°C in YPD medium.

extract_protocol:
Total RNA was isolated from 5ml of exponentially grown yeast culture (OD600 = 0.5-1.0). The cells were harvested (4°C; 14,000 rpm), washed with ice-cold buffer (50mM sodium acetate pH 5.2, 10mM EDTA pH 8.0) and stored at -80°C. RNA was extracted with hot phenol and depleted of total ribosomal RNA (rRNA) with the Ribo-Zero Gold rRNA Removal Kit Yeast (Illumina). Residual DNA was removed with DNase I (30min, 37°C, New England Bioloabs) and further purified with the RNeasy Kit (Qiagen). RNA concentrations were measured with a NanoDrop 2000c UV-Vis Spectrophotometer (Thermo Scientific), and RNA quality and integrity examined with a 2100 Bioanalyzer.
Libraries were prepared according to the Illumina Script seq manual. Briefly 5μg of total RNA was depleted of total ribosomal RNA (rRNA) with the Ribo-Zero Gold rRNA Removal Kit Yeast.  Two µl of rRNA-depleted RNA was then converted into a cDNA library with the ScriptSeq v2 RNA-Seq Library Preparation Kit (Illumina). cDNA was PCR-amplified and converted into double-strand cDNA using a forward primer hybridizing to the cDNA’s 3’-end and a reverse primer containing a 5’-Illumina index barcode. The cDNAs were then treated with Exonuclease I (37°C, 15min)(Illumina) and purified with MinElute PCR Purification Kit (Qiagen). The concentration of the cDNA library was quantified with a Qubit Fluorometer (Invitrogen) and its quality examined on a 2100 Bioanalyzer using the High Sensitivity DNA assay (Agilent Technologies).

treatment_protocol: To induce the degradation of Rio1-AID, 500μM auxin (Sigma-Aldrich) was added to the RIO1-AID PADH1-OsTIR1 culture (not added to the control culture).

tag: protocol

value: control


title: D1_S11827

source_name: RIO1-AID PADH1-OsTIR1 strain treated for 1h with 500uM auxin.

value: depletion of Rio1


title: Be_1

description:
Be_1.bam
MATa ade2-1 trp1-1 can1-100 his3-11,15 leu2-3,112 ura3-1, RIO1-AID, PADH1-OsTIR1.

library_source: genomic

data_processing:
Sequence reads were mapped using bwa-0.6.2
The peaks were called using SICER 1.1 with the following parameters: 1 200 150 0.8 600 0.01
Genome_build: sacCer3
Supplementary_files_format_and_content: .bed

molecule: genomic DNA

source_name: Saccharomyces cerevisiae parent strain endogenously expressing untagged Rio1 (Input DNA)

growth_protocol: Wld-type RIO1 and RIO1-AID PADH1-OsTIR1 yeast strains (genetic background: MATa ade2-1 trp1-1 can1-100 his3-11,15 leu2-3,112 ura3-1) were grown exponentially till an OD600 = 1 in YPD medium at 23°C.

extract_protocol:
Lysates were clarified from sonicated nuclei and Rio1-AID::DNA complexes isolated with an anti-AID antibody (CosmoBio, Catalog No. BRS-APC004AM, 100ul) bound to protein A agarose beads (Life Technologies).
Libraries were prepared according to Illumina protocolsl. In short, 1-5ng of input and chromatin immunoprecipitated DNA was blunt-ended and phosphorylated with T4 DNA Polymerase and T4 Polynucleotide Kinase, respectively. A single adenine was added to the 3'-ends using DNA Polymerase I Klenow allowing for ligation to an adapter containing a single tyrosine overhang. The ligation products were purified by Agencourt AMPure XP beads, and the DNA PCR-amplified (PfuUltra II Fusion HS DNA Polymerase) to enrich for fragments with adapters on both ends (Biomek FX, Beckman Coulter). cDNA library concentrations were measured with a Qubit ds DNA HS kit and its size distribution and quality evaluated on a Bioanalyzer 2100 prior to cluster generation.

tag: endogenously expressing

value: Rio1 (untagged)


title: GP_BF_12_ADR

value: female


title: GP_NF_09_ADR


title: Ip_1

description:
the peak.bed file is called using Be_1.bam as INPUT
MATa ade2-1 trp1-1 can1-100 his3-11,15 leu2-3,112 ura3-1, RIO1-AID, PADH1-OsTIR1.

source_name: Saccharomyces cerevisiae endogenously expressing AID-Rio1 (Rio1-AID immunoprecipitated DNA)

tag: chip antibody

value: anti-AID antibody (CosmoBio, Catalog No. BRS-APC004AM, 100ul)


title: Seaweed 1 sample 1

city: Leiden

first: Ron

middle: P

last: Dirks

address: Sylviusweg 74

country: Netherlands

institute: Future Genomics Technologies BV

description:
Sample 4
Origin of specimen: commercial salmon farm (Meridian Salmon, Furnace, UK)
DiffExpr_diet_sw1_versus_control_Ssal_ref.xlsx
DiffExpr_diet_sw1_versus_control.xlsx

data_processing:
Illumina Casava software used for basecalling: SCS2.2.38/RTA1.18.61
Reads were aligned to Salmo salar cDNA sequences downloaded from NCBI (strategy 1) or to a de novo assembled Salmo salar head kidney cDNA contig reference (strategy 2) using TopHat (version 2.0.5) (Trapnell et al., 2009)
The resulting files were filtered using SAMtools (version 0.1.18) (Li et al., 2009) to exclude secondary alignment of reads
Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq (version 0.5.3p9) (Anders and Huber, 2014)
Differentially expressed genes were identified using DESeq (Anders and Huber, 2010) and data were further processed using Microsoft Excel
Genome_build: Salmo_salar_head_kidney_cDNA.fa (strategy 2)
Supplementary_files_format_and_content: (Strategy 1) DiffExpr_diet_sw1_versus_control_Ssal_ref.xlsx and DiffExpr_diet_sw2_versus_control_Ssal_ref.xlsx: Microsoft Office Excel file (.xlsx) with the following columns: Gene; Sample x; Sample x; Sample x; Sample x; Sample x; Sample x; baseMean; baseMeanA; baseMeanB; foldChange; log2FoldChange; pval; padj
Supplementary_files_format_and_content: (Strategy 2) DiffExpr_diet_sw1_versus_control.xlsx and DiffExpr_diet_sw2_versus_control.xlsx: Microsoft Office Excel file (.xlsx) with the following columns: Contig ID; Description; Sample x; Sample x; Sample x; Sample x; Sample x; Sample x; baseMean; baseMeanA; baseMeanB; foldChange; log2FoldChange; pval; padj

organism: Salmo salar

source_name: head kidney

extract_protocol:
Head kidney was dissected from each individual, and stored in RNAlater (Ambion) at -80ºC till RNA extraction. Total RNA was isolated from homogenized samples (TissueRuptor, Qiagen) using the miRNeasy mini kit according to the manufacturer’s instructions (Qiagen), and analyzed with an Agilent Bioanalyzer 2100 total RNA Nano series II chip (Agilent). A transcriptome library for each sample was prepared from 2 microgram total RNA, using the TruSeq™ RNA Sample Prep Kit v2 following the manufacturer’s instructions (Illumina Inc.).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: head kidney

tag: diet

value: LPS-challenged Salmo salar specimens after a 42-day seaweed


title: Seaweed 2 sample 3

description:
Sample 9
Origin of specimen: commercial salmon farm (Meridian Salmon, Furnace, UK)
DiffExpr_diet_sw2_versus_control_Ssal_ref.xlsx
DiffExpr_diet_sw2_versus_control.xlsx


title: Seaweed 1 sample 3

description:
Sample 6
Origin of specimen: commercial salmon farm (Meridian Salmon, Furnace, UK)
DiffExpr_diet_sw1_versus_control_Ssal_ref.xlsx
DiffExpr_diet_sw1_versus_control.xlsx


title: Fishmeal-based control sample 3

description:
Sample 3
Origin of specimen: commercial salmon farm (Meridian Salmon, Furnace, UK)
DiffExpr_diet_sw1_versus_control_Ssal_ref.xlsx
DiffExpr_diet_sw2_versus_control_Ssal_ref.xlsx
DiffExpr_diet_sw1_versus_control.xlsx
DiffExpr_diet_sw2_versus_control.xlsx


title: GP_BF_15_ADR


title: Seaweed 1 sample 2

description:
Sample 5
Origin of specimen: commercial salmon farm (Meridian Salmon, Furnace, UK)
DiffExpr_diet_sw1_versus_control_Ssal_ref.xlsx
DiffExpr_diet_sw1_versus_control.xlsx


title: DNAM-1- NK subsets from 17Day AML Spleen

city: Tianjin

first: Guo Guang

last: Zheng

state: Tianjin

address: Blood Hospital,288 Nanjing Road,Heping District

department: Institute of Hematology & Blood Hospital

country: China

institute: Chinese Academy of Medical Science& Peking Union  Medical College

data_processing:
Base calling was done by BGISEQ-500.
Read pairs with low quality in either read were filtered out (10% bases with N or 50% bases with Q5).
Alignment was performed against RefSeq by bowtie2 (version 2.2.5).
FPKM values of each gene for each sample were measured via RSEM (version v1.2.12).
Genome_build: RefSeq
Supplementary_files_format_and_content: *txt: Tab-delimited text files include FPKMs.

organism: Mus musculus

source_name: DNAM-1- NK cells, AML spleen

extract_protocol:
Sorted DNAM-1+ and DNAM-1- NK cells were harvested and resuspended in 350ul RLT and 3.5ul β-Me. Total RNA was exacted by QIAGEN RNeasy Mini Kit (CAT 74103).
1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISEQ-500 protocols.

treatment_protocol: GFP+ leukemia cells were isolated from leukemia mice and transplanted into 6-8 weeks old C57BL/6J mice (1×10e6 cells/mouse) without irradiation. All mice suffered AML with a survival time of 35 to 40 days. DNAM-1+ and DNAM-1- NK cells were sorted from spleen of leukemia mice at 0d and 17d.

tag: strain/background

value: 6-8 weeks

tag: time point post-transplantation

value: day 17

value: AML spleen

tag: cell type

value: DNAM-1- natural killer cells


title: WT3_S11826


title: Seaweed 2 sample 2

description:
Sample 8
Origin of specimen: commercial salmon farm (Meridian Salmon, Furnace, UK)
DiffExpr_diet_sw2_versus_control_Ssal_ref.xlsx
DiffExpr_diet_sw2_versus_control.xlsx


title: WT1_S11824


title: DNAM-1+ NK subsets from Normal Spleen

source_name: DNAM-1+ NK cells, normal spleen

value: day 0

value: Normal spleen

value: DNAM-1+ natural killer cells


title: RNA-seq_Ssrp1-KD_rep1 (ERCC spike-in)

status: Public on Jun 13 2018

city: Cologne

last: Tessarz

state: Nordrhein-Westfalen

address: Joseph-Stelzman-Str 9b

institute: Max Planck Institute

description:
processed data file: RNAseq.limma.allgenes.tab
processed data file: Normalized.counts.RNA-seq.Control_vs_Ssrp1KD.txt

data_processing:
RNA-seq  files were aligned using STAR (v 2.5.1b). Counts were normalized using edgeR and differential expression was performed with limma.
Genome_build: mm10

source_name: mESCs

growth_protocol: The E14 cell line (mESCs) was cultured at 37 °C, 7.5% CO2, on 0.1% gelatin coated plates, in DMEM + GlutaMax™ (Gibco) with 15% fetal bovine serum (Gibco), MEM non- essential amino acids (Gibco), penicillin/streptomycin (Gibco), 550 µM 2-mercaptoethanol (Gibco), and 10 ng/ml of leukaemia inhibitory factor (LIF) (eBioscience). 293T (HEK), N2a, and B16 cell lines were cultured at 37 °C, 5% CO2 in DMEM + GlutaMax™ (Gibco) with 10% fetal bovine serum (Gibco), and penicillin/streptomycin (Gibco).

extract_protocol: Forty-eight hours (48h) after transfection, puromycin (2 µg /ml) selection was applied for an additional 24h period, before cell collection and RNA preparation. Total RNA was obtained via phenol-chloroform extraction (QIAzol Lysis Reagent – QIAGEN) followed by purification via Quick-RNA™ MicroPrep (Zymo Research). ERCC spike-in controls were added according to the manufacturer instructions

tag: cell line

value: E14 cell line

value: Ssrp1 knock down


title: RNA-seq_Ssrp1-KD_rep4 (ERCC spike-in)


title: DNAM-1+ NK subsets from 17Day AML Spleen

source_name: DNAM-1+ NK cells, AML spleen


title: RNA-seq_Ssrp1-KD_rep2 (ERCC spike-in)


title: RNA-seq_Ssrp1-KD_rep3 (ERCC spike-in)


title: Fishmeal-based control sample 1

description:
Sample 1
Origin of specimen: commercial salmon farm (Meridian Salmon, Furnace, UK)
DiffExpr_diet_sw1_versus_control_Ssal_ref.xlsx
DiffExpr_diet_sw2_versus_control_Ssal_ref.xlsx
DiffExpr_diet_sw1_versus_control.xlsx
DiffExpr_diet_sw2_versus_control.xlsx


title: Fishmeal-based control sample 2

description:
Sample 2
Origin of specimen: commercial salmon farm (Meridian Salmon, Furnace, UK)
DiffExpr_diet_sw1_versus_control_Ssal_ref.xlsx
DiffExpr_diet_sw2_versus_control_Ssal_ref.xlsx
DiffExpr_diet_sw1_versus_control.xlsx
DiffExpr_diet_sw2_versus_control.xlsx


title: D3_S11829


title: RNA-seq_Control_rep4 (ERCC spike-in)


title: D2_S11828


title: RNA-seq_Control_rep3 (ERCC spike-in)


title: Seaweed 2 sample 1

description:
Sample 7
Origin of specimen: commercial salmon farm (Meridian Salmon, Furnace, UK)
DiffExpr_diet_sw2_versus_control_Ssal_ref.xlsx
DiffExpr_diet_sw2_versus_control.xlsx


title: RNA-seq_Control_rep1 (ERCC spike-in)


title: Patient 43, conv sample, technical replicate 2

city: New York

first: Andrew

last: Kasarskis

state: New York

address: 1425 Madison Ave

department: Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Sequencer-generated base call (BCL) files were converted to FASTQ files and the multiplexed samples were separated using bcl2fastq
Demultiplexed fastq were assessed for sequencing quality using FastQC (version 0.11.4, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
The fastq files were quality filtered by using FASTAX Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/) with the invocation fastq_quality_filter -q 30 -p 50 -v -Q 33
Sequencing reads that met all quality control requirements were aligned to the latest human reference genome (GRCh38) using HISAT2 (version 2.0.4)
Gene expression in units of overlapping read counts per million were obtained by using the htseq-count script from HTseq on SAM files of preprocessed RNA-seq alignments.
Counts per million were normalized using the voom methodology and expression profiles were modeled using mixed-effect models in limma (version 3.30.6)
Genome_build: GRCh38
Supplementary_files_format_and_content: csv file with the following output: lgFCH_AcuteVsConv: log2 of the fold change in expression between acute and convalescent timepoints, FCH_AcuteVsConv: fold change in expression between acute and convalescent timepoints, pvals_AcuteVsConv, fdrs_AcuteVsConv, StatusFCH2FDR0.05_AcuteVsConv, a cutoff for |fold change| >2 and FDR <0.05. It is -1 if the gene is fold change <-2 and FDR <0.05, and it is +1 if the gene is fold change >2 and FDR <0.05. Otherwise it is 0.

organism: Homo sapiens

source_name: Whole blood

extract_protocol:
Whole blood collected in PAXgene Boold RNA Tube
Total RNA was extracted from PAXgene RNA blood with the PAXgene Blood RNA Kit (Qiagen) by following manufacturers’ instructions including DNase digestion and an additional clean-up using RNeasy MinElute kit (Qiagen). Purified RNA samples were quantified by Qubit 3.0 fluorometer with RNA High Sensitivity Assay kit (Thermo-Fisher). The quality of the RNA was confirmed by TapeStation 2200 with the RNA High Sensitivity ScreenTape (Agilent Technologies).
To prepare the 96 samples’ libraries, ribosomal RNA (rRNA) and globin mRNA were removed from 200ng total RNA, and the remaining RNA was fragmented and primed for cDNA synthesis using TruSeq Total Stranded RNA HT kit with Ribo-Zero Globin on a Microlab STAR automated liquid handling system (Hamilton). The libraries were barcoded with TruSeq HT indices to allow for multiplexing and ligation-mediated PCR was performed to enrich barcoded libraries for 15 cycles, then purified with the Agencourt AMPure XP beads system (Beckman Coulter). The libraries were assessed for quality with the high sensitivity DNA chip in a TapeStation 2200 (Agilent) and quantified with KAPA Library Quantification Kits for Illumina platforms (Kapa Biosystems). The libraries were diluted to 2nM and combined equimolarly in pools of 12.

tag: timepoint

value: 15-17d post symptom onset

tag: age (years)

tag: gender

value: M

tag: severity

value: severe

tag: acute viral load (log10 dilutions)

tag: convalescent chik igg titer (log10 dilutions)


title: Patient 43, conv sample, technical replicate 1


title: Patient 43, acute sample, technical replicate 2

value: 1-2d post symptom onset


title: Patient 42, conv sample, technical replicate 2

value: non-severe


title: Patient 41, conv sample, technical replicate 1

value: F


title: Patient 43, acute sample, technical replicate 1


title: Patient 41, acute sample, technical replicate 2


title: Patient 41, conv sample, technical replicate 2


title: Patient 42, conv sample, technical replicate 1


title: Patient 39, acute sample, technical replicate 2


title: RNA-seq_Control_rep2 (ERCC spike-in)

value: control


title: Patient 40, conv sample, technical replicate 2


title: Patient 41, acute sample, technical replicate 1


title: Patient 38, acute sample, technical replicate 1


title: Patient 39, conv sample, technical replicate 1


title: Patient 40, conv sample, technical replicate 1


title: Patient 38, acute sample, technical replicate 2


title: Patient 38, conv sample, technical replicate 1


title: Patient 39, conv sample, technical replicate 2


title: Patient 42, acute sample, technical replicate 1


title: Patient 40, acute sample, technical replicate 1


title: Patient 37, conv sample, technical replicate 2


title: Patient 37, conv sample, technical replicate 1


title: Patient 37, acute sample, technical replicate 2


title: Patient 38, conv sample, technical replicate 2


title: Patient 39, acute sample, technical replicate 1


title: Patient 36, conv sample, technical replicate 2


title: Patient 36, conv sample, technical replicate 1


title: Patient 37, acute sample, technical replicate 1


title: Patient 36, acute sample, technical replicate 2


title: Patient 35, acute sample, technical replicate 2


title: Patient 35, conv sample, technical replicate 1


title: Patient 36, acute sample, technical replicate 1


title: Patient 35, acute sample, technical replicate 1


title: Patient 34, acute sample, technical replicate 2


title: Patient 34, conv sample, technical replicate 2


title: Patient 34, acute sample, technical replicate 1


title: Patient 33, conv sample, technical replicate 1


title: Patient 33, acute sample, technical replicate 2


title: Patient 42, acute sample, technical replicate 2


title: Patient 33, acute sample, technical replicate 1


title: Patient 32, conv sample, technical replicate 2


title: Patient 35, conv sample, technical replicate 2


title: Patient 32, acute sample, technical replicate 1


title: Patient 32, conv sample, technical replicate 1


title: Patient 31, conv sample, technical replicate 2


title: Patient 34, conv sample, technical replicate 1


title: Patient 33, conv sample, technical replicate 2


title: Patient 31, conv sample, technical replicate 1


title: Patient 32, acute sample, technical replicate 2


title: Patient 31, acute sample, technical replicate 2


title: Patient 40, acute sample, technical replicate 2


title: Patient 31, acute sample, technical replicate 1


title: Patient 30, conv sample, technical replicate 1


title: Patient 30, conv sample, technical replicate 2


title: Patient 30, acute sample, technical replicate 1


title: Patient 30, acute sample, technical replicate 2


title: Patient 29, acute sample, technical replicate 2


title: Patient 29, conv sample, technical replicate 1


title: Patient 29, acute sample, technical replicate 1


title: Patient 28, acute sample, technical replicate 2


title: Patient 28, conv sample, technical replicate 1


title: Patient 27, conv sample, technical replicate 1


title: Patient 27, conv sample, technical replicate 2


title: Patient 25, acute sample, technical replicate 2


title: Patient 26, acute sample, technical replicate 1


title: Patient 26, conv sample, technical replicate 1


title: Patient 27, acute sample, technical replicate 1


title: Patient 26, conv sample, technical replicate 2


title: Patient 26, acute sample, technical replicate 2


title: Patient 25, conv sample, technical replicate 1


title: Patient 25, conv sample, technical replicate 2


title: Patient 27, acute sample, technical replicate 2


title: DGRP-551_50d_s11

city: LEUVEN

first: Stein

last: Aerts

address: Herestraat 49, bus 602

department: Center for Brain & Disease Research

country: Belgium

institute: KULeuven/VIB

data_processing:
The 10X samples were each processed (alignment, barcode assignment and UMI counting) with Cell Ranger (version 2.0.0) count pipeline. All 10X samples were then merged with Cell Ranger (version 2.0.0) aggr pipeline.
The Drop-seq samples were each processed (alignment, barcode assignment and UMI counting) with the Drop-seq tools (version 1.12) developped by Jim Nemesh from McCarroll lab. Gene expression matrices where outer joined.
For the ATAC samples the raw reads were first filtered and scanned for adapters using fastq‐mcf from the ea‐utils r819 package. Read quality was then checked using FastQC 0.11.4. The reads were mapped to the Drosophila genome (dm6) using STAR 2.5.1. The outputted BAM file from STAR was then indexedand sorted using Samtools 1.2. Using genomeCoverageBed from Bedtools 2.23.0, the BAM file was converted to a BedGraph file. For fast, visualization in the IGV GenomeBrowser, the BedGraph file was further processed to a BigWig file using bedGraphtoBigWig.
Genome_build: dm6 (dmel_r6.16_FB2017_03)
Supplementary_files_format_and_content: 10X DGRP-551 + w1118 high quality dataset (57k) raw UMI count matrix stored in compressed Market Exchange Format (MEX). It also contains TSV files with genes and barcode sequences corresponding to row and column indices, respectively
10X DGRP-551 + w1118 large dataset (157k) raw UMI count matrix stored in compressed Market Exchange Format (MEX). It also contains TSV files with genes and barcode sequences corresponding to row and column indices, respectively
CEL-seq2 FAC-sorted R23E10 neurons raw count matrix
SMART-seq2 FAC-sorted R23E10 neurons raw count matrix
Adapted SMART-seq2 FAC-sorted R23E10 neurons raw count matrix
Drop-seq DGRP-551 dataset raw UMI matrix
ATAC-seq bigWig files

organism: Drosophila melanogaster

source_name: Adult Brain

extract_protocol:
Adult flies were anesthetised by placing them in ice cold glass dishes, heads were removed and brains were dissected removing any cuticle, retina and trachea. Dissected brains were placed in ice cold PBS. Two brains were used for each ATAC-seq reaction, one male and one female. ATAC-seq was performed as previously described in Davie and Jacobs et al 2015 (PLOS Genetics)
ATAC-seq

treatment_protocol: Flies were grown on molasses based flyfood at 25'C with a 12hour/12hour day night cycle

tag: tissue

value: brain

tag: age

value: 50 Days


title: DGRP-820_50d_s12

tag: genotype


title: DGRP-820_0d_s10

value: 0 Days


title: Patient 29, conv sample, technical replicate 2


title: DGRP-913_50d_s14


title: Patient 24, conv sample, technical replicate 2


title: Patient 24, conv sample, technical replicate 1


title: Patient 28, conv sample, technical replicate 2


title: Patient 24, acute sample, technical replicate 2


title: DGRP-913_0d_s9


title: Patient 28, acute sample, technical replicate 1


title: DGRP-907_50d_s13


title: Patient 23, conv sample, technical replicate 2


title: Patient 24, acute sample, technical replicate 1


title: DGRP-907_0d_s8


title: Patient 25, acute sample, technical replicate 1


title: Patient 23, conv sample, technical replicate 1


title: Patient 23, acute sample, technical replicate 2


title: Patient 22, conv sample, technical replicate 2


title: w1118_9d_r2

extract_protocol:
Adult flies were anesthetised by placing them in ice cold glass dishes, heads were removed and brains were dissected removing any cuticle, retina and trachea. Dissected brains were placed in ice cold PBS. When 40 brains were collected, brains were dissociated at 25'C for 2 hours in a mix of Collagenase (75µl @ 100mg/ml) and Dispase (50µl @ 3mg/ml), the sample was pipette mixed every 15 minutes. Cells washed in PBS twice centrifuging at 800 xg) and resuspended in 400µl PBS. A single cell suspension was obtained by filtering with an 11µm cell strainer.
Drop-seq and 10x Genomics CHROMIUM Single Cell 3’ Solution V2 Chemistry

value: 9 Days


title: w1118_6d_r3

value: 6 Days


title: w1118_9d_r3


title: Patient 22, conv sample, technical replicate 1


title: w1118_15d_r1

value: 15 Days


title: w1118_9d_r1


title: w1118_30d_r1

value: 30 Days


title: Patient 23, acute sample, technical replicate 1


title: Patient 22, acute sample, technical replicate 1


title: Patient 21, acute sample, technical replicate 2


title: Patient 21, conv sample, technical replicate 2


title: w1118_6d_r2


title: w1118_3d_r2

value: 3 Days


title: w1118_3d_r3


title: w1118_6d_r1


title: w1118_3d_r1


title: Patient 21, acute sample, technical replicate 1


title: Patient 21, conv sample, technical replicate 1


title: Patient 20, conv sample, technical replicate 2


title: w1118_1d_r1

value: 1 Day


title: DGRP-551_50d_r1


title: Patient 22, acute sample, technical replicate 2


title: Patient 20, acute sample, technical replicate 2


title: w1118_0d_r2

value: < 8 Hours


title: DGRP-551_30d_r2


title: Patient 20, acute sample, technical replicate 1


title: DGRP-551_9d_r1


title: DGRP-551_6d_r2


title: DGRP-551_6d_r1


title: DGRP-551_3d_r2


title: Patient 19, conv sample, technical replicate 1

value: 15-17d post symptom onset


title: Patient 19, acute sample, technical replicate 2

value: M


title: Patient 19, acute sample, technical replicate 1

value: severe


title: DGRP-551_3d_r1


title: Patient 19, conv sample, technical replicate 2


title: Patient 18, conv sample, technical replicate 2


title: DGRP-551_0d_r2


title: Patient 18, acute sample, technical replicate 2

value: 1-2d post symptom onset


title: Patient 17, conv sample, technical replicate 2


title: Patient 18, acute sample, technical replicate 1

value: non-severe


title: Patient 17, conv sample, technical replicate 1


title: Patient 18, conv sample, technical replicate 1


title: DGRP-551_1d_r1


title: Patient 17, acute sample, technical replicate 2


title: Patient 17, acute sample, technical replicate 1


title: DNAM-1- NK subsets from Normal Spleen

source_name: DNAM-1- NK cells, normal spleen

value: 6-8 weeks

value: day 0

value: Normal spleen

value: DNAM-1- natural killer cells


title: Patient 20, conv sample, technical replicate 1


title: Patient 16, conv sample, technical replicate 2


title: Patient 16, conv sample, technical replicate 1


title: Patient 16, acute sample, technical replicate 2


title: Patient 16, acute sample, technical replicate 1


title: Patient 15, conv sample, technical replicate 2


title: AS0h_T_2_3READS

city: Newark

first: Bin

last: Tian

state: NJ

address: 205 South Orange Ave.

department: Department of Microbiology, Biochemistry and Molecular Genetics

institute: Rutgers New Jersey Medical School

description:
Analysis of stress-induced APA
total RNA

data_processing:
Adapter trimming performed using Cutadapt
3'READs reads were aligned to mm9 using bowtie2
For 3'READs data, reads with a mapping quality score (MAPQ) ≥10 were kept for further analysis. Reads with ≥2 non-genomic 5’Ts after alignment were called polyA site supporting (PASS) reads. pAs within 24 nt of each other were clustered. pAs with less than 5 PASS reads in all the samples were first trimmed.
RNAseq reads were aligned to mm9 using STAR
genome build: mm9
Supplementary_files_format_and_content: tab-delimited text files include reads count for each pAs/gene/PoI II position

source_name: Fibroblast

extract_protocol:
TRIzol
3'READS: The 3’READS procedure has been described in (Zheng et al., 2016). Briefly, Poly(A)+ RNA in 0.1-15 µg of total RNA was captured using 10 µl of oligo(dT)25 magnetic beads in 100 µl 1x binding buffer (10 mM Tris-Cl, pH7.5, 150 mM NaCl, 1 mM EDTA, and 0.05% TWEEN 20) and fragmented on the beads using 1.5 U of RNase III in 30 µl RNase III buffer (10 mM Tris-Cl pH8.3, 60 mM NaCl, 10 mM MgCl2, and 1 mM DTT) at 37 °C for 15 min. After washing away unbound RNA fragments with binding buffer, poly(A)+ fragments were eluted from the beads with TE buffer (10 mM Tris-Cl, 1 mM EDTA, pH 7.5) and precipitated with ethanol, followed by ligation to 3 pmol of heat-denatured 5’ adapter (5’-CCUUGGCACCCGAGAAUUCCANNNN) in the presence of 1 mM ATP, 0.1 µl of SuperaseIn, and 0.25 µl of T4 RNA ligase 1 in a 5 µl reaction at 22 °C for 1 h. The ligation products were captured by 10 pmol of biotin-T15-(+TT)5 attached to 12 µl of Dynabeads MyOne Streptavidin C1. After washing with washing buffer (10 mM Tris-Cl pH7.5, 1 mM NaCl, 1 mM EDTA, and 0.05% TWEEN 20), RNA fragments on the beads were incubated with 0.01 U/µl of RNase H at 37 °C for 30 min in 30 µl of RNase H buffer (50 mM Tris-Cl pH 7.5, 5 mM NaCl, 10 mM MgCl2, and 10 mM DTT). After washing with RNase H buffer, RNA fragments were eluted from the beads in elution buffer (1 mM NaCl, 1 mM EDTA, and 0.05% TWEEN 20) at 50 °C, precipitated with ethanol, and then ligated to 3 pmol of heat-denatured 5’ adenylated 3’ adapter (5’-rApp/NNNGATCGTCGGACTGTAGAACTCTGAAC/3ddC) with 0.25 µl T4 RNA ligase 2 (truncated KQ version) at 22 °C for 1 h in a 5 µl reaction containing 15% PEG 8000 and 0.2 µl of SuperaseIn. The ligation products were then precipitated and reverse transcribed using M-MLV reverse transcriptase, followed by PCR amplification using Phusion high-fidelity DNA polymerase and bar-coded PCR primers for 13-18 cycles (13 cycles for 5 µg input, 15 cycles for 1 µg input, and 18 cycles for inputs below 1 µg).   PCR products were size-selected twice with AMPure XP beads, using 0.6 volumes of beads (relative to the PCR reaction volume) to remove large DNA molecules and an additional 0.4 volumes of beads to remove small DNA molecules. The eluted DNA was selected again with 1 volume of AMPure XP beads to further remove small DNA molecules. The size and quantity of the libraries eluted from the AMPure beads were examined using a high sensitivity DNA kit on an Agilent Bioanalyzer. Libraries were sequenced on an Illumina NextSeq 500 (1x75 bases).
RNA-seq: Poly(A)+ RNA in 5 µg of total RNA was purified twice using 10 µl of oligo(dT)25 magnetic beads (NEB) following the manufacturer’s protocol. RNA was then fragmented by partial alkaline hydrolysis (94 °C for 2 min), 3’ dephosphorylated with shrimp alkaline phosphatase, and 5’ phosphorylated with T4 PNK. The RNA fragments were sequentially ligated to a 5’ adenylated 3' blocked 3' adapter (5’-Aden/NNNNNNGATCGTCGGACTGTAGAACTCTGAAC/3ddC, where N is a random nucleotide) with RNA ligase 2 truncated, KQ (200 U/µl) and to a 5′ adaptor (5’-CCUUGGCACCCGAGAAUUCCA) with T4 RNA ligase I. Reverse transcription of ligation product, cDNA amplification by PCR, and library purification were performed as described above for the 3’READS procedure.

treatment_protocol: Untreated: cells were cultured in normal medium; Sodium Arsenite treatment: 250 µM, 1 h; Recovery: After 1 h sodium arsenite treatment, cells were washed and cultured in normal medium again; 4sU labeling: 1 h (before harvest) culture in medium containing 50  µM of 4-sU.

tag: treatment

value: Sodium Arsenite treated, 0 h recovery

tag: strain


title: NT_TIA1_2_3READS

description: Analysis of stress-induced TIA1 binding in NIH3T3 cells

molecule: cytoplasmic RNA

value: Untreated, TIA1 RIP


title: NT_TIA1_1_3READS


title: NT0h_T_2_3READS

value: Untreated, 0 h recovery


title: Patient 15, conv sample, technical replicate 1


title: Patient 15, acute sample, technical replicate 2


title: NT0h_T_1_3READS


title: Patient 15, acute sample, technical replicate 1


title: AS_TIA1_2_3READS

value: Sodium Arsenite treated, 0 h recovery,TIA1 RIP


title: Ip_2

tag: endogenously expressing

tag: chip antibody

value: anti-AID antibody (CosmoBio, Catalog No. BRS-APC004AM, 100ul)


title: DRPA2

city: Beijing

first: Jiapei

last: Yuan

state: Beijing

address: Tsinghua Yuan

institute: Tsinghua University

description: Whole cell poly(A)+ RNA

data_processing:
Remove reads contain N and adapter sequence
Remove reads mapped to rRNA
Map to Rice genome using Tophat2
Remove duplicated reads
Calculate RPKM using DEGSeq
Do the differential expression using DESeq2
Genome_build: Os-Nipponbare-Reference-IRGSP-1.0
Supplementary_files_format_and_content: Coordinates and expression values of annotated and novel lncRNAs

organism: Oryza sativa Japonica Group

source_name: Seedlings

growth_protocol: We plant the Oryza sativa japonica on the ½ MS medium in a growth chamber under conditions of 12 hours light at 28℃ and 12 hours dark at 22℃ for 2 weeks.

extract_protocol:
The total RNAs were extracted with the Trizol reagent (Invitrogen). After total RNA extraction, ribosomal RNAs were removed using RiboMinus™ Plant Kit repeated two times. The poly(A)+ and poly(A)- constituent were separated with oligo(dT) magnetic beads (Oligotex mRNA Mini Kit, QIAGEN).
dUTP based strand-specific library construction protocol

treatment_protocol: Drought, high-salt, cold, heat, highlight stress treatment.

value: Seedlings

value: 2 weeks

tag: ecotype

value: japanica

value: Drought (air-dried)


title: AS_TIA1_1_3READS


title: AS0h_T_1_3READS


title: Patient 14, acute sample, technical replicate 2

value: M


title: Patient 14, acute sample, technical replicate 1

value: severe


title: Patient 14, conv sample, technical replicate 2

value: 15-17d post symptom onset


title: AS_input_2_3READS


title: Patient 13, conv sample, technical replicate 2

value: non-severe


title: NT_input_2_3READS

value: Untreated


title: AS_input_1_3READS


title: Patient 13, acute sample, technical replicate 2

value: 1-2d post symptom onset


title: Patient 13, conv sample, technical replicate 1


title: Patient 14, conv sample, technical replicate 1


title: DRNA2

description: Whole cell poly(A)- RNA


title: C2C12P_T_2_3READS

description: Analysis of APA during C2C12 differentiation

source_name: Myoblast


title: Patient 13, acute sample, technical replicate 1


title: C2C12D_T_3_3READS


title: Patient 12, conv sample, technical replicate 2


title: C2C12D_T_2_3READS


title: Patient 12, conv sample, technical replicate 1


title: Patient 12, acute sample, technical replicate 1


title: Patient 11, conv sample, technical replicate 2


title: Patient 12, acute sample, technical replicate 2


title: C2C12D_NT0h_C_1_3READS

description: Analysis of stress-induced APA in proliferating and differentiated C2C12 cells


title: C2C12D_NT4h_C_1_3READS

value: Untreated, 4 h recovery


title: C2C12D_AS4h_C_1_3READS

value: Sodium Arsenite treated, 4 h recovery


title: C2C12D_AS0h_C_1_3READS

value: Sodium Arsenite treated, 0 h recovery


title: C2C12P_AS4h_C_1_3READS


title: NT_input_1_3READS


title: C2C12P_AS0h_C_1_3READS


title: C2C12P_T_3_3READS


title: Patient 11, conv sample, technical replicate 1


title: Patient 11, acute sample, technical replicate 2


title: Patient 11, acute sample, technical replicate 1


title: Patient 10, conv sample, technical replicate 2


title: Patient 10, conv sample, technical replicate 1


title: C2C12P_NT0h_C_1_3READS


title: Patient 10, acute sample, technical replicate 2


title: AS4h_Ft_2_3READS

description:
Analysis of differential decay of APA isoforms
unlabeled RNA (Flowthrough fraction)

value: Sodium Arsenite treated, 4 h recovery, with 4sU labeling.


title: AS0h_Ft_2_3READS

value: Sodium Arsenite treated, 0 h recovery, with 4sU labeling.


title: NT0h_Ft_2_3READS

value: Untreated, 0 h recovery, with 4sU labeling.


title: AS4h_4sU_2_3READS

description:
Analysis of differential decay of APA isoforms
4sU-labeled RNA


title: Patient 9, conv sample, technical replicate 2


title: Patient 9, conv sample, technical replicate 1


title: Patient 9, acute sample, technical replicate 2


title: Patient 9, acute sample, technical replicate 1


title: NT4h_4sU_2_3READS

value: Untreated, 4 h recovery, with 4sU labeling.


title: NT0h_4sU_2_3READS


title: Patient 8, conv sample, technical replicate 2


title: AS12h_T_4_3READS

description:
Analysis of stress-induced APA, time course
total RNA

value: Sodium Arsenite treated, 12 h recovery


title: AS24h_T_4_3READS

value: Sodium Arsenite treated, 24 h recovery


title: C2C12P_NT4h_C_1_3READS


title: Patient 8, conv sample, technical replicate 1


title: AS8h_T_4_3READS

value: Sodium Arsenite treated, 8 h recovery


title: Patient 8, acute sample, technical replicate 1


title: NT4h_Ft_2_3READS


title: Patient 8, acute sample, technical replicate 2


title: AS4h_T_4_3READS


title: AS0h_T_4_3READS


title: Patient 7, conv sample, technical replicate 2

value: F


title: NT0h_T_4_3READS

value: Untreated, 0 h recovery


title: Patient 10, acute sample, technical replicate 1

value: M


title: Patient 7, conv sample, technical replicate 1

value: 15-17d post symptom onset

value: severe


title: NT4h_T_3_RNAseq

description:
Gene expression analysis
total RNA


title: AS4h_T_3_RNAseq

description:
Gene expression analysis
total RNA


title: Patient 7, acute sample, technical replicate 2


title: Patient 7, acute sample, technical replicate 1


title: Patient 6, conv sample, technical replicate 2

value: non-severe


title: Patient 6, acute sample, technical replicate 2

value: 1-2d post symptom onset


title: AS0h_4sU_2_3READS


title: AS0h_T_3_RNAseq

description:
Gene expression analysis
total RNA


title: Patient 6, conv sample, technical replicate 1


title: NT0h_T_3_RNAseq

description:
Gene expression analysis
total RNA


title: Patient 6, acute sample, technical replicate 1


title: Patient 5, conv sample, technical replicate 2


title: Patient 5, acute sample, technical replicate 2


title: Patient 4, conv sample, technical replicate 2


title: Patient 4, acute sample, technical replicate 1


title: Patient 3, conv sample, technical replicate 2


title: Patient 4, acute sample, technical replicate 2


title: Patient 5, acute sample, technical replicate 1


title: Patient 3, acute sample, technical replicate 2


title: Patient 3, conv sample, technical replicate 1


title: Patient 2, conv sample, technical replicate 1


title: Patient 1, conv sample, technical replicate 2


title: Patient 2, acute sample, technical replicate 1


title: Patient 1, conv sample, technical replicate 1


title: Patient 3, acute sample, technical replicate 1


title: ATAC-seq_Ssrp1-KD_rep2

data_processing:
Sequenced paired mates were mapped on mm10 genome build using Bowtie2 with the following parameters: –X 2000. Reads corresponding to nucleosome free regions were selected via the “ATACseqQC” R package.  All the ATAC-seq BAM files were converted to bigwig, binned (1 bp), and normalised to x1 sequencing depth using Deeptools (v 2.4). Duplicated reads were removed. Chromatin accessibility profiles were visualised using R (v 3.3.0).
Genome_build: mm10

extract_protocol: Biological replicates were obtained from two independent transfection experiments for each shRNA vector.  ATAC-seq was performed on 50,000 cells as previously described (Buenrostro et al, 2013). All samples were PCR amplified for 9 cycles were paired-end sequenced on an Illumina Hi-Seq 2500 platform.

value: E14 cell line


title: ATAC-seq_Control_rep2

value: control


title: Patient 2, acute sample, technical replicate 2


title: ATAC-seq_Ssrp1-KD_rep1


title: ATAC-seq_Control_rep1


title: Patient 1, acute sample, technical replicate 2


title: Patient 1, acute sample, technical replicate 1


title: RNA-seq- NPC2

description: processed data file: RNAseq.limma.NPC-WT.tab

data_processing:
RNA-seq files were aligned using STAR (v 2.4.1b). Counts were normalised using edgeR and differential expression was performed with limma.
Genome_build: mm10

source_name: early stage Neural progenitor cells

growth_protocol: The E14 cell line (mESCs) was cultured at 37 °C, 7.5% CO2, on 0.1% gelatin coated plates, in DMEM + GlutaMax™ (Gibco) with 15% fetal bovine serum (Gibco), MEM non- essential amino acids (Gibco), penicillin/streptomycin (Gibco), 550 µM 2-mercaptoethanol . (Gibco), and 10 ng/ml of leukaemia inhibitory factor (LIF) (eBioscience). 293T (HEK), N2a, and B16 cell lines were cultured at 37 °C, 5% CO2 in DMEM + GlutaMax™ (Gibco) with 10% fetal bovine serum (Gibco), and penicillin/streptomycin (Gibco). Early Neuronal Precursor Cells (NPCs) were generated as previously described  (Bibel, Richter, Lacroix, & Barde, 2007). Briefly, embryoid bodies were created with the hanging drop technique and were further treated with 1 µM retinoic acid (RA) for 4 days. RA-treated embryoid bodies were trypsinised and cultured in DMEM + GlutaMax™ (Gibco) with 15% fetal bovine serum without LIF for 3 days.

extract_protocol:
Cell collection and RNA preparation. Total RNA was obtained via phenol-chloroform extraction (QIAzol Lysis Reagent – QIAGEN) followed by purification via Quick-RNA™ MicroPrep (Zymo Research).
Library preparation and ribosomal depletion were performed via the NEBNext Directional RNA Ultra Kit (NEB) and the RiboZero Kit (Illumina) according to the manufacturer’s instructions, respectively. Three different biological replicates  were prepared and processed for transcriptome analysis.


title: RNA-seq- NPC1


title: RNA-seq- NPC3


title: polysome_asy_T30_Input_rep2

city: madison

first: Audrey

last: Gasch

state: wi

address: 425G Henry mall

department: genetics

institute: university of wisconsin, madison

description: Gasch 634

data_processing:
Sequencing reads were processed with Trimmomatic version 0.32
Trimmed sequencing reads were mapped to the S288c reference V64-1-1, using Bowtie2.
HTseq version 0.6.1 was used to sum read counts per gene
For spike-in samples, Saccharomyces cerevisiae sequencing reads were normalized by reads from Schizosaccharomyces pombe spike-in control
For others, RPKM is used to calculate log2 fold change
Supplementary_files_format_and_content: Excel files include raw reads for each gene and each sample.

source_name: S. cerevisiae cells, Spike-in with S.pombe RNA

growth_protocol: All strains were grown in YPD for 7-10 generations before treatments or stress

extract_protocol:
For RNA-seq: RNA was extracted with hot phenol protocol; RNA was rRNA-depleted with Epicentre's Ribo-Zero rRNA Removal Kit (Human/Mouse/Rat). For polysome-seq: RNA was extraced with phenol and choloform mixture; RNA was rRNA-depleted with illumina TruSeq Stranded Total RNA library Prep Kit.
cDNA library was prepared with Epicentre's Script-seq V2 H/M/R Complete Kit (Human/Mouse/Rat) for RNA-seq samples, or  illumina TruSeq Stranded Total RNA library Prep Kit for polysome-seq samples

treatment_protocol: 2 hr treatement of alpha factor (25uM), nocodazole(10ug/ml), cycholoheximide (indicated) as indicated.

tag: stress

value: NaCl


title: Patient 4, conv sample, technical replicate 1


title: polysome_asy_T30_5R_rep2

description: Gasch 632


title: Patient 5, conv sample, technical replicate 1


title: polysome_asy_T30_6R>_rep2

description: Gasch 633


title: Patient 2, conv sample, technical replicate 2


title: polysome_asy_T30_4R_rep2

description: Gasch 631


title: RNA-seq E14 chromatin_1

description:
Sample 1
nascent RNA
processed data file: raw_counts_combined_chromatin_RNA-seq_samples.txt

data_processing:
RNA-seq files were aligned using STAR (v 2.4.1b). Raw counts were obtained from featureCounts of the Rsubread package (R/Bioconductor).
Genome_build: mm10
Supplementary_files_format_and_content: text file with raw counts

growth_protocol: The E14 cell line (mESCs) was cultured at 37 °C, 7.5% CO2, on 0.1% gelatin coated plates, in DMEM + GlutaMax™ (Gibco) with 15% fetal bovine serum (Gibco), MEM non- essential amino acids (Gibco), penicillin/streptomycin (Gibco), 550 µM 2-mercaptoethanol (Gibco), and 10 ng/ml of leukaemia inhibitory factor (LIF) (eBioscience).

extract_protocol:
Cell fractionation was performed as described in (Pandya-Jones & Black, RNA, 2009), (Bhatt et al., Cell, 2012) and based on (Wuarin & Schibler, MCB, 1994) with modifications. All subsequent steps have been conducted on ice or at 4°C and in the presence of 25 µM α-amanitin (Sigma, A2263), 50 Units SUPERaseIN (Life Technologies, AM2696) and Protease inhibitors cOmplete (Roche, 11873580001) according to manufacturer’s instructions using RNAse free equipment. All buffers have been pre-chilled on ice before use. The cell pellet corresponding to 1x107 cells was gently resuspended in 200 µl cytoplasmic lysis buffer (0.15% NP-40, 10 mM Tris-HCl pH 7.0, 150 mM NaCl). The cell lysate was incubated for 5 min on ice, layered onto 500 µl sucrose buffer (10 mM Tris-HCl pH 7.0, 150 mM NaCl, 25% sucrose) and centrifuged at 16,000 g for 10 min. The supernatant corresponding to the cytoplasmic fraction was carefully removed.
Sequencing library preparation was performed as described in (Mayer & Churchman, 2016)

tag: cell compartment

value: chromatin


title: polysome_asy_T30_80S_rep2

description: Gasch 628


title: polysome_asy_T30_60S_rep2

description: Gasch 627


title: polysome_asy_T30_40S_rep2

description: Gasch 626


title: polysome_asy_T30_RNP_rep2

description: Gasch 625


title: Mock20-2

city: Hamilton

first: Craig

last: Martens

state: MT

address: 903 S. 4th St

department: DIR

institute: NIAID

data_processing:
Illumina Casava1.8.2 software was used for basecalling
Reads were processed using fastx toolkit to trim for adapter and low quality bases and filter for low quality reads.
Processed reads were mapped to the Mus musculus and murine norovirus genomes using Tophat v2.0.14
Reads mapping to genes were counted using htseq-count
Gene normalization and differential expression analysis were performed using Deseq2
Genome_build: UCSC mm10
Supplementary_files_format_and_content: tab delimited text file containing deseq2 normalized values in a single matrix format.

extract_protocol:
RNA was extracted using Qiagen AllPrep DNA/RNA kit with an additional on-column Dnase I treatment
Total RNA libraries were prepared using the TruSeq Stranded Total RNA kit with Ribo-Zero Gold rRNA depletion (Illumina Inc., San Diego, CA)

value: Mock infected 20 hour time point


title: MNV20-3

value: MNV infected 20 hour time point


title: Mock20-1


title: polysome_asy_T0_Input_rep2

description: Gasch 624


title: NET-seq_Control_rep2

description: nascent RNA

data_processing:
Library strategy: NET-seq
NET-seq files were aligned using STAR (v 2.4.2a). BAM files were converted to bigwig (1 bp bin), filtered by strand and normalised to x1 sequencing depth.
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig

extract_protocol: NET-seq libraries were prepared as previously described (Mayer & Churchman, 2016) with a few modifications. Briefly, chromatin associated nascent RNA was extracted through cell fractionation in the presence of α-amanitin, protease and RNAase inhibitors. > 90% recovery of ligated RNA and cDNA was achieved from 15 % TBE-Urea (Invitrogen) and 10% TBE-Urea (Invitrogen), respectively, by adding RNA recovery buffer (Zymo Research, R1070-1-10) to the excised gel slices and further incubating at 70°C (1500 rpm) for 15 min. Gel slurry was transferred through a Zymo-Spin IV Column (Zymo Research, C1007-50) and further precipitated for subsequent library preparation steps. cDNA containing the 3’ end sequences of a subset of mature and heavily sequenced snRNAs, snoRNAs, and rRNAs, were specifically depleted using biotinylated DNA oligos (Supplementary Table 6). Oligo-depleted circularised cDNA was amplified via PCR (5 cycles) and double stranded DNA was run on a 4% low melt agarose gel. The final NET-seq library running at ~150 bp was extracted and further purified using the ZymoClean Gel DNA recovery kit (Zymo Research)

tag: cell line


title: NET-seq_Control_rep1

description: nascent RNA


title: MNV20-2


title: RNA-seq E14 chromatin_2

description:
Sample 2
nascent RNA
processed data file: raw_counts_combined_chromatin_RNA-seq_samples.txt


title: polysome_asy_T0_6R>_rep2

description: Gasch 623


title: polysome_asy_T0_5R_rep2

description: Gasch 622


title: NET-seq_Ssrp1-KD_rep2

description: nascent RNA


title: polysome_asy_T0_4R_rep2

description: Gasch 621


title: MNV14-3

value: MNV infected 14 hour time point


title: polysome_asy_T0_3R_rep2

description: Gasch 620


title: MNV14-1


title: polysome_asy_T30_3R_rep2

description: Gasch 630


title: polysome_asy_T30_2R_rep2

description: Gasch 629


title: MNV8-2

value: MNV infected 8 hour time point


title: NET-seq_Ssrp1-KD_rep1

description: nascent RNA


title: polysome_asy_T0_80S_rep2

description: Gasch 618


title: MNV8-3


title: polysome_asy_T0_60S_rep2

description: Gasch 617


title: polysome_asy_T0_RNP_rep2

description: Gasch 615


title: Mock0-2

value: Mock infected Zero time point


title: polysome_alpha_T0_Input_rep1

description: Gasch 604

value: alpha


title: Mock0-1


title: MNV0-2

value: MNV infected Zero time point


title: MNV20-1


title: polysome_alpha_T0_4R_rep1

description: Gasch 601


title: polysome_alpha_T0_6R>_rep1

description: Gasch 603


title: polysome_alpha_T0_5R_rep1

description: Gasch 602


title: polysome_alpha_T0_3R_rep1

description: Gasch 600


title: DGRP-551_0d_3f

value: brain

value: 0 Days


title: polysome_asy_T0_2R_rep2

description: Gasch 619


title: polysome_alpha_T0_2R_rep1

description: Gasch 599


title: Ssrp1_ChIP_seq_rep1,rep2

description: ChIP antibody: Anti-Ssrp1 (Biolegends)

data_processing:
ChIP-seq files were aligned using Bowtie2 (v 2.2.6). BAM files were converted to bigwig (10 bp bin) and normalised to x1 sequencing depth. Duplicated reads were removed.
Genome_build: mm10

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 20 min followed by quenching for 5 min with the addition of glycine to a final concentration of 0.125 M. After washing with PBS buffer, cells were collected and lysed in Cell Lysis buffer (5 mM Tris pH8.0, 85 mM KCl, 0.5% NP40 ) with proteinase inhibitors (10 µl/mL Phenylmethylsulfonyl fluoride (PMSF), 1 µl/mL Leupeptin and 1 µl/mL Pepstatin). Pellets were spun for 5 min at 5000 rpm at 4°C. Nuclei were lysed in Nuclei Lysis Buffer (1% SDS, 10 mM EDTA, 50 mM Tris HCl) and samples were sonicated for 12 min. Samples were centrifuged for 20 min at 13,000 rpm at 4°C and the supernatant was diluted in IP buffer (0.01% SDS, 1.1% Triton-X-100, 1.2 mM EDTA, 16.7 mM Tris HCl, 167 mM NaCl) and the appropriate antibody was added and left overnight with rotation at 4°C. Protein A/G Dynabeads (Invitrogen) were added for 1h and after extensive washed samples were eluted in Elution Buffer (1% SDS, 0.1 M NaHCO3). 20 µL of 5 M NaCl were added and samples were reverse-crosslinked at 65°C for 4h. Following phenol-chloroform extraction and ethanol precipitation, DNA was incubated at 37°C for 4h with RNAse (Sigma).
Approximately 10-20 ng of ChIP material was used for library preparation. End-repair and adaptor ligation was prepared as described previously with a few modifications (Tessarz, et al). Double sided size selections (~200 – 650bp) were performed using the MagSI-NGS Dynabeads (MagnaMedics, #MD61021) according to the manufacturer’s instructions. Purified adapter-ligated ChIP material was run on a high sensitivity DNA chip on a 2200 TapeStation (Agilent) to assess size distribution and adaptor contamination.


title: MNV14-2


title: DGRP-551_0d_3m


title: MNV8-1


title: polysome_alpha_T0_80S_rep1

description: Gasch 598


title: DGRP-551_0d_s2


title: polysome_alpha_T0_60S_rep1

description: Gasch 597


title: polysome_asy_T0_40S_rep2

description: Gasch 616


title: 17_nrp1ox

first: Balazs

last: Balint

state: Csongrad

address: Vallalkozok street

country: Hungary

institute: Seqomics Ltd

data_processing:
Basecall was carried out using bcl2fastq version 1.8.4
Raw data quality assessment and read trimming (with an error probability threshold of 0.05) was carried out in CLC Genomics Workbench Tool (v 8.5.1)
Alignment was carried out in CLC Genomics Workbench Tool (v 8.5.1). Reference genome: TAIR10.30. Mapping parameters: read length fraction 0.8 sequence similarity fraction: 0.8, maximum number of hits per read:30
Total gene read” RNA-Seq count data was imported from CLC into R version 3.2.0.  Subsequently, data normalization based on “trimmed mean of M-values” was carried out using package edgeR (version 3.2.2). Log transformation was carried out with the “voom” function of “limma” package (version 3.18.13).
List of differentially expressed genes in each comparison was generated with edgeR functions “exactTest” and “topTags”. Genes showing at least two-fold gene expression change with an FDR value below 0.05 were considered as significant.
Genome_build: TAIR10
Supplementary_files_format_and_content: comma separated RNA-Seq read count table from CLC Genomics Workbench Tool is available on the sample records.  The matrix of log2 CPM values from edgeR is available on the series record.

organism: Arabidopsis thaliana

source_name: aboveground plant organs

growth_protocol: Seeds of Arabidopsis plants were sown into pots and kept 3 days at 5oC in dark, then put into a growth chamber (8 h photoperiod light/16 h dark, 190 μmol/m2/s) with the temperature of 20oC) and the plants were grown for the next 40 to 100 days depending on the type of the experiment.

extract_protocol:
Total RNA was extracted using Quick RNATM Mini Prep kit (Zymo Research, Irvine, California, USA).
PolyA mRNA sequencing was performed using TrueSeq RNA Library Preparation Kit v2 (Illumina, San Diego, California, USA) according to the manufacturer’s instructions. Briefly, RNA quality and quantity measurements were performed using RNA ScreenTape and Reagents on TapeStation (all from Agilent, Santa Clara, California, USA) and Qubit (Thermo Fisher); only high quality (RIN >8.0) total RNA samples were processed. Next, RNA was DNaseI (Thermo Fisher) treated and the mRNA was purified and fragmented. First strand cDNA synthesis was performed using SuperScript II (Thermo Fisher) followed by second strand cDNA synthesis, end repair, 3’-end adenylation, adapter ligation and PCR amplification. All the purification steps were performed using AmPureXP Beads (Backman Coulter, Brea, California, USA). Final libraries were quality checked using D1000 ScreenTape and Reagents on TapeStation (all from Agilent)

value: Columbia

value: Helianthus annuus GUbB1 promoter:atnrp1 overexpressor

value: aboveground plant organs


title: DGRP-551_0d_s22


title: polysome_alpha_T0_40S_rep1

description: Gasch 596


title: 18_nrp1ox


title: DGRP-551_30d_r1 Drop-Seq

value: 30 Days


title: MNV0-3


title: MNV0-1


title: polysome_alpha_T0_RNP_rep1

description: Gasch 595


title: Input_ChIP_seq_rep1,rep2

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 20 min followed by quenching for 5 min with the addition of glycine to a final concentration of 0.125 M. After washing with PBS buffer, cells were collected and lysed in Cell Lysis buffer (5 mM Tris pH8.0, 85 mM KCl, 0.5% NP40 ) with proteinase inhibitors (10 µl/mL Phenylmethylsulfonyl fluoride (PMSF), 1 µl/mL Leupeptin and 1 µl/mL Pepstatin). Pellets were spun for 5 min at 5000 rpm at 4°C. Nuclei were lysed in Nuclei Lysis Buffer (1% SDS, 10 mM EDTA, 50 mM Tris HCl) and samples were sonicated for 12 min. 20 µL of 5 M NaCl were added and samples were reverse-crosslinked at 65°C for 4h. Following phenol-chloroform extraction and ethanol precipitation, DNA was incubated at 37°C for 4h with RNAse (Sigma).
Approximately 10-20 ng of ChIP material was used for library preparation. End-repair and adaptor ligation was prepared as described previously with a few modifications (Tessarz, et al). Double sided size selections (~200 – 650bp) were performed using the MagSI-NGS Dynabeads (MagnaMedics, #MD61021) according to the manufacturer’s instructions. Purified adapter-ligated ChIP material was run on a high sensitivity DNA chip on a 2200 TapeStation (Agilent) to assess size distribution and adaptor contamination.

value: E14 cell line


title: 13_nrpmut

value: nrp1-1 nrp2-1 double T-DNA-insertion mutant


title: Supt16_ChIP_seq_rep1,rep2

description: ChIP antibody: Anti-Supt16 (Cell Signaling)


title: polysome_asy_T30_Input_rep1

description: Gasch 594

value: NaCl


title: w1118_0d_r1

value: < 8 Hours


title: 12_wt

value: wild-type


title: DGRP-551_15d_r1

value: 15 Days


title: polysome_asy_T30_6R>_rep1

description: Gasch 593


title: 10_wt


title: polysome_asy_T30_4R_rep1

description: Gasch 591


title: DGRP-551_0d_r1


title: polysome_asy_T30_5R_rep1

description: Gasch 592


title: polysome_asy_T30_2R_rep1

description: Gasch 589


title: polysome_asy_T30_3R_rep1

description: Gasch 590


title: Japanica_Seedling_sRNA

description: Whole cell small RNA

source_name: Leaves of seedlings

value: Leaves of seedlings

value: 2 weeks

value: japanica

value: No treatment


title: Highlight_sRNA

description: Whole cell small RNA

value: Seedlings

value: Highlight (50000 Lux)


title: polysome_asy_T30_80S_rep1

description: Gasch 588


title: Japanica_Root_sRNA

description: Whole cell small RNA

source_name: Roots of seedlings

value: Roots of seedlings


title: polysome_asy_T30_60S_rep1

description: Gasch 587


title: polysome_asy_T30_RNP_rep1

description: Gasch 585


title: polysome_asy_T30_40S_rep1

description: Gasch 586


title: 15_nrpmut

value: Columbia


title: Heat_sRNA

description: Whole cell small RNA

value: Heat (50℃)


title: Japanica_Panicle_sRNA

description: Whole cell small RNA

source_name: Panicles of seedlings

value: Panicles of seedlings


title: Drought_sRNA

description: Whole cell small RNA

value: Drought (air-dried)


title: DGRP-551_0d_r1 Drop-Seq

value: brain

value: 0 Days


title: Cold_sRNA

description: Whole cell small RNA

value: Cold (4℃)


title: NaCl_sRNA

description: Whole cell small RNA

value: High-salt (300 mM NaCl)


title: DGRP-551_30d_r1

value: 30 Days


title: WT_sRNA

description: Whole cell small RNA


title: asy_T0(NaCl)_Spombe_rep3

source_name: S. cerevisiae cells, Spike-in with S.pombe cells

value: NaCl


title: asy_T30(NaCl)_Spombe_rep3


title: alpha_T30(NaCl)_Spombe_rep3

value: alpha


title: alpha_T0(NaCl)_Spombe_rep3


title: CHX_0.1_T30_Spombe_rep1

value: cycholoheximide


title: japanicarootNUC

description: Nuclear total RNA

value: 2 weeks

value: japanica


title: japanicarootPA

description: Whole cell poly(A)+ RNA

value: No treatment


title: CHX_0.2_T0_Spombe_rep1


title: CHX_0.1_T0_Spombe_rep1


title: japanicapaniclePA

description: Whole cell poly(A)+ RNA


title: alpha_T30(NaCl)_Spombe_rep2


title: CHX_0.2_T30_Spombe_rep1


title: japanicarootNA

description: Whole cell poly(A)- RNA


title: japanicapanicleNUC

description: Nuclear total RNA


title: alpha_T0(NaCl)_Spombe_rep2


title: asy_T30(NaCl)_Spombe_rep2


title: japanicapanicleNA

description: Whole cell poly(A)- RNA


title: japanicaNUC

description: Nuclear total RNA

value: Leaves of seedlings


title: japanicaNA

description: Whole cell poly(A)- RNA


title: japanicaPA

description: Whole cell poly(A)+ RNA


title: NACLNUC

description: Nuclear total RNA

value: Seedlings


title: NACLPA

description: Whole cell poly(A)+ RNA


title: alpha_T30(NaCl)_Spombe_rep1

description: Gasch 265


title: alpha_T0(NaCl)_Spombe_rep1

description: Gasch 264


title: asy_T0(NaCl)_Spombe_rep2


title: NACLNA

description: Whole cell poly(A)- RNA


title: asy_T30(NaCl)_Spombe_rep1

description: Gasch 263


title: asy_T0(NaCl)_Spombe_rep1

description: Gasch 262


title: LIGHTPA

description: Whole cell poly(A)+ RNA

value: Highlight (50000 Lux)


title: Noc(3.5h)_T30_rep2

source_name: S. cerevisiae cells

value: nocodazole


title: LIGHTNUC

description: Nuclear total RNA


title: LIGHTNA

description: Whole cell poly(A)- RNA


title: Noc(3.5h)_T0_rep2


title: CHX_0.2_T0_rep1


title: CHX_0.1_T30_rep2


title: HEATPA

description: Whole cell poly(A)+ RNA

value: Heat (50℃)


title: HEATNA

description: Whole cell poly(A)- RNA


title: CHX_0.1_T0_rep2


title: Noc(3.5h)_T30_rep1

description: Gasch 273


title: COPA

description: Whole cell poly(A)+ RNA


title: DRPA

description: Whole cell poly(A)+ RNA

value: Drought (air-dried)


title: CHX_0.1_T30_rep1

description: Gasch 269


title: DRNA

description: Whole cell poly(A)- RNA


title: Noc(3.5h)_T0_rep1

description: Gasch 272


title: CHX_0.1_T0_rep1

description: Gasch 268


title: CONUC

description: Nuclear total RNA


title: CKPA

description: Whole cell poly(A)+ RNA


title: CHX_0.2_T30_rep1


title: gar2deletion_Cnp1_2

city: Hangzhou

first: Min

last: Lu

state: Zhejiang

address: Yuhangtang road 866

institute: Zhejiang University, Life Sciences Institute

data_processing:
Ion Torrent software (Torrent_Suite 4.0.2) used for basecalling.
Remove low quality reads and trim reads to ensure uniformity, then align ChIP-seq reads to ASM294v2 genome assembly using bwa (burrows-wheeler alignment) tools.
Remove duplicate reads at the same position and randomly samle down the ChIP-seq reads by using MACS2.
Callpeaks and peak pileup using MACS2.
Genome_build: ASM294v2
Supplementary_files_format_and_content: Bedgraph files were generated using MACS2.

organism: Schizosaccharomyces pombe

source_name: Exponentially growth cells

growth_protocol: Cells were cultured at 29℃ in rich medium and harvested.

extract_protocol:
Cells were lysed and added 30 U/µl Micrococcal Nuclease (Thermo Fisher) to digest chromatin into mononucleosomes. Anti-Cnp1 (from Allshire lab) was used in ChIPs.
Libraries of DNA were prepared using commercial high throughput library preparation kit (KAPA) according to the protocal.

treatment_protocol: Zymolase (final concentration 0.25 mg/ml) was added to digest the yeast cell walls.

value: Anti-Cnp1 (from Allshire lab)


title: CONA

description: Whole cell poly(A)- RNA


title: epe1deletion_2

extract_protocol:
Cells were lysed and added 30 U/µl Micrococcal Nuclease (Thermo Fisher) to digest chromatin into mononucleosomes. Anti-H3K9me2 (ab1220, Abcam) was used in ChIPs.
Libraries of DNA were prepared using commercial high throughput library preparation kit (KAPA) according to the protocal.

value: Anti-H3K9me2 (ab1229, Abcam)


title: alpha-0.5N_t30(NaCl)_rep2

description: Gasch 187


title: CKNA

description: Whole cell poly(A)- RNA


title: ccp1deletion_Cnp1_2


title: DRNUC

description: Nuclear total RNA


title: Noc-0.5N_t30(NaCl)_rep2

description: Gasch 191


title: epe1deletion_1

value: Anti-H3K9me2 (ab1228, Abcam)


title: Noc-T0(NaCl)_rep2

description: Gasch 190


title: gar2deletion_Cnp1_1


title: alpha-0.7N_t30(NaCl)_rep2

description: Gasch 188


title: polysome_asy_T0_6R>_rep1

description: Gasch 582


title: ccp1deletion_Cnp1_1


title: Noc-T10(37c)(HeatShock)_rep2

description: Gasch 185

value: HeatShock


title: alpha-T0(NaCl)_rep2

description: Gasch 186


title: Noc-0.7N_t30(NaCl)_rep2

description: Gasch 192


title: HEATNUC

description: Nuclear total RNA


title: polysome_asy_T0_5R_rep1

description: Gasch 581


title: polysome_asy_T0_Input_rep1

description: Gasch 583


title: Noc-T10(33c)(HeatShock)_rep2

description: Gasch 184


title: wild-type_Cnp1_1


title: wild-type_Cnp1_2


title: Noc-T0(HeatShock)_rep2

description: Gasch 183


title: CKNUC

description: Nuclear total RNA


title: alpha-T10(37c)(HeatShock)_rep2

description: Gasch 182


title: polysome_asy_T0_3R_rep1

description: Gasch 579


title: alpha-T10(33c)(HeatShock)_rep2

description: Gasch 181


title: polysome_asy_T0_2R_rep1

description: Gasch 578


title: ccp1-myc(test)_2

data_processing:
Ion Torrent software (Torrent_Suite 4.0.2) used for basecalling.
Remove low quality reads and trim reads to ensure uniformity, then align ChIP-seq reads to ASM294v2 genome assembly using bwa (burrows-wheeler alignment) tools.
Remove duplicate reads at the same position and randomly samle down the ChIP-seq reads by using MACS2.
Callpeaks using MACS2.
Genome_build: ASM294v2
Supplementary_files_format_and_content: Bedgraph files were generated using MACS2.

growth_protocol: Cells were cultured at were cultured at 29℃ in rich medium.

extract_protocol:
Using bead beater to lyse the cells, lysates were sonicated until chromatin is sheared to 200~400bp fragments (Diagenode Bioruptor Pico).
Libraries of DNA were prepared using commercial high throughput library preparation kit (KAPA) according to the protocal.

treatment_protocol: Cells were fixed with 1% paraformaldehyde solution (pFA), then quenched the fixation reaction with 125 mM glycine.

value: Anti-Myc (ab9135, Abcam)

tag: genotype/variation

value: ccp1-myc (C-terminal fusion)


title: polysome_asy_T0_80S_rep1

description: Gasch 577

value: NaCl


title: ccp1-myc(test)_1

value: Anti-Myc (ab9134, Abcam)


title: polysome_asy_T0_4R_rep1

description: Gasch 580


title: polysome_asy_T0_60S_rep1

description: Gasch 576


title: no_tag(control)_2

value: Anti-Myc (ab9133, Abcam)

value: wild-type


title: dbl5deletion_1

value: Anti-H3K9me2 (ab1222, Abcam)


title: Noc_T40(HeatShock)_rep1

description: Gasch 179


title: no_tag(control)_1

value: Anti-Myc (ab9132, Abcam)


title: polysome_asy_T0_40S_rep1

description: Gasch 575


title: Noc_T30(HeatShock)_rep1

description: Gasch 178


title: ccp1gar2deletion_2

value: Anti-H3K9me2 (ab1227, Abcam)


title: polysome_asy_T0_RNP_rep1

description: Gasch 574


title: ccp1gar2deletion_1

value: Anti-H3K9me2 (ab1226, Abcam)


title: gar2deletion_2

value: Anti-H3K9me2 (ab1225, Abcam)


title: Noc_T20(HeatShock)_rep1

description: Gasch 177

value: nocodazole


title: Noc_t0'(HeatShock)_rep1

description: Gasch 174


title: Noc_T10(HeatShock)_rep1

description: Gasch 176


title: alpha_T40(HeatShock)_rep1

description: Gasch 173

value: alpha


title: ccp1deletion_1


title: alpha_T30(HeatShock)_rep1

description: Gasch 172


title: alpha_T20(HeatShock)_rep1

description: Gasch 171


title: Noc_T0(HeatShock)_rep1

description: Gasch 175


title: ccp1deletion_2

value: Anti-H3K9me2 (ab1223, Abcam)


title: alpha-T0(HeatShock)_rep2

description: Gasch 180


title: wild-type_2

value: Anti-H3K9me2 (ab1221, Abcam)


title: alpha_T10(HeatShock)_rep1

description: Gasch 170


title: wild-type_1

value: Anti-H3K9me2 (ab1220, Abcam)


title: alpha_t0'(HeatShock)_rep1

description: Gasch 168

value: HeatShock


title: alpha_T0(HeatShock)_rep1

description: Gasch 169


title: Noc_T30(NaCl)_rep1

description: Gasch 163


title: Noc_T15(NaCl)_rep1

description: Gasch 162


title: Noc_T60(NaCl)_rep1

description: Gasch 165


title: Noc_T0(NaCl)_rep1

description: Gasch 161


title: Noc_T45(NaCl)_rep1

description: Gasch 164


title: Noc_t0'(NaCl)_rep1

description: Gasch 160


title: asy_T0(HeatShock)_rep1

description: Gasch 166


title: alpha_T30(NaCl)_rep1

description: Gasch 157


title: alpha_T45(NaCl)_rep1

description: Gasch 158


title: alpha_T60(NaCl)_rep1

description: Gasch 159


title: alpha_T15(NaCl)_rep1

description: Gasch 156


title: alpha_T0(NaCl)_rep1

description: Gasch 155


title: gar2deletion_1

value: Anti-H3K9me2 (ab1224, Abcam)


title: alpha_t0'(NaCl)_rep1

description: Gasch 154


title: asy_T0(NaCl)_rep1

description: Gasch 152


title: RNA-seq_Ssrp1-KD_rep1-4

data_processing:
RNA-seq  files were aligned using STAR (v 2.5.1b). Counts were normalised using edgeR and differential expression was performed with limma. For cryptic transcription visualisation, replicates( per condition) were merged, converted to bigwig, binned (10 bp), split by strand (forward/reverse), and RPKM normalised
Genome_build: mm10

source_name: mESCs

extract_protocol: Fourty-eight hours (48h) after transfection, puromycin (2 µg /ml) selection was applied for an additional 24h period, before cell collection and RNA preparation. Total RNA was obtained via phenol-chloroform extraction (QIAzol Lysis Reagent – QIAGEN) followed by purification via Quick-RNA™ MicroPrep (Zymo Research)

value: E14 cell line

value: Ssrp1 knock down


title: MNase-seq_Control_rep1,rep2

data_processing:
MNase-seq BAM files were merged per condition, converted to bigwig, binned (1 bp), smoothed (20-bp window), and normalised to x1 sequencing depth. Mononucleosomes were selected according to fragment length (135-170 bp). Duplicated reads were removed.
Genome_build: mm10

extract_protocol:
Biological replicates were obtained from two independent transfection experiments for each shRNA vector. Briefly, ~5 million cells were crosslinked with 1% formaldehyde for 20 min followed by quenching for 5 min with the addition of glycine to a final concentration of 0.125 M. After washing with PBS buffer, cells were collected and lysed in Cell Lysis buffer (5 mM Tris pH8.0, 85 mM KCl, 0.5% NP40 ) with proteinase inhibitors (10 µl/mL Phenylmethylsulfonyl fluoride (PMSF), 1 µl/mL Leupeptin and 1 µl/mL Pepstatin). Nuclei were gathered by centrifugation (5000 rpm for 2 min) and were treated with 10 Kunitz Units of micrococcal nuclease (NEB, #M0247S) per 10^6 cells for 5 min at 37°C. The reaction was stopped with the addition of 60 µl 50 mM EDTA, 25 µl 5 M NaCl, 15 µl 20% NP-40 and incubated on a rotator for 1h at room temperature to release soluble nucleosomes. Samples were centrifuged for 5 min at 10,000 g and supernatant was transferred to a new tube. Samples were reverse-crosslinked by incubating overnight at 65°C with 0.5% SDS and proteinase K. Following phenol-chloroform extraction and ethanol precipitation, DNA was incubated at 37°C for 4h with RNAse (Sigma). All the samples were run in a 2% agarose gel and fragments <200 bp were extracted and purified using the NucleoSpin® Gel and PCR Clean-up kit (Macherey-Nagel) according to the manufacturer’s instructions.
Purified DNA (500 ng) was used for library preparation as described previously (Tessarz, et al). The only difference was the PCR amplification step where we used the same conditions as mentioned in Henikoff et al but with only three amplification cycles.

value: control


title: siD1-2

first: Yang

address: 8th fuxing road

institute: PLA general hospital

description: Barcode: GTCCGCA

data_processing:
The  RAW-data was processed to map to Rattus norvegicus assembly 5.0.75 by Tophat  v2.0.8
The data was dealed by cuffldiff  v2.0.2 to calculate  Fragments Kilobase of exon model per millon mapped reads (FPKM)
Supplementary_files_format_and_content: FPKMs

organism: Rattus

source_name: mesangial cell

growth_protocol: mesangial cells were cultured in 15% FBS 1640

extract_protocol:
Trizol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: siRNA was transfected to inhibit the expression of DBP and NC siRNA was applied as control

value: Wistar

tag: passage

value: DBP knock-down

tag: cell type

value: mesangial cells


title: MNase-seq_Ssrp1-KD_rep1,rep2


title: RNA-seq_Control_rep1-4

growth_protocol: The E14 cell line (mESCs) was cultured at 37 °C, 7.5% CO2, on 0.1% gelatin coated plates, in DMEM + GlutaMax™ (Gibco) with 15% fetal bovine serum (Gibco), MEM non- essential amino acids (Gibco), penicillin/streptomycin (Gibco), 550 µM 2-mercaptoethanol (Gibco), and 10 ng/ml of leukaemia inhibitory factor (LIF) (eBioscience)


title: siD1-3

description: Barcode: GTTTCGG


title: siD1-1

description: Barcode: GTCCGCA


title: NC1

description: Barcode: TTAGGCA


title: NC2

description: Barcode: GATCAGA


title: NC3

description: Barcode: CGTACGT


title: asy_T10(HeatShock)_rep1

description: Gasch 167


title: SNU601-mir1271-mimic3

status: Public on Jun 12 2018

city: Daejeon

first: Jong Hwan

last: Kim

address: 125 Gwahak-ro, Yuseong-gu

department: Genome structure research center

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

data_processing:
Illumina Casava1.7 software used for basecalling.
mapped to hg19 whole genome using STAR v2.5.1.
Gene expression levels were calculated count-per-million (CPM) values normalized with trimmed mean of M-values (TMM) using a edgeR v.3.12.1. The CPM values are on log2 scale.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include CPM values for each Sample

source_name: gastric cancer cell line

extract_protocol:
MBD2-immunoprecipitated chromatin fragments were extracted for MBD-seq. RNAs were isolated using the mirVana miRNA Isolation Kit (Thermo Fisher Scientific)
We collected MBD2-immunoprecipitated chromatin fragments and genomic libraries were constructed using the TruSeq ChIP Sample Prep Kit (Illumina).RNAs were isolated using the mirVana miRNA Isolation Kit (Thermo Fisher Scientific) and libraries were prepared using the Illumina TruSeq Small RNA Sample Prep Kit.

treatment_protocol: Synthetic mimic of mir-1271 were purchased from the Thermo Fisher Scientific. 2×105 cells onto a 6-well plate (SPL) were transfected with 100 pmoles of miRNA using Lipofectamine® RNAiMAX (Invitrogen).

tag: molecular subtype

value: total RNA


title: SNU601-mir1271-mimic2


title: MKN74-mir1271-control3


title: SNU601-mir1271-control3


title: MKN74-mir1271-mimic3


title: MKN74-mir1271-mimic2


title: MKN74-mir1271-control2


title: asy_T30(NaCl)_rep1

description: Gasch 153

value: NaCl


title: DO+C CD19+ B cells; Sample_04_CD19

city: Ulm

first: Medhanie

middle: Assmelash

last: Mulaw

address: Albert-Einstein-Allee 11

institute: University of Ulm

data_processing:
Standard Illumina software used for basecalling and demultiplexing
Sequenced reads were trimmed for adaptor sequence, then mapped to mm10 using tophat
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) calculation, normalization, and differential expression analysis were calculated using Cufflinks and cuffdiff
Genome_build: mm10
Supplementary_files_format_and_content: Two tab-delimited text files (one for CD4 and one for CD19) with FPKM values of genes across all samples

source_name: sorted splenic CD19+ B cells

extract_protocol:
transplantation protocol: HSCs were isolated from young and aged B6.SJL mice. They were cultured for 16 hrs in HBSS + 10% FBS ± 5µM CASIN at 37°C (5% CO2, 3% O2). Subsequently, 600 LT-HSCs were transplanted into sublethally (6,5 Gy) irradiated RAG1-/- mice
cell isolation protocol: 12 weeks after transplantation, 50.000 naïve CD4+ T cells and CD19+ B cells were sorted in Ultra Culture medium
RNA was extracted from sorted cells using the RNeasy Micro Kit (Quiagen) following manufacturer's protocol
cDNA was processed with the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech). cDNA libraries were prepared using the Nextera XT DNA Library Prep Kit (Illumina)

value: RAG1-/- mouse transplanted with DO+C HSCS isolated from B6.SJL

value: splenic CD19+ B cells


title: DY CD19+ B cells; Sample_08_CD19

value: RAG1-/- mouse transplanted with DY HSCS isolated from B6.SJL


title: DO CD19+ B cells; Sample_06_CD19

value: RAG1-/- mouse transplanted with DO HSCS isolated from B6.SJL


title: DO CD19+ B cells; Sample_05_CD19


title: DY CD19+ B cells; Sample_09_CD19


title: DO CD19+ B cells; Sample_07_CD19


title: DY CD19+ B cells; Sample_10_CD19


title: DO+C CD19+ B cells; Sample_03_CD19


title: DO+C CD19+ B cells; Sample_01_CD19


title: SNU601-mir1271-control2


title: DO+C naive CD4+ T cells; Sample_03_CD4

source_name: sorted splenic naive CD4+ T cells

value: splenic naive CD4+ T cells


title: DO+C naive CD4+ T cells; Sample_04_CD4


title: DO naive CD4+ T cells; Sample_05_CD4


title: DO+C naive CD4+ T cells; Sample_01_CD4


title: DY naive CD4+ T cells; Sample_10_CD4


title: DO naive CD4+ T cells; Sample_06_CD4


title: DY naive CD4+ T cells; Sample_08_CD4


title: DY naive CD4+ T cells; Sample_09_CD4


title: DO naive CD4+ T cells; Sample_07_CD4


title: KO.rep1 [ChIP-seq]

city: Worcester

first: Kensuke

last: Futai

state: MA

address: 364 Plantation St

department: Neurobiology

institute: University of Massachusetts Medical School

description: processed data: ChIP-seq_IDRpeaks.bed

data_processing:
Basecalls performed using Illumina CASAVA version 1.8
RNA-seq: reads were quality trimmed/filtered using FASTX-Toolkit with quality score cutoff of 20
RNA-seq: filtered reads were mapped to mm10 whole genome using tophat v.2.0.9 with parameters --library-type fr-secondstrand
RNA-seq: read counts were calculated for each sample using HTSeq v.0.6.1 with UCSC gene annotation
ChIP-seq: reads were aligned to the mm10 genome using bowtie v.2.2.4 with default parameters
ChIP-seq: peaks were called using IDR analysis protocol described in Li Q et al., Ann Appl Stat, 2011. In short, all three KO samples were pooled and used as control for peak callings. Peaks were called on individual WT replicates, pooled WT replicate, pseudoreplicates of individual WT replicates, and pseudoreplicates of pooled WT replicate. At least 100k peaks were called for each sample using macs v.2.1.0 with relaxed threshold: -p 0.05 --nomodel --extsize 165. IDR threshold of 0.01 and 0.0025 were used for self-consistency and pooled-consistency test respectively to determine the number of final peaks called.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw read counts generated from HTSeq for each sample; bed file includes ChIP-seq peaks from IDR analysis (columns in bed file are: column1:chromosome; column2:start; column3:end; column4:-log10(pvalue))

growth_protocol: Mice were housed in animal facility with 12 h light/dark cycles and food ab libitum

extract_protocol:
Hippocampus was rapidly dissected from mice on ice, and crosslinked by 2 mM DSG for 20 min, followed by the addition of 1.5% formaldehyde during the last 10 min of DSG crosslinking. Nuclei preparation and chromatin digestion steps followed SimpleChIP Plus Enzymatic Chromatin IP Kit protocol (Cell Signaling). Chromatin was digested to 100 to 500bp fragments using MNase (micrococcal nuclease) and was immunoprecipitated with 10μg anti-L3mbtl1 antibody.
ChIP-seq library barcode: ACTTGA (lane1). Libraries were prepared from 10ng ChIP'd DNA using NEBNext Ultra DNA Library Prep Kit. Size selection was performed before amplification. Final approximate fragment length is 165bp.

treatment_protocol: no treatment

tag: strain background

tag: developmental stages

value: post natal day 7-8

tag: tissue/cell type

value: hippocampus


title: KO.rep2 [ChIP-seq]

description: processed data: ChIP-seq_IDRpeaks.bed

extract_protocol:
Hippocampus was rapidly dissected from mice on ice, and crosslinked by 2 mM DSG for 20 min, followed by the addition of 1.5% formaldehyde during the last 10 min of DSG crosslinking. Nuclei preparation and chromatin digestion steps followed SimpleChIP Plus Enzymatic Chromatin IP Kit protocol (Cell Signaling). Chromatin was digested to 100 to 500bp fragments using MNase (micrococcal nuclease) and was immunoprecipitated with 10μg anti-L3mbtl1 antibody.
ChIP-seq library barcode: CTTGTA (lane1). Libraries were prepared from 10ng ChIP'd DNA using NEBNext Ultra DNA Library Prep Kit. Size selection was performed before amplification. Final approximate fragment length is 165bp.


title: WT.rep2 [ChIP-seq]

description: processed data: ChIP-seq_IDRpeaks.bed

extract_protocol:
Hippocampus was rapidly dissected from mice on ice, and crosslinked by 2 mM DSG for 20 min, followed by the addition of 1.5% formaldehyde during the last 10 min of DSG crosslinking. Nuclei preparation and chromatin digestion steps followed SimpleChIP Plus Enzymatic Chromatin IP Kit protocol (Cell Signaling). Chromatin was digested to 100 to 500bp fragments using MNase (micrococcal nuclease) and was immunoprecipitated with 10μg anti-L3mbtl1 antibody.
ChIP-seq library barcode: GATCAG (lane1). Libraries were prepared from 10ng ChIP'd DNA using NEBNext Ultra DNA Library Prep Kit. Size selection was performed before amplification. Final approximate fragment length is 165bp.

value: wild type


title: WT.rep3 [ChIP-seq]

description: processed data: ChIP-seq_IDRpeaks.bed

extract_protocol:
Hippocampus was rapidly dissected from mice on ice, and crosslinked by 2 mM DSG for 20 min, followed by the addition of 1.5% formaldehyde during the last 10 min of DSG crosslinking. Nuclei preparation and chromatin digestion steps followed SimpleChIP Plus Enzymatic Chromatin IP Kit protocol (Cell Signaling). Chromatin was digested to 100 to 500bp fragments using MNase (micrococcal nuclease) and was immunoprecipitated with 10μg anti-L3mbtl1 antibody.
ChIP-seq library barcode: TGACCA (lane2). Libraries were prepared from 10ng ChIP'd DNA using NEBNext Ultra DNA Library Prep Kit. Size selection was performed before amplification. Final approximate fragment length is 165bp.


title: PTX.rep4 [RNA-seq]

source_name: hippocampal primary cultures_PTX

growth_protocol: Primary hippocampal cultures were prepared from postnatal day 0-1 mouse and maintained in 2% B27 supplement containing medium for 14 days in vitro

extract_protocol:
Total RNA was extracted from hippocampal primary cultures using RNAqueous Micro Kit (Ambion) and rRNA was depleted using RiboZero Kit (Illumina).
RNA-seq library barcode: GGCTAC. Libraries were prepared from 15ng rRNA-depleted RNA according to ScriptSeq v2 protocol.

treatment_protocol: treated with 100 μM picrotoxin for 15 hours

value: days in vitro 14

tag: treated with

value: Picrotoxin

value: hippocampal primary cultures


title: PTX.rep2 [RNA-seq]

extract_protocol:
Total RNA was extracted from hippocampal primary cultures using RNAqueous Micro Kit (Ambion) and rRNA was depleted using RiboZero Kit (Illumina).
RNA-seq library barcode: TTAGGC. Libraries were prepared from 15ng rRNA-depleted RNA according to ScriptSeq v2 protocol.


title: WT.rep1 [ChIP-seq]

description: processed data: ChIP-seq_IDRpeaks.bed

extract_protocol:
Hippocampus was rapidly dissected from mice on ice, and crosslinked by 2 mM DSG for 20 min, followed by the addition of 1.5% formaldehyde during the last 10 min of DSG crosslinking. Nuclei preparation and chromatin digestion steps followed SimpleChIP Plus Enzymatic Chromatin IP Kit protocol (Cell Signaling). Chromatin was digested to 100 to 500bp fragments using MNase (micrococcal nuclease). 40μg digested chromatin was immunoprecipitated with 10μg anti-L3mbtl1 antibody.
ChIP-seq library barcode: CAGATC (lane1). Libraries were prepared from 10ng ChIP'd DNA using NEBNext Ultra DNA Library Prep Kit. Size selection was performed before amplification. Final approximate fragment length is 165bp.


title: PTX.rep3 [RNA-seq]

extract_protocol:
Total RNA was extracted from hippocampal primary cultures using RNAqueous Micro Kit (Ambion) and rRNA was depleted using RiboZero Kit (Illumina).
RNA-seq library barcode: GATCAG.  Libraries were prepared from 15ng rRNA-depleted RNA according to ScriptSeq v2 protocol.


title: CTRL.rep4 [RNA-seq]

source_name: hippocampal primary cultures_control

extract_protocol:
Total RNA was extracted from hippocampal primary cultures using RNAqueous Micro Kit (Ambion) and rRNA was depleted using RiboZero Kit (Illumina).
RNA-seq library barcode: CTTGTA. Libraries were prepared from 15ng rRNA-depleted RNA according to ScriptSeq v2 protocol.

treatment_protocol: treated with 0.1% DMSO for 15 hours

value: DMSO control


title: CTRL.rep2 [RNA-seq]

extract_protocol:
Total RNA was extracted from hippocampal primary cultures using RNAqueous Micro Kit (Ambion) and rRNA was depleted using RiboZero Kit (Illumina).
RNA-seq library barcode: TGACCA. Libraries were prepared from 15ng rRNA-depleted RNA according to ScriptSeq v2 protocol.


title: CTRL.rep1 [RNA-seq]

extract_protocol:
Total RNA was extracted from hippocampal primary cultures using RNAqueous Micro Kit (Ambion) and rRNA was depleted using RiboZero Kit (Illumina).
RNA-seq library barcode: CGATGT. Libraries were prepared from 15ng rRNA-depleted RNA according to ScriptSeq v2 protocol.


title: SUSP_4

city: Uppsala

first: Gustav

last: Arvidsson

state: Uppsala

address: Husargatan 3

department: Department of Medical Sciences

country: Sweden

institute: Uppsala Universitet

description:
Sample_4D
hg19_count_table.csv, mm10_count_table.csv

data_processing:
Short reads were indexed using the species-based short read separation software Xenome (v1.0.1) for human and mouse based on UCSC reference genomes as specified below.
Species-specific PE short reads of human and murine origin were aligned to reference genomes hg19 and mm10 respectively using the splice aware short read aligner Tophat2 (2.0.11) with Bowtie2 (v2.2.2) and Samtools (v0.1.19) using PE read input and default options
Species specific read pairs per feature were counted using summarizeOverlaps from the Bioconductor (v2.14) package GenomicAlignments (v1.0.6). Annotated genes were acquired through Bioconductor packages TxDb.Hsapiens.UCSC.hg19.knownGene (v2.14.0) and TxDb.Mmusculus.UCSC.mm10.knownGene (v2.14.0).
Data was pairwise interrogated for differentially expressed genes using the Bioconductor package Deseq (v1.16.0).
Genome_build: hg19 (GRCh37) and mm10 (GRCm38) were obtained from the UCSC Genome Browser FTP server
Supplementary_files_format_and_content: hg19_count_table.csv: RAW read count table per feature for all samples after species-based separation of reads of human origin and alignment to hg19
Supplementary_files_format_and_content: mm10_count_table.csv: RAW read count table per feature for all samples after species-based separation of reads of murine origin and alignment to mm10

organism:
Homo sapiens
Mus musculus

source_name: MS-5, Jeko-1 (suspension fraction)

growth_protocol: MS-5 cells and Jeko-1 cells mono- or co-cultured in αMEM-glutamax (Gibco) supplemented with 10% H.I. FBS (Gibco), 2mM sodium pyruvate, 100U/mL penicillin and 100µg/mL streptomycin (Gibco). All cells were cultivated in a humidified incubator at 37°C and 5% CO2.

extract_protocol:
Total RNA was extracted using RNeasy (Qiagen) with QIAshredders following the protocol supplied by the manufacturer.
Libraries were constructed using Illumina Truseq 2.0 reagents according to manufacturers protocol, mRNA was purified by poly-T oligo-attached magnetic beads.

treatment_protocol: 5x10^5 MS-5 stromal cells were seeded 24h in advance to 10cm dishes (TPP) and 5x10^6 Jeko-1 cells were subsequently added. RNA was extracted following 24h of incubation at 37 degrees 5% CO2.

tag: cultivation

value: co-culture of two cell lines


title: dCas9-sgM5_1

city: Memphis

first: Beisi

last: Xu

state: Tennessee

address: 262 Danny Thomas Pl

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hosipital

data_processing:
Basecalls performed using CASAVA
After trimming nextra adapter with cutadapt(v 1.13), we used BWA (version 0.5.9-r26-dev, default parameter) to align the ChIP-Seq reads to mouse genome mm9(MGSCv37 from Sanger), Picard(version 1.65(1160)) then have been used for marking duplicated reads. Then only non-duplicated reads with have been kept by samtools (parameter “-q 1 -F 1804” version 0.1.18 (r982:295)).
center 80bp of nucleosome free reads were used generate bigwig file to view on IGV (version 2.3.40).
Genome_build: mm9(MGSCv37)
Supplementary_files_format_and_content: bigwig

source_name: retina

growth_protocol: Cells were cultured on ultra-low attachment dishes using N2B27 complete medium (Invitrogen), and human recombinant basic fibroblast growth factor (FGF) and epidermal growth factor (EGF) (PeproTech) were added to the culture medium every 2 days.

extract_protocol:
chromatin was prepared for shearing using the truChIP Chromatin Shearing Reagent Kit (Covaris,part number 520154); chromatin sheared by Covaris L-Series Focused-ultrasonicator; 350 Watts, 200 cycles per burst, 15% Duty Cycle, for 20 minutes
material indexed by standard illumina protocols and sent for HiSeq

treatment_protocol: 2x10^7 cells were fixed in 1% formaldehyde for 5 minutes

tag: guide rna

value: dCas9 (clontech, catalog number 632606)


title: dCas9-sgM5_2

tag: strain


title: ADH_4

description:
Sample_4C
hg19_count_table.csv, mm10_count_table.csv

source_name: MS-5, Jeko-1 (adherent fraction)


title: Parental_H3K4me3_ChIP

city: shanghai

first: wang

last: yujie

state: Shanghai

address: Chi Feng road No:65

institute: Shanghai JiaYin Biological technology co., LTD

data_processing:
ChIP-seq reads were aligned to the hg19 reference genome using BWA(0.7.10)
Sam files were converted to Bam format using Samtools and used for peak calling
MACS2 version 2.1.1 was used to call peaks with the sonicated input as a control and an initial threshold q-value of 0.01 as cutoff
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files were generated using MACS

growth_protocol: HL-60 were grown in DMEM supplemented with 10%FBS, at 37 °C in a humidified atmosphere with 5% CO2

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: myeloblast

value: parental

value: H3K4me3 (Abcam, ab8580)


title: JMJD3_KO_H3K27me3_ChIP

value: JMJD3 KO

value: H3K4me3 (Abcam, ab6002)


title: Parental_H3K27me3_ChIP


title: JMJD3_KO_K3K4me3_ChIP


title: HL-60_C/EBPβ_input

tag: gentoype/variation

value: C/EBPβ-overexpressed


title: JMJD3_KO_input

tag: chip antibody


title: CTRL.rep3 [RNA-seq]

extract_protocol:
Total RNA was extracted from hippocampal primary cultures using RNAqueous Micro Kit (Ambion) and rRNA was depleted using RiboZero Kit (Illumina).
RNA-seq library barcode: TAGCTT. Libraries were prepared from 15ng rRNA-depleted RNA according to ScriptSeq v2 protocol.


title: PTX.rep1 [RNA-seq]

extract_protocol:
Total RNA was extracted from hippocampal primary cultures using RNAqueous Micro Kit (Ambion) and rRNA was depleted using RiboZero Kit (Illumina).
RNA-seq library barcode: ATCACG. Libraries were prepared from 15ng rRNA-depleted RNA according to ScriptSeq v2 protocol.


title: KO.rep3 [ChIP-seq]

description: processed data: ChIP-seq_IDRpeaks.bed

extract_protocol:
Hippocampus was rapidly dissected from mice on ice, and crosslinked by 2 mM DSG for 20 min, followed by the addition of 1.5% formaldehyde during the last 10 min of DSG crosslinking. Nuclei preparation and chromatin digestion steps followed SimpleChIP Plus Enzymatic Chromatin IP Kit protocol (Cell Signaling). Chromatin was digested to 100 to 500bp fragments using MNase (micrococcal nuclease) and was immunoprecipitated with 10μg anti-L3mbtl1 antibody.
ChIP-seq library barcode: CAGATC (lane2). Libraries were prepared from 10ng ChIP'd DNA using NEBNext Ultra DNA Library Prep Kit. Size selection was performed before amplification. Final approximate fragment length is 165bp.


title: Parental_input


title: dCas9-sgM7_2


title: ADH_1

description:
Sample_1C
hg19_count_table.csv, mm10_count_table.csv


title: SUSP_2

description:
Sample_2D
hg19_count_table.csv, mm10_count_table.csv


title: SUSP_3

description:
Sample_3D
hg19_count_table.csv, mm10_count_table.csv


title: ADH_3

description:
Sample_3C
hg19_count_table.csv, mm10_count_table.csv


title: ADH_2

description:
Sample_2C
hg19_count_table.csv, mm10_count_table.csv


title: dCas9-sgM9


title: SUSP_1

description:
Sample_1D
hg19_count_table.csv, mm10_count_table.csv


title: SEP_2

description:
Sample_2B
hg19_count_table.csv, mm10_count_table.csv

source_name: -, Jeko-1

value: mono-cultured cell line

value: mantle cell lymphoma cell line