title: G98_M1

description: Liver DNase-I released fragments

source_name: DNase of male mouse liver_3 h vehicle_pool1_G98_M1


title: G91_M2

status: Public on Apr 09 2018

type: SRA

city: Boston

first: David

middle: J.

last: Waxman

state: MA

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

country: USA

institute: Boston University

description: Liver DNase-I released fragments

library_source: genomic

data_processing:
27 h data sets were processed as single end reads, by using read1 (R1) only, for consistency with the 3 h data sets. Sequence reads were mapped to the mouse genome (mm9) using Bowtie
Peaks were called using MACS2
Genome_build: mm9
Supplementary_files_format_and_content: Excel spreadhseet; MACS2 output (peaks discovered and statistics per peak)

molecule: genomic DNA

organism: Mus musculus

source_name: DNase of female mouse liver_3 h vehicle_pool2_G91_M2

extract_protocol:
DNA fragments were released from regions hypersensitive to DNase-I cutting and purified using a two step process: 1) sucrose gradient to isolate fragments less than 1-kb; followed by 2) SPRI bead purification isolating DNA fragments 125-400 bp
NEBNext Ultra DNA library prep kit for Illumina
SE50 or PE50 DNase-Seq. Sample from 27 h data sets were processed as single end reads by using read1 (R1) only.

treatment_protocol: Male and female CD1 (ICR) mice were obtained from Charles River Labs (Wilmington, MA) at 7 weeks of age. Mice were injected i.p. with 3 mg/kg TCPOBOP or vehicle alone (1% DMSO in corn oil)  between 8:00-8:45 AM on Day 1 and liver was collected between 11:00-11:45 AM on Day 1 (3 h) or between 11:00-11:45 AM on Day 2 (27 h). Nuclei were isolated and stored at -80C prior to DNase-I digestion.

tag: strain

value: CD-1 (Charles River)

tag: treatment

value: Vehicle (1% DMSO in corn oil)_ 3 h exposure

tag: Sex

value: female

tag: age

value: 7 weeks

tag: tissue

value: liver


title: G91_M4

description: Liver DNase-I released fragments

source_name: DNase of female mouse liver_3 h TCPOBOP_pool2_G91_M4

value: 3 mg/kg TCPOBOP_ 3 h exposure


title: G91_M1

description: Liver DNase-I released fragments

source_name: DNase of female mouse liver_3 h vehicle_pool1_G91_M1


title: Non-Reactive CMV specific CD8 lymphocyte

city: Bruce

first: Kristine

last: Hardy

state: ACT

address: University of Canberra

country: Australia

institute: University of Canberra

description: NonReactive

data_processing:
Adapters stripped using trimmomatic
Reads mapped with Bowtie2. Only uniquely mapped reads used.
Duplicates removed using Picard
bedgraph files from HOMER, reads extended 200bp.
Peaks called against TI, called with MACS2 (-broad) and filtered on q value < 0.01 and >=3 fold enrichment.
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph files show tag densities for the different cell types for FAIRE and Total Input (TI). Bed files are peaks for FAIRE against TI.

organism: Homo sapiens

source_name: CD8 lymphocyte

extract_protocol:
Cells were cross-linked with 1% formaldehyde for 10 minutes, the reaction is then quenched by adding 2.5M glycine (final concentration of 125mM). Fixed cells were lysed in 500ul SDS lysis buffer and chromatin bound DNA was then sheared by sonication. Nucleosome free DNA (FAIRE DNA) was extracted by using phenol-chloroform and reverse-crosslinked at 65oC. The Zymo-SpinTM I kit (Zymo Research) was then used to purify FAIRE DNA.
FAIRE DNA, and the corresponding total input, were used to prepare the FAIRE-seq DNA library using the NEBNext® Ultra DNA Library Prep Kit for Illumina® (New England BioLabs)

treatment_protocol: To detect or isolate CMV-specific or naïve T cells, PBMCs were incubated with APC- or PE-conjugated MHC class I multimers specific for the HLA A*01:01-restricted epitope VTEHDTLLY, HLA A*02:01-restricted epitope NLVPMVATV, HLA B*07:02-restricted epitopes TPRVTGGGAM and RPHERNGFTVL, or the HLA B*08:01-restricted epitope ELKRKMIYM (MHC-multimers were supplied by Immudex, Copenhagen, Denmark, or generated in-house). Cells were incubated with PerCP-Cy5.5-conjugated anti-CD8 (eBioscience; Thermo Fisher Scientific, Waltham, MA), Alexa-Fluor-700- or Pacific Blue-conjugated anti-CD4 (BD Biosciences), live/dead near IR (Thermo Fisher Scientific), PE-Cy7 CCR7 (BD Biosciences; Thermo Fisher Scientific), and CD45RA-FITC (BD Biosciences).

tag: cell type

value: T cells

tag: cell markers


title: Total Input

description: TI


title: Reactive CMV specific CD8 lymphocyte

description: Reactive


title: EIF5A_2

city: Copenhagen N

first: Imke

last: Tiessen

address: Ole Maaløes Vej 5

department: Biotech Research and Innovation Centre (BRIC)

country: Denmark

institute: University of Copenhagen

library_source: transcriptomic

data_processing:
Raw RNA-seq data was subjected to quality control filters applying threshold of Phred (quality) >= 25.
Prior to mapping, Illumina adapters were removed and the reads were trimmed using cutadapt.
Read mapping was performed with bowtie2 (version 2.2.4).
Counting of reads was performed using Bam files in HTSeq (using gencode hg19 gene annotations). Read counts were analysed by DESeq2in R environment.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files containing RNA seq peaks

molecule: total RNA

source_name: MCF-7 cells

growth_protocol: MCF-7 cells (stably expressing with eGFP-LC3) were cultured in RPMI L-Glutamine media, supplemented with 6 % FBS.

extract_protocol:
Total RNA from three biological replicates was purified and depleted for ribosomal RNA using the Illumina Ribo-Zero Magnetic Gold rRNA removal kit (MRZG12324).
Libraries were built using the Illumina TruSeq kit (RPHMR12126) according to the manufacturer’s protocol.

treatment_protocol: Cells were reverse transfected for 72 h with 10 nM silencer-select siRNAs against EIF5A or scramble using Lipofectamine2000. Media was renewed after 24 h.

tag: cell line

tag: transfection

value: siRNA-mediated knockdown of EIF5A


title: Naive CD8 lymphocyte

description: Naive

value: CD8+CD45RA+ CCR7+


title: EIF5A_3


title: CTRL_1

value: control siRNA


title: EIF5A_1


title: CTRL_3


title: CTRL_2


title: G115_M4

description: Liver DNase-I released fragments

source_name: DNase of male mouse liver_27 h TCPOBOP_pool2_G115_M4

value: 3 mg/kg TCPOBOP_27 h exposure

value: male


title: G98_M3

description: Liver DNase-I released fragments

source_name: DNase of male mouse liver_3 h TCPOBOP_pool1_G98_M3


title: M3_p1_3

city: Freiburg im Breisgau

first: Josip

middle: Stefan

last: Herman

address: Stuebeweg 51

department: Quantitative Single Cell Biology

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

description: Library of 96 cells

data_processing:
For image aquisition, intensity extraction and basecalling HiSeq Control Software  2.0.2, RTA 2.4.11 / Recipe Fragment 2.0.0.2 was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14
Paired end reads were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all RefSeq gene models based on the mouse genome release mm10 downloaded from the UCSC genome browser. All isoforms of the same gene were merged to a single gene locus.
The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction (Baker et al., 2005). Reads mapping to multiple loci were discarded.
The left read contains the barcode information: the first six bases corresponded to the cell specific barcode followed by six bases representing the unique molecular identifier (UMI). The remainder of the left read contains a polyT stretch. The left read was not used for mapping to the reference transcriptome.
For each cell barcode, the number of UMIs per transcript were counted and aggregated across all transcripts derived from the same gene locus.
Based on binomial statistics, the number of observed UMIs were converted into transcript counts (Grün et al., 2014).
genome build: mm10
Supplementary_files_format_and_content: CSV files, columns represent each cell barcode (total barcodes used = 192), rows represent the geneid and the values in the file are the quantified number of transcripts.

source_name: Bone marrow-derived lymphoid progenitors

growth_protocol: Hematopoietic progenitors were isolated from C57BL/6J wildtype mice.

extract_protocol:
Bone marrow of 5-week old male C57BL/6J wildtype mice purchased from Charles River or from in house breedings of C57BL/6J wildtype mice was isolated from femora and tibiae by flushing using 1x MojoSort™ Buffer (BioLegend®, 480017). Hematopoietic progenitors were enriched using the MojoSort™ Mouse Hematopoietic Progenitor Cell Isolation Kit (BioLegend®, 480004), stained and sorted according to different surface markers.
The amplified RNA (aRNA) was reversely transcribed in order to generate libraries for sequencing, as previously described. 1 µl of custom random hexamer RT primers (GCCTTGGCACCCGAGAATTCCANNNNNN) and 0.5 µl of 10mM dNTP were added to the aRNA. The samples were incubated at 65˚C for 5 min and cooled to 4˚C afterwards. Thereafter 4 µl of First Strand Reaction Mix containing SuperScript™ II Reverse Transcriptase and Buffer (Invitrogen, 18064014) and RnaseOUT™ (Invitrogen, 10777019) was added and samples were first incubated at 25˚C for 10 min followed by incubation at 42˚C for 1 hour. To every sample 2 µl of one uniquely indexed RPI index primer and 2 µl of RP1 primer (TruSeq Library Prep, sequences available from Illumina), 25 µl of Phusion® High-Fidelity PCR Master Mix with HF Buffer (NEB, M0531) and 11 µl of nuclease-free water were added. PCR was performed using 98˚C for 30 s as initial step, followed by 11 cycles of amplification (98˚C for 10 s, 60˚C for 30 s, 72˚C for 30 s) and a final extension at 72˚C for 10 min. To each sample 1 volume (50 µl) of Agencourt® AMPure XP beads (Beckman Coulter, A63881) was added and the samples were incubated at 25˚C for 15 min. The samples were incubated for 5 min on a magnetic stand (96 well format), the supernatant was removed and the beads were washed twice by adding 180 µl of 80 % ethanol and by incubating for 40 s. Ethanol was removed and beads were dried for 10 min at room temperature. DNA was eluted with 25 µl nuclease-free water and the purification was repeated with an adjusted volume of magnetic beads (25 µl). After the final step the samples were eluted in 10 µl nuclease-free water. DNA concentration and fragment size were determined using the Qubit® dsDNA HS Assay Kit (Invitrogen, Q32854) and the Agilent High Sensitivity DNA Kit for Bioanalyzer (Agilent Technologies, 5067-4627), respectively. Libraries were sequenced on an Illumina HiSeq 2500 System in high output run mode at a depth of 150000 to 200000 reads per cell.
CEL-Seq2 (Hashimshony et al. 2016, Genome Biology, DOI: 10.1186/s13059-016-0938-8)

treatment_protocol: no treatment

value: bone marrow

tag: surface marker

value: cells from different gates based on Sca-1,c-Kit, Flt3 expression

tag: illumina barcode

tag: barcode sequence

value: GGCTAC


title: ES_2_1fold

description: Library of 48 cells

value: no surface marker, only FSC & SSC

value: CGATGT


title: NP1_10

description: Library of 96 cells

value: Lin neg, Sca lo/neg, c-Kit lo, Flt3+

value: TAGCTT


title: M3_p1_4

description: Library of 96 cells

value: CTTGTA


title: NP1_9

description: Library of 96 cells

value: GATCAG


title: M3_p1_2

description: Library of 96 cells


title: M3_p1_1

description: Library of 96 cells


title: ES_2_7fold

description: Library of 48 cells

value: TGACCA


title: M1_p1_4

description: Library of 96 cells


title: M1_p1_3

description: Library of 96 cells

value: TTAGGC


title: M1_p1_2

description: Library of 96 cells


title: M1_p2_34

description: Library of 192 cells

value: CAGATC


title: M1_p2_1

description: Library of 96 cells

value: ACAGTG


title: M1_p2_2

description: Library of 96 cells

value: GCCAAT


title: ES_2_10fold

description: Library of 48 cells


title: CLP2

description: Library of 192 cells

value: Lin neg, Sca-1 lo, c-Kit lo,


title: M1_p1_1

description: Library of 96 cells

value: ATCACG


title: CLP1

description: Library of 192 cells


title: LMPP2_2

description: Library of 192 cells

value: Lin neg, Sca-1 hi, c-Kit hi, Flt3 pos


title: ES_2_5fold

description: Library of 48 cells

value: bone marrow


title: LMPP2_1

description: Library of 192 cells


title: LMPP1_1

description: Library of 192 cells


title: LSK2

description: Library of 192 cells

value: Lin neg, Sca-1 hi, c-Kit hi


title: LSK1

description: Library of 192 cells

value: ACTTGA


title: Line5-14 Tet1/2 dKO + DMSO + Nanog rep1

city: New York

first: Richard

last: Koche

state: New York

institute: Memorial Sloan Kettering Cancer Center

data_processing:
ATAC-seq reads were filtered for quality and 3' trimmed for adapter sequences.
Reads were aligned to mouse assembly mm9 using bowtie2 (v2.2.2) with default parameters.
To create density files, the reads were extended to 200 bp, the signal was then normalized to ten million mapped reads and converted to BigWig using BEDTools.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: BigWig files containing read densities normalized to 10 million reads.

source_name: mESC, Tet1/2 double KO + Nanog Tg, DMSO

growth_protocol: ESCs were maintained on gelatin-coated plates in serum/LIF (S/L) medium containing Knockout DMEM (Gibco) supplemented with 10% ESC-qualified FBS (Gemini), penicillin/streptomycin (Life Technologies), 0.1 mM 2-mercaptoethanol, 2 mM L-glutamine (Life Technologies) and 1000 U/mL LIF (Millipore).

extract_protocol:
Cell nuclei were fresh prepared from 50,000 cells as previously described (Buenrostro et al. 2013 Nature Methods).
ATAC-seq was performed as previously described (Buenrostro et al. 2013 Nature Methods). For each sample, cell nuclei were prepared from 50,000 cells, and incubated with 2.5 uL transposase (Illumina) in a 50 uL reaction for 30 min at 37°C. Following purification of transposase fragmented DNA, the library was amplified by PCR and subjected to high-throughput sequencing using Illumina HiSeq 2500 platform.

treatment_protocol: For culture in 2i (S/L+2i), S/L medium was supplemented with 2i: 3 µM CHIR99021 (Stemgent) and 1 µM PD0325901 (Stemgent). Cells were adapted to S/L+2i for at least three passages prior to experiments and were maintained in S/L+2i for no more than 9 passages. For BET inhibitor treatment, cells were treated with JQ1 at 500 nM for 24 hours (vs DMSO vehicle control).

value: embryonic stem cells

tag: genotype/variation

value: Tet1/2 double KO + Nanog Tg

value: DMSO


title: Line5-14 Tet1/2 dKO + DMSO + Nanog rep2


title: Line5-14 Tet1/2 dKO + JQ1 + Nanog rep1

source_name: mESC, Tet1/2 double KO + Nanog Tg, JQ1


title: Line5-14 Tet1/2 dKO + JQ1 + Nanog rep2


title: Line5-14 Tet1/2 dKO + JQ1 rep2


title: Line5-14 Tet1/2 dKO + JQ1 rep1


title: Line5-9 Tet1/2 dKO + DMSO + Nanog rep2


title: Line5-14 Tet1/2 dKO + DMSO rep1


title: Line5-9 Tet1/2 dKO + JQ1 + Nanog rep2


title: Line5-9 Tet1/2 dKO + DMSO + Nanog rep1


title: Line5-9 Tet1/2 dKO + JQ1 + Nanog rep1


title: 171_SG_S3_MO_12_B2

city: Udine

first: Emanuele

last: De Paoli

state: UDINE

address: via delle Scienze 206

department: Agricultural, Food, Environmental and Animal Sciences

country: Italy

institute: University of Udine

data_processing:
Quality of raw sequencing data was evaluated with the FastQC software (Babraham Institute, Cambridge, UK).
Adaptor sequences were removed using the TRIM GALORE program (Babraham Institute, Cambridge, UK) with default settings and hard-trimmed from position 1 to 5 nt to improve data quality
Cleaned reads were aligned to the grapevine reference genome (Jaillon et al., 2007) using the bisulfite alignment program Bismark v0.14.5 (Krueger et al., 2011; Babraham Institute, Cambridge, UK)
Alignments were deduplicated and converted into single-cytosine methylation maps by ancillary methods of the Bismark package (deduplicate_bismark and bismark_methylation_extractor respectively) with default settings
Genome_build: Viti vinifera Genoscope 12X
Supplementary_files_format_and_content: Methylkit profile files

organism: Vitis vinifera

source_name: Sangiovese; Mid-ripening; Riccione; 2012; Replicate B

growth_protocol: Grapevine berry samples were collected from 7/10-year-old vineyards located in Bolgheri - wine cellar Podere Guado al Melo (Tuscany coast), Montalcino - wine cellar Banfi Srl (Tuscany Apennines) and Riccione - wine cellar Valbruna Soc. Coop. Agricola (Romagna coast) during the 2011-2012 growing seasons at the same time of day (~ 11:00 am). Per each experimental site, berries of two different cultivars, Cabernet Sauvignon and Sangiovese, have been sampled. To avoid major environmental differences, the berry sampling was performed, in each farm, on adjacent vineyards for Cabernet Sauvignon and Sangiovese (Fig. 1a). The most relevant features per each vineyard are reported in Supplementary Table 1.

extract_protocol:
Genomic DNA was isolated from approximately 100 mg of berry pericarps by the Doyle&Doyle protocol (Focus, 1990)
Reduced Representation Bisulfite Sequencing (RRBS) libraries were constructed acccording to Gu et al. 2011 with modifications. DNA was digested with TaqI enzyme (recognition site T^CGA, NEB, Ipswich, MA, USA) at 65°C for 2 h. After purification using the QIAquick PCR Purification kit (QIAGEN, Germany), fragment ends were repaired and ligated using adapters and the protocol provided by the Ovation Ultralow Methyl-Seq DR Multiplex Kit (NuGEN, CA, USA). Ligated products corresponding to 100–1500 bp DNA fragments were purified by 2% Low-Range agarose gel electrophoresis. A final end-repair step of the purified fragments was performed using the same NuGEN kit. Bisulfite conversion was conducted using a EpiTect Fast DNA Bisulfite Kit (QIAGEN, Germany). The final RRBS libraries were generated by PCR amplification and validated by an Agilent 2100 Bioanalyzer (Agilent Technologies).
Reduced Representation Bisulfite Sequencing (RRBS) libraries sequenced using the Illumina HiSeq2500 platform (Illumina, San Diego, CA, USA) in paired-ended (PE), 125 bp runs

tag: cultivar

value: Sangiovese

tag: developmental stage

value: Mid-ripening, MR, berries developing color, BBCH 83

tag: area

value: Riccione, Romagna coast, Italy

tag: year


title: Line5-14 Tet1/2 dKO + DMSO rep2


title: 170_SG_S3_MO_12_B1

source_name: Sangiovese; Mid-ripening; Riccione; 2012; Replicate A


title: 165_SG_S3_MI_12_B2

source_name: Sangiovese; Mid-ripening; Montalcino; 2012; Replicate B

value: Montalcino, Tuscany Apennines, Italy


title: 167_SG_S3_MO_11_B1

source_name: Sangiovese; Mid-ripening; Riccione; 2011; Replicate A


title: 164_SG_S3_MI_12_B1

source_name: Sangiovese; Mid-ripening; Montalcino; 2012; Replicate A


title: Line5-9 Tet1/2 dKO + JQ1 rep2

source_name: mESC, Tet1/2 double KO, JQ1

value: Tet1/2 double KO


title: 161_SG_S3_MI_11_B1

source_name: Sangiovese; Mid-ripening; Montalcino; 2011; Replicate A


title: Line5-9 Tet1/2 dKO + DMSO rep2

source_name: mESC, Tet1/2 double KO, DMSO


title: Line5-9 Tet1/2 dKO + JQ1 rep1


title: 162_SG_S3_MI_11_B2

source_name: Sangiovese; Mid-ripening; Montalcino; 2011; Replicate B


title: Nanog transgene + JQ1 rep2

source_name: mESC, Nanog transgene, JQ1

value: Nanog transgene


title: 168_SG_S3_MO_11_B2

source_name: Sangiovese; Mid-ripening; Riccione; 2011; Replicate B


title: Line5-9 Tet1/2 dKO + DMSO rep1


title: Nanog transgene + JQ1 rep1


title: LMPP1_2

description: Library of 192 cells

tag: strain


title: Nanog transgene + DMSO rep2

source_name: mESC, Nanog transgene, DMSO

tag: treatment


title: 156_SG_S3_BO_11_B2

source_name: Sangiovese; Mid-ripening; Bolgheri; 2011; Replicate B

value: Bolgheri, Tuscany coast, Italy


title: 159_SG_S3_BO_12_B2

source_name: Sangiovese; Mid-ripening; Bolgheri; 2012; Replicate B


title: 152_SG_S2_MO_12_B1

source_name: Sangiovese; Pre-veraison; Riccione; 2012; Replicate A

value: Pre-veraison, PV, majority of berries touching, BBCH 79


title: 155_SG_S3_BO_11_B1

source_name: Sangiovese; Mid-ripening; Bolgheri; 2011; Replicate A


title: 150_SG_S2_MO_11_B2

source_name: Sangiovese; Pre-veraison; Riccione; 2011; Replicate B


title: 153_SG_S2_MO_12_B2

source_name: Sangiovese; Pre-veraison; Riccione; 2012; Replicate B


title: Nanog transgene + DMSO rep1


title: JQ1 (control for Nanog Tg) rep2

source_name: mESC, WT, JQ1

value: WT

value: JQ1 (control for Nanog Tg)


title: 147_SG_S2_MI_12_B2

source_name: Sangiovese; Pre-veraison; Montalcino; 2012; Replicate B


title: JQ1 (control for Nanog Tg) rep1


title: DMSO (control for Nanog Tg) rep2

source_name: mESC, WT, DMSO

value: DMSO (control for Nanog Tg)


title: 143_SG_S2_MI_11_B1

source_name: Sangiovese; Pre-veraison; Montalcino; 2011; Replicate A


title: 146_SG_S2_MI_12_B1

source_name: Sangiovese; Pre-veraison; Montalcino; 2012; Replicate A


title: 158_SG_S3_BO_12_B1

source_name: Sangiovese; Mid-ripening; Bolgheri; 2012; Replicate A


title: 140_SG_S2_BO_12_B1

source_name: Sangiovese; Pre-veraison; Bolgheri; 2012; Replicate A


title: Serum LIF + 2i + JQ1 rep2

source_name: mESC, WT, Serum LIF + 2i + JQ1

value: Serum LIF + 2i + JQ1


title: Serum LIF + 2i + JQ1 rep1


title: DMSO (control for Nanog Tg) rep1


title: 137_SG_S2_BO_11_B1

source_name: Sangiovese; Pre-veraison; Bolgheri; 2011; Replicate A


title: 135_CS_S3_MO_12_B2

source_name: Cabernet Sauvignon; Mid-ripening; Riccione; 2012; Replicate B

value: Cabernet Sauvignon


title: 129_CS_S3_MI_12_B2

source_name: Cabernet Sauvignon; Mid-ripening; Montalcino; 2012; Replicate B


title: 132_CS_S3_MO_11_B2

source_name: Cabernet Sauvignon; Mid-ripening; Riccione; 2011; Replicate B


title: 131_CS_S3_MO_11_B1

source_name: Cabernet Sauvignon; Mid-ripening; Riccione; 2011; Replicate A


title: Serum LIF + 2i rep2

source_name: mESC, WT, Serum LIF + 2i

value: Serum LIF + 2i


title: Serum LIF + JQ1 rep2

source_name: mESC, WT, Serum LIF + JQ1

value: embryonic stem cells

value: Serum LIF + JQ1


title: 149_SG_S2_MO_11_B1

source_name: Sangiovese; Pre-veraison; Riccione; 2011; Replicate A


title: 126_CS_S3_MI_11_B2

source_name: Cabernet Sauvignon; Mid-ripening; Montalcino; 2011; Replicate B


title: Serum LIF + JQ1 rep1


title: 122_CS_S3_BO_12_B1

source_name: Cabernet Sauvignon; Mid-ripening; Bolgheri; 2012; Replicate A


title: 123_CS_S3_BO_12_B2

source_name: Cabernet Sauvignon; Mid-ripening; Bolgheri; 2012; Replicate B


title: 125_CS_S3_MI_11_B1

source_name: Cabernet Sauvignon; Mid-ripening; Montalcino; 2011; Replicate A


title: Serum LIF + 2i rep1


title: 144_SG_S2_MI_11_B2

source_name: Sangiovese; Pre-veraison; Montalcino; 2011; Replicate B


title: WT treated with SQ109, rep2

city: East Lansing

first: Robert

middle: B.

last: Abramovitch

state: MI

address: 567 Wilson Road

department: Microbiology and Molecular Genetics

institute: Michigan State University

data_processing:
Illumina bcl2fastq (v1.8.4) was used to de-multiplexe and converte reads to FASTQ format
Trimmomatic (v0.30) was used to trim low quality bases and remove adapter sequences with a 4 bp sliding window, cutting when the read quality dropped below 15 or read length was less than 36 bp.
Bowtie was used to align trimmed reads to the M. tuberculosis CDC1551 genome (NCBI accession AE000516) with the -S option to produce SAM files as output.
SAMtools was used to calculate coverage depth (>98% coverage acrosss the genome for all samples).
HTSeq software suite was used to analyze aligned and determin counts per gene feature in the M. tuberculosis CDC1551 genome
R was used for statistical analysis and differential gene expression by fitting a negative binomial model to each set of conditions and testing for differences utilizing the edgeR package
Qualimap was used to analyze coverage against the reference genome, sequence depth and pearson's correlation coefficient between replicates
Genome_build: M. tuberculosis CDC1551 genome (NCBI accession AE000516)
Supplementary_files_format_and_content: Processed files are presented as .csv spreadsheets and represents the average of 2 biological replicates
Supplementary_files_format_and_content: SupplementalTableS1: Normalized counts and differential expression Pyruvate pH 7.0 vs Glycerol pH 7.0; Differentially regulated genes by HC2091 and SQ109 treatments
Supplementary_files_format_and_content: SupplementalTableS2: Normalized counts and differential expression Glycerol pH 5.7 vs Glycerol pH 7.0; Full processed gene tables for HC2091 and SQ109 treatments

organism: Mycobacterium tuberculosis

source_name: Bacterial cell

growth_protocol: Mtb strain CDC1551 was grown at 37ºC in T-25 vented, standing tissue culture flasks in 8 mL of buffered 7H9 medium to an OD600 of 0.1.

extract_protocol:
RNA was extracted using the method Rohde, Abramovitch and Russell, Cell Host and Microbe, 2007. Briefly, RNA was stabilized and isolated using a guanidine thiocyanate-based lysis buffer as previously described. Pelleted mycobacteria were lysed using 5 μg/ml lysozyme, hot Trizol, and physical disruption with silica beads in a BeadBeater. Total RNA was isolated by chloroform extraction followed by direct application to QIAGEN RNeasy column purification. Residual DNA contamination was removed using Turbo DNAfree DNase (Ambion). RNA quality and integrity were examined using an Agilent Bioanalyzer prior to subjecting samples to rRNA depletion using the Epicentre Ribo-Zero depletion kit.
cDNA libraries were constructed using the Illumina TruSeq RNA library preparation kit (v2), omitting the polyA selection step. Multiplexing sequences are included in the title of the associated fastq.gz files.
After library quality control, sample libraries were pooled and sequenced in one lane of an Illumina HiSeq 2500 Rapid Run flow cell (v1) in 50bp, single-end read format (SE50). After the sequencing run, reads were de-multiplexed and converted to FASTQ format using the Illumina bcl2fastq (v1.8.4) script.

treatment_protocol: Mtb cultures were subsequently treated with 10 µM HC2091 or SQ109. For the control, cultures treated with an equal amount of DMSO. Following a 24 h incubation period, RNA was isolated from the bacterial cultures and used for RNA-seq. For each condition, 2 biological replicates were performed.

tag: chemical treatment


title: 138_SG_S2_BO_11_B2

source_name: Sangiovese; Pre-veraison; Bolgheri; 2011; Replicate B


title: 119_CS_S3_BO_11_B1

source_name: Cabernet Sauvignon; Mid-ripening; Bolgheri; 2011; Replicate A


title: 134_CS_S3_MO_12_B1

source_name: Cabernet Sauvignon; Mid-ripening; Riccione; 2012; Replicate A


title: 141_SG_S2_BO_12_B2

source_name: Sangiovese; Pre-veraison; Bolgheri; 2012; Replicate B


title: 117_CS_S2_MO_12_B2

source_name: Cabernet Sauvignon; Pre-veraison; Riccione; 2012; Replicate B


title: WT treated with HC2091, rep2


title: WT treated with SQ109, rep1


title: 116_CS_S2_MO_12_B1

source_name: Cabernet Sauvignon; Pre-veraison; Riccione; 2012; Replicate A


title: Serum LIF rep1

source_name: mESC, WT, Serum LIF

value: Serum LIF


title: Serum LIF rep2


title: 113_CS_S2_MO_11_B1

source_name: Cabernet Sauvignon; Pre-veraison; Riccione; 2011; Replicate A


title: WT treated with DMSO, rep2

value: DMSO


title: 114_CS_S2_MO_11_B2

source_name: Cabernet Sauvignon; Pre-veraison; Riccione; 2011; Replicate B


title: 128_CS_S3_MI_12_B1

source_name: Cabernet Sauvignon; Mid-ripening; Montalcino; 2012; Replicate A

value: Mid-ripening, MR, berries developing color, BBCH 83


title: WT treated with DMSO, rep1


title: SL2iJQ-Med1

data_processing:
ChIP-seq reads were filtered for quality and 3' trimmed for adapter sequences.
Reads were aligned to mouse assembly mm9 using bowtie2 (v2.2.2) with default parameters.
To create density files, the reads were extended to 200 bp, the signal was then normalized to ten million mapped reads and converted to BigWig using BEDTools.
Genome_build: mm9
Supplementary_files_format_and_content: BigWig files containing read densities normalized to 10 million reads

source_name: mESC

growth_protocol: ESCs were maintained on gelatin-coated plates in serum/LIF (S/L) medium containing Knockout DMEM (Gibco) supplemented with 10% ESC-qualified FBS (Gemini), penicillin/streptomycin (Life Technologies), 0.1 mM 2-mercaptoethanol, 2 mM L-glutamine (Life Technologies) and 1000 U/mL LIF (Millipore).Ê

extract_protocol: ChIP-seq libraries were constructed with the NEBNext ChIP-seq library prep kit following the manufacturer’s recommended protocol (New England Biolabs, Ipswich, MA, USA).

tag: treatment medium

tag: chip antibody

value: anti-Med1, Bethyl Laboratories A300-793A


title: SLJQ-Med1-Input


title: SL2iJQ-Med1-Input


title: 120_CS_S3_BO_11_B2

source_name: Cabernet Sauvignon; Mid-ripening; Bolgheri; 2011; Replicate B


title: SLJQ-Med1


title: 111_CS_S2_MI_12_B2

source_name: Cabernet Sauvignon; Pre-veraison; Montalcino; 2012; Replicate B

value: Montalcino, Tuscany Apennines, Italy


title: 110_CS_S2_MI_12_B1

source_name: Cabernet Sauvignon; Pre-veraison; Montalcino; 2012; Replicate A


title: o11 rep3

city: Shanghai

first: Fan

last: Feng

address: 333 Nanchen Road

country: China

institute: Shanghai University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed using fastx（version:0.0.13）, then mapped to B73 RefGen_v3.24 using TopHat（version:2.0.9）.
Then quantified read counts per gene and normalized Fragments Per Kilobase exon per Million reads mapped (FPKM) values using Cufflinks TopHat（version:2.0.9）
Genome_build: Ensembl plants release-24 zea_mays
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Zea mays

source_name: kernel

extract_protocol:
RNA was extracted from pooled kernels at 15 DAP with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: kernel

tag: age

value: 15 DAP

tag: genotype

value: o11 homozygous mutant


title: SL2i-Med1-Input


title: o11 rep2


title: 108_CS_S2_MI_11_B2

source_name: Cabernet Sauvignon; Pre-veraison; Montalcino; 2011; Replicate B

value: Pre-veraison, PV, majority of berries touching, BBCH 79


title: SL2i-Med1


title: WT rep2

value: Wild-type


title: WT rep3


title: 107_CS_S2_MI_11_B1

source_name: Cabernet Sauvignon; Pre-veraison; Montalcino; 2011; Replicate A


title: SL-Med1


title: 105_CS_S2_BO_12_B2

source_name: Cabernet Sauvignon; Pre-veraison; Bolgheri; 2012; Replicate B

value: Bolgheri, Tuscany coast, Italy


title: SL-Med1-Input


title: WT treated with HC2091, rep1

source_name: Bacterial cell


title: SLJQ-Brd4-Input


title: 104_CS_S2_BO_12_B1

source_name: Cabernet Sauvignon; Pre-veraison; Bolgheri; 2012; Replicate A


title: 102_CS_S2_BO_11_B2

source_name: Cabernet Sauvignon; Pre-veraison; Bolgheri; 2011; Replicate B


title: SLJQ-Brd4

value: anti-Brd4, Bethyl Laboratories A301-985A50


title: SL2i-Brd4-Input


title: 101_CS_S2_BO_11_B1

source_name: Cabernet Sauvignon; Pre-veraison; Bolgheri; 2011; Replicate A


title: L1

city: Beiing

first: Yijun

last: Qi

address: NO.1 Qinghuayuan

department: School of Life Sciences

institute: Tsinghua University

data_processing:
Small RNA-Seq: The adapter sequences were trimmed by cutadapt 1.12. Only reads in the size of 18-30 nt were retained for further analysis. Clean small RNA reads were mapped to the Arabidopsis genome (TAIR10) with bowtie allowing no mismatches (Langmead et al., 2009)
Bisulfite-Seq: Bisulfite sequencing reads were mapped to Arabidopsis genome (TAIR10) by BRAT-BW(Harris et al., 2012) with parameters -m 3 -i 0 -a 1000, allowing up to three mismatches. Only uniquely mapped reads were retained for further methylation analysis. Copy-duplicates were removed by Remove-dupl command of BRAT-BW package. Acgt-count command of BRAT-BW was used to calculate fractional DNA methylation levels.
Genome_build: TAIR10
Supplementary_files_format_and_content: For BS-seq data, our files were generated by acgt-count command of BRAT-BW and their format is 'Chr,Start,End,Context:Coverage,Methylation level,Strand'. For sRNA-Seq data, the text files contain genome-matched unique sequences and their counts.

organism: Arabidopsis thaliana

source_name: 13-day-old seedlings

growth_protocol: All plants were grown in Murashige and Skoog (MS) medium at 16-h-light/8-h-dark photoperiod.

extract_protocol:
Genomic DNA was isolated using a DNeasy Plant kit (Qiagen) according to the manufacturer’s instructions.
For whole-genome bisulfite sequencing, genomic DNA was isolated using a DNeasy Plant kit (Qiagen) according to the manufacturer’s instructions. For small RNA deep sequencing, small RNAs were extracted by Trizol reagent (Invitrogen), resolved on a 15% denaturing PAGE gel, and visualized by SYBR-Gold (Invitrogen) staining. Gel slices within the range of 18-30 nt were excised, and the RNAs were eluted and purified for small RNA library construction.
For whole-genome bisulfite sequencing, the libraries were constructed using an Accel-NGS® Methyl-Seq DNA Library Kit (Swift Biosciences). Small RNA libraries were constructed as described(Mi et al., 2008)

value: wild-type

tag: ecotype


title: qqt2-2


title: nrpb/d/e11-1 rep2

description: PEG-enriched RNA

extract_protocol:
Small RNAs were extracted from whole plants by Trizol reagent (Invitrogen), resolved on a 15% denaturing PAGE gel, and visualized by SYBR-Gold (Invitrogen) staining. Gel slices within the range of 18-30 nt were excised, and the RNAs were eluted and purified for small RNA library construction.
For whole-genome bisulfite sequencing, genomic DNA was isolated using a DNeasy Plant kit (Qiagen) according to the manufacturer’s instructions. For small RNA deep sequencing, small RNAs were extracted by Trizol reagent (Invitrogen), resolved on a 15% denaturing PAGE gel, and visualized by SYBR-Gold (Invitrogen) staining. Gel slices within the range of 18-30 nt were excised, and the RNAs were eluted and purified for small RNA library construction.
For whole-genome bisulfite sequencing, the libraries were constructed using an Accel-NGS® Methyl-Seq DNA Library Kit (Swift Biosciences). Small RNA libraries were constructed as described(Mi et al., 2008)


title: iyo-4


title: SL2i-Brd4


title: qqt2-2 rep2

description: PEG-enriched RNA


title: SL-Brd4


title: o11 rep1

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to B73 RefGen_v3.24 using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of fragments falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: reads mapped to mapped to B73 RefGen_v3.24; Ensembl plants release-24 zea_mays
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: WT rep1


title: iyo-4 rep2

description: PEG-enriched RNA


title: hybrid striped bass pooled liver biological rep5

city: Auburn

first: Jason

last: Abernathy

state: AL

address: 990 Wire Road

institute: USDA-ARS

data_processing:
Base-calling and demultiplexing were performed using the native software on the Illumina sequencer.
Raw reads were processed for quality control using the Trim Galore! software version 0.4.3. This software was used to trim low-quality ends from reads in addition to Illumina adapter removal. Quality trimming was then specified at phred Q20.
Sequences after QC were clustered into transcripts using Trinity software version 2.4.0
Transcripts were annotated by the Trinotate software version 3.0.2.
Protein coding transcripts were selected from Trinotate analysis and clustered using CD-HIT version 4.6.6 and BUSCO version 2.0 software packages to create a HSB liver transcriptome.
Bowtie2 version 2.3.1 was used for alignment of reads to the HSB liver transcriptome using the alignment parameters as recommended by eXpress software version 1.5.1.
Alignment files were piped into the eXpress version 1.5.1 software using the default parameters to generate read counts.
Effective read counts output from the eXpress version 1.5.1 software were used to calculate fold-change using the DESeq2 package in R-Bioconductor Release 3.3.3.
Genome_build: HSB liver transcriptome created using all six RNAseq datasets
Supplementary_files_format_and_content: Tab-delimited text file of effective read counts, rounded to the nearest whole number
Supplementary_files_format_and_content: FASTA file of the HSB liver transcriptome

organism: Morone chrysops x Morone saxatilis

source_name: section from whole liver

extract_protocol:
Tissue samples were excised, flash-frozen in liquid nitrogen and stored at -80°C until usage. Samples were processed using the Qiagen RNeasy Plus Mini Kit per the manufacturer's recommendation for total RNA isolation. Samples were treated with RNase free DNase I (Qiagen) to remove genomic DNA.
Total RNA was standardized to 2 µg each sample. Sequencing libraries were then prepared using the Illumina TruSeq RNA Sample Preparation Kit as per the protocol. Samples were barcoded using Illumina TruSeq Indexed adapters.

tag: growth

value: small

value: liver


title: hybrid striped bass pooled liver biological rep6


title: L1 rep2

description: PEG-enriched RNA


title: hybrid striped bass pooled liver biological rep3

value: large


title: nrpb/d/e11-1


title: hybrid striped bass pooled liver biological rep4


title: qqt2-2 rep1

description: PEG-enriched RNA


title: hybrid striped bass pooled liver biological rep2


title: L1 rep1

description: PEG-enriched RNA


title: 1D

status: Public on Apr 08 2018

city: Bron

first: Bertrand

middle: Pierre-Yves

last: PAIN

address: 18, Avenue du  Doyen Lépine

country: France

institute: U1208, INSERM

data_processing:
The raw files were convereted into Fastq files (fastq.gz) and demultiplexed using Bcl2fastq 2.0 software (Illumina)
Quality control was performed on Fastq files using the FastQC v0.11.5 software
Sequenced reads were pseudoaligned against ref_mRNA of galGal5 using kallisto v0.43.0 with parameters -t 4 -b 100 –rf-stranded
Normalized counts and DE genes were calculated using DESeq2
Genome_build: ref_mRNA of galGal5
Supplementary_files_format_and_content: Normalized counts and DE genes were calculated using DESeq2

organism: Gallus gallus

source_name: in vitro reprogrammed cells

growth_protocol: Cells were isolated and maintained as described in Fuet et al., (2017). Submitted and in Vautherot et al., (2017). PLoS ONE 12(4): e0175259. https://doi.org/10.1371/journal.  pone.0175259

extract_protocol:
Total RNAs were prepared by Trizol extraction using standard protocols
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: somatically reprogrammed stem cell


title: iyo-4 rep1

description: PEG-enriched RNA


title: 1A


title: PGC

source_name: in vitro culture

value: primordial germ cell (PGCs)


title: 3F


title: BP45

value: chicken embryonic stem cell (cESC)


title: hybrid striped bass pooled liver biological rep1


title: BC

source_name: Stages EGK-X - EGKXII embryos

value: blastodermal cell (BCs)


title: CEF

value: primary chicken embryonic fibroblasts (CEF)


title: nrpb/d/e11-1 rep1

description: PEG-enriched RNA


title: SL-Brd4-Input

source_name: mESC

value: Serum LIF


title: VYSS_01-CBS6039_TotalDNA

city: Durham

middle: Blake

last: Billmyre

state: North Carolina

address: 312 CARL Bldg

department: Molecular Genetics and Microbiology

institute: Duke University Medical Center

data_processing:
Processing/demultiplexing with bcl2fastq ver 1.8.4
Sequences were aligned using bwa sampe ver 0.7.10
SAMs were converted to BAM using samtools
BAMS were cleaned and sorted using picard tools version 1.115
Peaks were called using MACS2 with the broad peaks setting
Genome_build: CBS6039 C. amylolentus
Supplementary_files_format_and_content: Differential peaks between total and chip samples called with the broad peak setting of MACS2 in bed format

organism: Cryptococcus amylolentus

source_name: vegetative cells

growth_protocol: 100 mL cultures were grown from a single colony at 30 C until OD600

extract_protocol:
Cell were crosslinked with 37% formaldehyde prior to spheroplasting with lysing enzyme. DNA was sheared using a sonicator, decrosslinked and phenol/chloroform extracted. IP was performed using RFP-TRAP beads.
Libraries were prepared using the TruSeq ChIP preparation kit from Illumina.

value: CBS6309 CSE4::MCHERRY

tag: antibody


title: VYSS_02-CBS6039_Cse4IP

value: RFP-trap beads (Chromotek, Rta-20)


title: 3E


title: Cardiomyocytes_1

status: Public on Apr 06 2018

city: Belen de Escobar

first: Santiago

last: Miriuka

state: Buenos Aires

address: Ruta 9 Km 52.5

department: LIAN-CONICET

country: Argentina

institute: FLENI

description: small RNA

data_processing:
For the sequencing we used the Illumina HiSeq2500 1x50, one lane, and each sample got more than 8.5 million reads.
Raw data was processed following the CAP-miRSeq pipeline. Briefly, the reads were analyzed with FASTQC v0.11.4  for quality check pre and post adapter trimming. Trimming was achieved with Cutadapt v1.9.1. The alignment was done using Bowtie v1.1.2  and the mapping using miRDeep2 (miRbase version 21). Finally, read counts for each sample were normalized (PRM) and differential expression analyses were performed with edgeR.
miRNA expression counts are normalized as Counts per Million within each sample (1000000 * raw_counts/total_raw_counts).
Genome_build: Hg19
Supplementary_files_format_and_content: Tab-delimited text file. The first column is the mature name of the microRNA, the second is the precursor name and the third is the miRbase link for each microRNA. From 4th   to 12th  column are the normalized read counts: three replicates of Pluripotent cells (4th to 6th)  followed by three replicates of the mesoderm progenitor cells (7th to 9th) and finally three replicates of cardiomyocytes (10th to 12th).

source_name: Cardiac Progenitor Cells

growth_protocol: hESC were differentiated to cardiomyocytes by cultering cells in suspension embryoid bodies (EB) formed by forced aggregation. EB were cultured in suspension in StemPro with mesoderm induction factors, BMP4 (10ng/ml), activin A (3ng/ml) and  bFGF (5ng/ml) during 4 days. At day 5 they were plated in gelatin coated plates with the addition of the Wnt inhibitor IWR-1 (5µM). From day 6 until day 21, cells were cultured in StemPro supplemented with the cardiac differentiation factors VEGF (5ng/µl), bFGF (10ng/ml) and IWR-1 (5µM). Cardiomyocytes were purified by Zeocin selection.

extract_protocol:
The small RNA molecules were extracted with mirVana™ miRNA Isolation Kit (Ambion, Thermo Fisher Scientific) following the manufacturer's protocols.
Libraries were prepared using the NEBNext small RNA library prep for Illumina, following manufacturer's protocols. Briefly, 200 ng of RNA were used as input. The 3' and 5' adaptors were ligated sequentially and  barcode primers 1 to 9 illumina compatible were use for the PCR. After this the clean up and size selection was made by gel following manufacturer's protocols.

value: Cardiac Progenitor Cells (hES-derived cells)

tag: cell line

value: H9-hTnnTZ-pGZ-D2 WiCell


title: Cardiomyocytes_2

description: small RNA


title: Endogenous_Microglia_2

status: Public on Apr 07 2018

city: Charlottesville

first: Christopher

last: Overall

state: Virginia

address: 409 Lane Road

department: Neuroscience

institute: University of Virginia

data_processing:
Base calling an quality scoring performed by real-Time Analysis (RTA) v2.
Raw FASTQ sequencing reads were chastity filtered to remove clusters having outlying intensity corresponding to bases other than the called base.
Filtered reads were assessed for quality using FastQC.
Reads were splice-aware aligned to the UCSC mm9 genome using STAR.
Reads overlapping Gencode mm9 gene regions were counted using HTSeq.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text file with the raw counts.

source_name: FACS sorted microglia

growth_protocol: C57BL/6J mice were maintained in vivarium conditions for 8 months post bone marrow transplant.

extract_protocol:
RNA was isolated using RNAeasy mini kit (Qiagen)
Ovation RNA-Seq System V2 kit (Nugen) for initial RNA amplification. After purification, the cDNA was fragemented and further library steps performed.

treatment_protocol: Bone marrow transplant was performed on wild type C57BL/6J mice with UBC-GFP bone marrow (C57BL/6 background), and engrafted macrophages and microglia were isolated from whole brain 8 months later.

value: Whole brain

value: microglia

value: 9 months (8 months post-transplant)

value: wild type


title: Engrafted_Macrophage_2

source_name: FACS sorted CNS engrafted macrophages

value: engrafted macrophage


title: Endogenous_Microglia_1


title: Engrafted_Macrophage_3


title: Engrafted_Macrophage_1


title: MPC_3

description: small RNA

source_name: Mesoderm Progenitor Cells

growth_protocol: hESC were grown on matrigel with StemPro hESC FSM media (Thermo Scientific) to induce differentiation, supplemented with human VEGF, bFGF, BMP4, and activin A (all at 10 ng/mL; Thermo Scientific) during the first 24 hours and for the next 2.5 days activin A was removed. After mesoderm induction, CD326−CD56+ cells were typically isolated by fluorescence acti- vated cell sorting (FACS) at day 3.5.

value: Mesoderm Progenitor Cells (hES-derived cells)

value: H9 (WA09) WiCell


title: Cardiomyocytes_3

description: small RNA


title: PSC_1

description: small RNA

source_name: Pluripotent Stem Cells

growth_protocol: hESC were grown on matrigel coated plates (growth factor reduced, no phenol red; BD Biosciences) and cultured in  mTesR (Stem Cell Technologies), a defined medium for embryonic stem cells.

value: Pluripotent Stem Cells (modified hES)


title: PSC_3

description: small RNA


title: MPC_1

description: small RNA


title: MPC_2

description: small RNA


title: PSC_2

description: small RNA


title: jc2929_MCF7_Input_AZD2014

city: Cambridge

last: Carroll

address: Li Ka Shing Centre, Robinson Way

country: United Kingdom

institute: Cancer Research UK, Cambridge Institute

data_processing:
Reads were mapped to hg38 genome using Bowtie2 version 2.2.6 (Langmead B and  Salzberg S., 2012).
Aligned reads with the mapping quality less than 5 were filtered out.
The read alignments from three replicates were combined into single library and peaks were called with MACS2 version 2.0.10.20131216 (Zhang Y1 at al., 2008) using sequences from MCF7 chromatin extracts as a background input control.
The peaks yielded with MACS2 q value <= 1e-4 were selected for downstream analysis.
Meme version 4.9.1 (Timothy et al., 2009) was used to detect known and discover novel binding motifs amongst tag-enriched sequences.
For visualizing tag density and signal distribution heatmap the read coverage in a window of +/- 2.5 or 5 kb region flanking the tag midpoint was generated using the bin size of 1/100 of the window length.
Differential binding analysis (Diffbind) was performed as described previously (Brown and Stark, 2011).
Genome_build: GRCh38
Supplementary_files_format_and_content: peaks.narrowPeak

source_name: MCF7 input AZD2014

growth_protocol: MCF7 cells were grown in DMEM supplemented with 10% FBS, 1%pen/strep, 2mM L-glutamine.

extract_protocol:
Cells were crosslinked for 10min using 1% formaldehyde. After sonication, chromatin immunoprecipitation was performed using a polyclonal ERa antibody over night. After decrosslinking at 65 C over night followed by RNase A and proteinase K treatment, immunoprecipitated DNA was purified by phenol-chloroform extraction.
DNA was prepared for Illumina sequencing on the HiSeq 2500 using the ThruPLEX DNA-seq kit according to the manufacturer's instructions.

treatment_protocol: Asynchronous cells were treated for 2 hours with vehicle (DMSO), 500nM RAD001, or 500nM AZD2014

value: Breast cancer

tag: passages

value: Input

tag: agent

value: Treatment with AZD201


title: jc2928_MCF7_Input_RAD001

source_name: MCF7 input RAD001

value: Treatment with RAD001


title: jc2926_MCF7_ER_AZD2014

source_name: ERa AZD2014 treatment

value: ERa sc-543


title: jc2927_MCF7_Input_Veh

source_name: MCF7 input

value: No treatment


title: BP25

value: chicken embryonic stem cell (cESC)


title: jc2923_MCF7_Input_AZD2014


title: jc2921_MCF7_Input_Veh


title: jc2922_MCF7_Input_RAD001


title: jc2924_MCF7_ER_Veh

source_name: ERa untreated


title: jc2919_MCF7_ER_RAD001

source_name: ERa RAD001 treatment


title: jc2917_MCF7_Input_AZD2014


title: jc2918_MCF7_ER_Veh


title: jc2916_MCF7_Input_RAD001


title: jc2909_MCF7_Input_Veh


title: jc2913_MCF7_ER_RAD001


title: jc2915_MCF7_Input_Veh


title: jc2908_MCF7_ER_AZD2014


title: jc2910_MCF7_Input_RAD001


title: jc2914_MCF7_ER_AZD2014


title: jc2912_MCF7_ER_Veh


title: jc2911_MCF7_Input_AZD2014


title: jc2907_MCF7_ER_RAD001


title: jc2925_MCF7_ER_RAD001


title: jc2920_MCF7_ER_AZD2014


title: iTreg_72_rep3

city: Espoo

first: Sini

last: Rautio

address: Konemiehentie 2

country: Finland

institute: Aalto University

data_processing:
Paired-end reads were aligned with Tophat (version 2.0.8b) and Bowtie2 (version 2.1.0) to human reference genome (hg19) and Gencode transcriptome (v19).  Based on calculation for one million reads, we set the mean insert size and standard deviation for each sample separately.
Read counts were determined using HTSeq-count (version 0.6.1) with parameters “--stranded no --order name”
Bioconductor package edgeR was used for differential expression calling. Genes with RPKM <3 in at least two samples in both conditions were filtered out before differential expression calling.
Genome_build: hg19
Supplementary_files_format_and_content: Abundance measurements (rpkm.txt)

molecule: polyA RNA

source_name: Peripheral blood CD4+ cells 72h after activation and polarization towards iTreg

growth_protocol: Naive CD4+ T-cells (> 90% purity) were isolated from PBMCs. Cells were cultured in 24 well plates and activated in the absence (Th0 cells) or presence (iTreg cells) of the cytokines shown in the treatment protocol below. Cells were grown for up to 7 days.

extract_protocol:
RNA isolations were done using RNeasy Protect Cell Mini Kit (QIAGEN) (genomic DNA removal step was included)
Illumina TruSeq RNA sample prep kit v2

treatment_protocol: Naive CD4+ T cells were differentiated into iTreg cells in X-Vivo15 medium with 10% human serum, 10ng/ml TGFß, 10ng/ml IL-2 and 10nM all-trans-retanoic acid and Th0 cells were grown in X-Vivo15. Th0 and iTreg cultures were supplemented with 0.5µg/ml αCD3 and 0.5µg/ml αCD28. Cells were seeded at a density of 2x106 cells per well in a 24 well plate and incubated at 37°C.

value: Peripheral blood

tag: biological replicate

value: human biological replicate:3


title: Th0_96_rep3

source_name: Peripheral blood CD4+ cells 96h after activation


title: iTreg_24_rep3

source_name: Peripheral blood CD4+ cells 24h after activation and polarization towards iTreg


title: Th0_12_rep3

source_name: Peripheral blood CD4+ cells 12h after activation


title: iTreg_96_rep3

source_name: Peripheral blood CD4+ cells 96h after activation and polarization towards iTreg


title: Th0_72_rep3

source_name: Peripheral blood CD4+ cells 72h after activation


title: Th0_48_rep3

source_name: Peripheral blood CD4+ cells 48h after activation


title: Th0_24_rep3

source_name: Peripheral blood CD4+ cells 24h after activation


title: iTreg_12_rep3

source_name: Peripheral blood CD4+ cells 12h after activation and polarization towards iTreg


title: iTreg_120_rep3

source_name: Peripheral blood CD4+ cells 120h after activation and polarization towards iTreg


title: iTreg_6_rep3

source_name: Peripheral blood CD4+ cells 6h after activation and polarization towards iTreg


title: iTreg_2_rep3

source_name: Peripheral blood CD4+ cells 2h after activation and polarization towards iTreg


title: Th0_120_rep3

source_name: Peripheral blood CD4+ cells 120h after activation


title: Th0_2_rep3

source_name: Peripheral blood CD4+ cells 2h after activation


title: jc2906_MCF7_ER_Veh


title: Th0_1_rep3

source_name: Peripheral blood CD4+ cells 1h after activation


title: Th0_6_rep3

source_name: Peripheral blood CD4+ cells 6h after activation


title: Thp_rep3

source_name: Peripheral blood CD4+ cells without any treatments


title: iTreg_120_rep2

value: human biological replicate:2


title: iTreg_1_rep3

source_name: Peripheral blood CD4+ cells 1h after activation and polarization towards iTreg


title: Th0_0.5_rep3

source_name: Peripheral blood CD4+ cells 0.5h after activation


title: iTreg_48_rep3

source_name: Peripheral blood CD4+ cells 48h after activation and polarization towards iTreg


title: iTreg_0.5_rep3

source_name: Peripheral blood CD4+ cells 0.5h after activation and polarization towards iTreg


title: iTreg_72_rep2

source_name: Peripheral blood CD4+ cells 72h after activation and polarization towards iTreg


title: Th0_120_rep2


title: iTreg_48_rep2


title: Th0_96_rep2

source_name: Peripheral blood CD4+ cells 96h after activation


title: iTreg_12_rep2


title: Th0_24_rep2


title: Th0_6_rep2


title: Thp_rep2


title: Th0_48_rep2

source_name: Peripheral blood CD4+ cells 48h after activation


title: Th0_0.5_rep2


title: iTreg_24_rep2

source_name: Peripheral blood CD4+ cells 24h after activation and polarization towards iTreg


title: Th0_12_rep2

source_name: Peripheral blood CD4+ cells 12h after activation


title: iTreg_72_rep1

value: human biological replicate:1


title: iTreg_48_rep1


title: iTreg_0.5_rep2


title: iTreg_6_rep2


title: Th0_96_rep1


title: Th0_72_rep2

source_name: Peripheral blood CD4+ cells 72h after activation


title: Th0_120_rep1


title: Th0_12_rep1


title: Th0_1_rep2


title: iTreg_120_rep1

source_name: Peripheral blood CD4+ cells 120h after activation and polarization towards iTreg


title: iTreg_6_rep1

source_name: Peripheral blood CD4+ cells 6h after activation and polarization towards iTreg


title: iTreg_96_rep2

source_name: Peripheral blood CD4+ cells 96h after activation and polarization towards iTreg


title: Th0_6_rep1


title: Th0_2_rep2

source_name: Peripheral blood CD4+ cells 2h after activation


title: Th0_72_rep1


title: iTreg_96_rep1


title: Th0_48_rep1


title: iTreg_2_rep2

source_name: Peripheral blood CD4+ cells 2h after activation and polarization towards iTreg


title: iTreg_24_rep1


title: Th0_24_rep1

source_name: Peripheral blood CD4+ cells 24h after activation


title: iTreg_12_rep1

source_name: Peripheral blood CD4+ cells 12h after activation and polarization towards iTreg


title: iTreg_1_rep2

source_name: Peripheral blood CD4+ cells 1h after activation and polarization towards iTreg


title: iTreg_2_rep1


title: Th0_1_rep1

source_name: Peripheral blood CD4+ cells 1h after activation


title: iTreg_0.5_rep1


title: Th0_2_rep1


title: iTreg_1_rep1


title: Thp_rep1

source_name: Peripheral blood CD4+ cells without any treatments


title: G04_T05_D

city: Stockholm

first: Francesco

last: Marabita

address: Karolinska University Hospital

country: Sweden

institute: Karolinska Institutet

description: 2d stim TGFB ATRA donor D

data_processing:
Illumina HiSeq Control/Real Time Analysis software was used for base calling.
Demuliplexing and bcl to fastq conversion was performed with the bcl2fastq Conversion Software v1.8.4
FASTQ files were quality- and adapter-trimmed using Trim Galore!. Reads were aligned with TopHat2 (2.0.11) using hg19 genome index and GENCODE v19 transcriptome model. Discordant alignments were removed. Alignment metrics and statistic were extracted from the BAM files using Picard tools and preseq.
Alignments from BAM files were summarized to the GENCODE v19 genes with the summarizeOverlaps function of the GenomicAlignments package.
Raw counts were imported in DESeq2, after removing the genes with zero counts in all samples. Normalization was obtained with the DESeq2 size factors.
Genome_build: hg19
Supplementary_files_format_and_content: Processed data text files contain raw or DESeq2-normalized counts for GENCODE v19 genes.

source_name: CD4+ T cells

growth_protocol: Peripheral blood mononuclear cells (PMBCs) were isolated by gradient centrifucation from healthy donor buffy coats. Naive CD4+ T cell and CD25high nTregs subsets were isolated using magnetic activated cell sorting (MACS). Cells were rested for several hours before plating.

extract_protocol:
At the indicated time points, cells were collected by centrifugation, washed twice with PBS and lysed in RLT buffer supplemented with beta-mercaptoethanol. Lysates were homogenized using QiaShredder columns and stored at -80°C until processing. RNA and proteins were extracted with the AllPrep DNA/RNA/Protein Mini Kit, with the following modifications. Centrifugations were carried out at 9600 x g except protein precipitation at 20800 x g. RNA was eluted with 40 µl RNase-free water and elution was repeated with the first eluate. An aliquot of RNA was taken for nanodrop, bioanalyzer and qRT-PCR, RNA was frozen on dry ice and stored at -80°C.
One microgram of RNA per sample (except for the 2h time point samples of Donor 2: 500 to 900 ng) was used for library preparation with the TruSeq Stranded mRNA HT kit (Illumina), with Dual Indexing adapters (8-plex). As control, an ERCC Spike-In Control Mix was used. Libraries were purified from excess sequencing adapters with Agencourt AMPure XP beads. Library concentration was measured on a Qubit 2.0 Fluorometer and library quality and size were determined by using an Agilent High Sensitivity DNA Kit on a 2100 Bioanalyzer. Libraries were quantified with the KAPA Library Quantification Kit.

treatment_protocol: Cells were stimulated with 5 µg/ml plate-bound anti-CD3 antibody, 1 µg/ml soluble anti-CD28 antibody and 100 IU/ml IL-2. ‘Mock’ control cells received no further compounds. For Treg-inducing conditions, TGF-β1 (5 ng/ml), ATRA (10 nM), Rapa (100 ng/ml) or sodium butyrate (100 µM) were added to the corresponding samples. Cells were plated in 96U-well plates in serum-free X-Vivo 15 medium supplememented with Glutamax. Cells were incubated for 2 hours to 6 days. At the indicated time points (2h, 6h, 24h, 48h, 6d), several wells per condition were pooled and cells were processed for RNA and protein extraction.

value: D

value: Male

value: naive CD4+ T cells

tag: lane


title: G03_T02_D

description: 2h stim TGFB donor D


title: G04_T04_D

description: 1d stim TGFB ATRA donor D


title: G03_T05_B

description: 2d stim TGFB donor B

value: B


title: G03_T02_B

description: 2h stim TGFB donor B


title: G05_T03_B

description: 6h stim TGFB ATRA Rapa donor B


title: G07_T01_B

description: 0h nTreg donor B

source_name: CD25high nTregs

value: CD25high nTregs


title: G05_T06_A

description: 6d stim TGFB ATRA Rapa donor A

value: A


title: Th0_0.5_rep1

source_name: Peripheral blood CD4+ cells 0.5h after activation


title: G05_T04_A

description: 1d stim TGFB ATRA Rapa donor A


title: G02_T02_A

description: 2h stim donor A


title: G06_T05_D

description: 2d stim TGFB Butyr donor D


title: G03_T06_A

description: 6d stim TGFB donor A


title: G04_T04_A

description: 1d stim TGFB ATRA donor A


title: G07_T01_D

description: 0h nTreg donor D


title: G04_T03_A

description: 6h stim TGFB ATRA donor A


title: G06_T04_D

description: 1d stim TGFB Butyr donor D


title: G05_T05_D

description: 2d stim TGFB ATRA Rapa donor D


title: G06_T03_D

description: 6h stim TGFB Butyr donor D


title: G06_T02_D

description: 2h stim TGFB Butyr donor D


title: G05_T06_D

description: 6d stim TGFB ATRA Rapa donor D


title: G06_T06_D

description: 6d stim TGFB Butyr donor D


title: G03_T04_B

description: 1d stim TGFB donor B


title: G02_T05_B

description: 2d stim donor B


title: G05_T02_D

description: 2h stim TGFB ATRA Rapa donor D


title: G04_T06_D

description: 6d stim TGFB ATRA donor D


title: G04_T03_D

description: 6h stim TGFB ATRA donor D


title: G05_T03_D

description: 6h stim TGFB ATRA Rapa donor D


title: G03_T06_D

description: 6d stim TGFB donor D


title: G03_T05_D

description: 2d stim TGFB donor D


title: G03_T04_D

description: 1d stim TGFB donor D


title: G02_T04_D

description: 1d stim donor D


title: G02_T06_D

description: 6d stim donor D


title: G02_T03_D

description: 6h stim donor D


title: G03_T03_D

description: 6h stim TGFB donor D


title: G02_T02_D

description: 2h stim donor D


title: G01_T01_D

description: 0h unstim donor D


title: G06_T06_B

description: 6d stim TGFB Butyr donor B


title: G06_T05_B

description: 2d stim TGFB Butyr donor B


title: G06_T03_B

description: 6h stim TGFB Butyr donor B


title: G05_T04_D

description: 1d stim TGFB ATRA Rapa donor D


title: G05_T02_B

description: 2h stim TGFB ATRA Rapa donor B


title: G05_T05_B

description: 2d stim TGFB ATRA Rapa donor B


title: G05_T04_B

description: 1d stim TGFB ATRA Rapa donor B


title: G05_T06_B

description: 6d stim TGFB ATRA Rapa donor B


title: G04_T03_B

description: 6h stim TGFB ATRA donor B


title: G04_T04_B

description: 1d stim TGFB ATRA donor B


title: G03_T06_B

description: 6d stim TGFB donor B


title: G04_T02_D

description: 2h stim TGFB ATRA donor D


title: G04_T06_B

description: 6d stim TGFB ATRA donor B


title: G03_T03_B

description: 6h stim TGFB donor B


title: G04_T02_B

description: 2h stim TGFB ATRA donor B


title: G02_T03_B

description: 6h stim donor B


title: G02_T05_D

description: 2d stim donor D


title: G02_T04_B

description: 1d stim donor B


title: G02_T02_B

description: 2h stim donor B


title: G01_T01_B

description: 0h unstim donor B


title: G06_T04_B

description: 1d stim TGFB Butyr donor B


title: G07_T01_A

description: 0h nTreg donor A


title: G06_T02_B

description: 2h stim TGFB Butyr donor B


title: G06_T04_A

description: 1d stim TGFB Butyr donor A


title: G06_T06_A

description: 6d stim TGFB Butyr donor A


title: G06_T02_A

description: 2h stim TGFB Butyr donor A


title: G06_T03_A

description: 6h stim TGFB Butyr donor A


title: G02_T06_B

description: 6d stim donor B


title: G05_T02_A

description: 2h stim TGFB ATRA Rapa donor A


title: G05_T05_A

description: 2d stim TGFB ATRA Rapa donor A


title: G04_T06_A

description: 6d stim TGFB ATRA donor A


title: G04_T05_A

description: 2d stim TGFB ATRA donor A


title: G04_T02_A

description: 2h stim TGFB ATRA donor A


title: G03_T04_A

description: 1d stim TGFB donor A


title: G03_T05_A

description: 2d stim TGFB donor A


title: G03_T03_A

description: 6h stim TGFB donor A


title: G02_T06_A

description: 6d stim donor A


title: G02_T03_A

description: 6h stim donor A


title: G01_T01_A

description: 0h unstim donor A


title: G02_T04_A

description: 1d stim donor A


title: G02_T05_A

description: 2d stim donor A


title: G05_T03_A

description: 6h stim TGFB ATRA Rapa donor A


title: G04_T05_B

description: 2d stim TGFB ATRA donor B


title: Mirlet7d_GOF_Exsoc10_sh_smallRNA_seq

city: Nancy Cedex

first: Guillermo

last: Barreto

address: 9, Avenue de la Forêt de Haye ‐ BP 20199

department: Campus Biologie-Santé. Faculté de Médecine

institute: CNRS Director of Research

description:
Custom LNA oligonucleotide from EXIGON
sh_plasmid

data_processing:
Low quality reads were filter out by using trimmomatic 95 with the following parameters (LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:17). High quality reads were mapped to the NONCODE V4.0 (http://www.noncode.org/download.php) for the ncRNAs. The unmapped reads from the ncRNAs database were extracted by samtools view (-f 4) and converted to bam files using samtools view (-Sb). The bam files were further converted to fastq files using SamToFastq.jar from picard-tools-1.119  (https://sourceforge.net/projects/picard/files/picard-tools/1.119/). These fastq files were further mapped to the protein coding database  GENECODE M1.
The mapping were performed with bwa (-n 1 -o 0 -e 0 -k 1 -t 4) parameters followed by bwa (sampe).
Sam files were converted to bam files by samtools and these files to bed format by the use of bamtobed tool. In order to extract the mature Mirlet7d sequence from the mapped smallRNA libraries.
The converted  bed files were crossed with the mature Mirlet7d sequence coordinate from mm9 by using Bedtools v2.15 (interspect -wa –v). The mapped reads to the sense strands were loaded to Rstudio to obtain reads between 15 to 35 bp long by the use of custom R-script.
FastaFrombed tool was used to convert the output file from the R-Script to a fasta file. Further, the degradation products were quantified with analyzeRepeats.pl with (analyzeRepeats.pl database.gtf mm9 -count genes -strand both and -rpkm). Database.gtf was NONCODE V4.0 for ncRNAs and GENECODE M1 for mRNAs quantification

growth_protocol: MLE-12 cells were kept at 37°c in DMEM: F12 medium containing 5 % Fetal Calf Serum, and 1% P/S (penicillin/Streptomycin)

extract_protocol:
MLE-12 cells nuclei were isolated by treating with hypotonic solution and later used for small RNA isolation by mirVana™ miRNA Isolation Kit, with phenol (ThermoFisher Scientific #AM1560)
smallRNA_seq:  libraries were prepared using the  Truseq small RNA Kit (Illumina). using 15-30 ng small RNAs (based on Bioanaylzer small RNA measurement).  Instead of gel-based cleanup of ligated cDNA, Size-selection was performed on LabChipXT (Perkin Elmer) with extraction window from 135bp - 175bp (insert size 10bp – 60bp)

treatment_protocol: MLE-12 cells were transfected with 25nM of microRNA (Random or Mirlet7d) and/or 2.5 ug shDNA plasmid (Control or Exosc10) and harsvested after 48 h.

tag: gof

tag: biotinylated microrna

tag: sh plasmid


title: Ctrl_empty_vector_GOF_smallRNA_seq

description: Custom LNA oligonucleotide from EXIGON

value: control


title: Mirlet7d_GOF_smallRNA_seq

description: Custom LNA oligonucleotide from EXIGON


title: G03_T02_A

description: 2h stim TGFB donor A


title: shExsoc10_smallRNA_seq

data_processing:
Low quality reads were filter out by using trimmomatic 95 with the following parameters (LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:17).
High quality reads were mapped to the NONCODE V4.0 (http://www.noncode.org/download.php) for the ncRNAs. The unmapped reads from the ncRNAs database were extracted by samtools view (-f 4) and converted to bam files using samtools view (-Sb). The bam files were further converted to fastq files using SamToFastq.jar from picard-tools-1.119 (https://sourceforge.net/projects/picard/files/picard-tools/1.119/). These fastq files were further mapped to the protein coding database GENECODE M1.
High quality reads were aligned to the mm9 genome by using bwa aln (-n 1 -o 0 -e 0 -k 1 -t 4), followed by bwa <sampe>
Sam files were converted to bam files using samtools view and sort.
bam files were converted to bed files using bamTobed program (default)
the negative ,mapped strand was obtained using grep <-> < output_sort.bed> [>] output_sort_NEGA.bed
custom R Script was used to filter mapped reads between 15 to 35 bp long
The converted bed files were crossed with the mature Mirlet7d sequence coordinate from mm9 by using Bedtools v2.15 (interspect -wa –v). The mapped reads to the sense strands were loaded to Rstudio to obtain reads between 15 to 35 bp long by the use of custom R-script.
genome build: NONCODE version V4.0 and GENECODE version M1
processed data files format and content: MakeTagDirectory (default)  followed by makeUCSCfile (default) from homer were used to obtained the Bedgraph file to load in the UCSC genome Browser

extract_protocol:
MLE-12 cells nuclei were isolated by treating with hypotonic solution and later used for small RNA isolation by mirVana™ miRNA Isolation Kit, with phenol (ThermoFisher Scientific #AM1560)
libraries were prepared using the  Truseq small RNA Kit (Illumina). using 15-30 ng small RNAs (based on Bioanaylzer small RNA measurement).  Instead of gel-based cleanup of ligated cDNA, Size-selection was performed on LabChipXT (Perkin Elmer) with extraction window from 135bp - 175bp (insert size 10bp – 60bp)

tag: cells

tag: sample type

value: treatment

value: sh Exosc10


title: Mirlet7d_ChIRP_MLE_12

description: Tilling Mirlet7d oligonucleotide from EXIGON

data_processing:
library strategy: ChIRP-seq
Visualization of raw reads was done using FastQC to check the quality of raw reads.
Raw reads were trimmed with fastx_trimmer -Q33 -f  13 -l 73
ChIRP_seq reads were aligned to the mm9 genome by the help of bowtie2 using default settings
The ouput mapped files were converted to bam files using samtools view -Sb and samtools sort.
Bam files were converted to bed files using bamTobed programm (default settings).
peak calls were performed with MACS14.1 using the P-value of p1e-3.
Annotation of the peaks was performed using annotatePeaks.pl from Homer.
The mapped files in bed format were used to create a Taq library using makeTagDirectory (default settings).
The makeUCSCfile command (default settings), to visualize the mapped files in the UCSC genome browser.
The peak file (Mirlet7d_ChIRP_seq_peaks_annot.txt) was obtained using annotatePeaks.pl from Homer (Default settings).
Genome_build: mm9
Supplementary_files_format_and_content: Bedgraph_UCSC files to load in the UCSC genome Browser

growth_protocol: MLE-12 cells were kept at 37°c in DMEM:F12 medium containing 5 % Fetal Calf Serum, and 1% P/S (penicillin/Streptomycin)

extract_protocol:
DNA was eluted with a cocktail of 100μg/ml RNase-A (Sigma-Aldrich). Chromatin was reverse crosslinked at 65°C overnight. DNA was then extracted purify the DNA with qiaquick columns according to manufacturer’s instructions.
ChIRP_seq: Libraries were prepared according to Illumina's instructions accompanying the Ovation Ultra Low Kit.

treatment_protocol: Chromatin from MLE-12 were incubated with 150pmol of probes (Biotinylated tilling oligo of mature Mirlet7d) at 37°C for 4h. Streptavidin-magnetic C1 beads (Invitrogen) were blocked with 500ng/μl yeast total RNA, and 1mg/ml BSA for 1h at room temperature, and washed three times again in nuclear lysis buffer before resuspended in its original volume. 100µl of washed/blocked C1 beads were added per 100pm ol of probes, and the whole reaction was mixed for another 30 min at 37°C. beads:biotin-probes:RNA:chromatin adducts were captured by magnets (Invitrogen) and washed five times with 40x beads volume of wash buffer.

tag: sample group

value: Mirlet7d_tylling Oligo


title: Mirlet7d_Input_MLE_12

data_processing:
library strategy: ChIRP-seq
Visualization of raw reads was done using FastQC to check the quality of raw reads.
Raw reads were trimmed with fastx_trimmer -Q33 -f  13 -l 73
ChIRP_seq reads were aligned to the mm9 genome by the help of bowtie2 using default settings
The ouput mapped files were converted to bam files using samtools view -Sb and samtools sort.
Bam files were converted to bed files using bamTobed programm (default settings).
peak calls were performed with MACS14.1 using the P-value of p1e-3.
Annotation of the peaks was performed using annotatePeaks.pl from Homer.
The mapped files in bed format were used to create a Taq library using makeTagDirectory (default settings).
The makeUCSCfile command (default settings), to visualize the mapped files in the UCSC genome browser.
Genome_build: mm9
Supplementary_files_format_and_content: Bedgraph_UCSC files to load in the UCSC genome Browser


title: G06_T05_A

description: 2d stim TGFB Butyr donor A


title: single cell mRNA d5_23_gf

city: Utrecht

first: Abel

last: Vertesy

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description:
cDNA of polyadenylated RNA
DP_mat.tsv.gz; DP_pat.tsv.gz; PP_matrix.tsv.gz; TPM_AllCells.tsv.gz; AllCells.Total.RefSeq.cout.tsv.gz

data_processing:
RNA: Single end reads obtained by SmartSeq2 were aligned to the transcriptome using BWA  with default parameters. The transcriptome model contained all RefSeq gene models based on the human genome release hg19 downloaded from the UCSC genome browser. All isoforms of the same gene were merged to a single gene locus. See online methods and supplementary of the manuscript for details.
Genome_build: hg19
Supplementary_files_format_and_content: tab separated values (.tsv)
Supplementary_files_format_and_content: Mapping results (transcript counts and rations) combining all mRNA-Seq experiments.
Supplementary_files_format_and_content: Dimensions: 108 single cells per columns, 23211 detected genes / 9673 detected genes (HGNC/ HUGO gene symbol) with allelic information per row.
Supplementary_files_format_and_content: rsem.fpkm_table_all.tsv.gz : Fragments per kilobase of exon per million mapped reads (FPKM) values for all uniquely mapped reads. software used:RSEM v1.2.16
Supplementary_files_format_and_content: rsem.tpm_table_all.tsv.gz : Transcript per million (TPM) values for all uniquely mapped reads. software used:RSEM v1.2.16
Supplementary_files_format_and_content: htseq.count_table_all.tsv.gz : Read Counts (uniquely mapped) software used:HTSeq 0.6.1p1
Supplementary_files_format_and_content: DP_mat.tsv.gz : Uniquely mapped read counts for maternal allelic reads software used:Custom scripts; will be available under https://github.com/vertesy/human_germ_cell_x-reactivation upon publication
Supplementary_files_format_and_content: DP_pat.tsv.gz : Uniquely mapped read counts for paternal allelic reads software used:Custom scripts; will be available under https://github.com/vertesy/human_germ_cell_x-reactivation upon publication
Supplementary_files_format_and_content: PP_matrix.tsv.gz : Paternal maternal read count ratios for allelic reads software used:Custom scripts; will be available under https://github.com/vertesy/human_germ_cell_x-reactivation upon publication

source_name: gonad

growth_protocol: Human Embryos with no medical indication

extract_protocol: Single cell isolation from human organs: The tissue culture dishes to use for the single cell picking were first coated for a couple of minutes at room temperature with 0.5% bovine serum albumin (BSA, Life Technologies, Carlsbad, USA) in PBS and then filled with Dulbecco’s Modified Eagle Medium/F12 Nutrient mixture (DMEM/F12, Life Technologies, Paisley, UK). Human gonads and adrenals were placed individually in tissue culture dishes and the organs were mechanically disrupted with sharp needles so that single cells were released. Single cells were then manually picked under a stereo microscope (Zeiss, Sliedrecht, the Netherlands) using a pulled glass capillary in picking volumes of ±0.5µl medium and transferred to ice-cold PCR tubes containing 2.0µl lysis buffer (1.9µl 0.2% TritonX-100 in water + 0.1µl Recombinant RNase inhibitor (TaKaRa 40U/µl Ref. 2313A) per tube), snap-frozen on dry ice and stored at -80°C.  Reverse transcription: Single-cell full-length cDNA libraries were prepared using the Smart-seq2 protocol (Picelli et al., 2013). Briefly, 2.1µl priming buffer mix (1µl 10mM dNTPs; 1µl 10µM Smarter oligo-dT primer was added to the cell lysate and incubated for 3 min at 72°C in a thermal cycler, and then put on ice. Reverse transcription (RT) was performed by the addition of 5.6µl Smart-Seq2 RT mix (0.5µl SuperScriptII (Invitrogen Cat. 18064-014); 2µl 5x SuperScriptII buffer; 0.5µl 100mM DTT; 2µl 5M betaine; 0.1µl 1mM MgCl2; 0.25µl Recombinant RNase inhibitor (TaKaRa 40U/µl Ref. 2313A); 0.1µl 100µM LNA strand switch primer; 0.15µl water, per reaction) and incubation (90 min 42°C; 10 “strand-switch” cycles of (2 min 50°C; 2 min 70°C); 4°C) in a thermal cycler.   cDNA amplification: cDNA amplification was performed by the addition of 15µl of Smart-Seq2 PCR mix (12.5µl 2x KAPA HiFi HotStart ReadyMix (KAPA Biosystems Ref. KK2602); 0.25µl 10µM ISPCR primers; 2.25µl water, per reaction) and incubation (3 min 98°C; 19 cycles of (20 s 98°C; 15s 67°C; 6 min 72°C); 5 min 70°C; 4°C) in a thermal cycler. The cDNA was purified using 0.7:1 volume of AMPure XP beads (Beckman Coulter, Ref. A63882) according to the manufacturer’s protocol (No. PT5163-1). The purified cDNA for each cell was inspected on an Agilent 2100 Bioanalyzer to determine cDNA concentration and size distribution, using Agilent High Sensitivity DNA chips (Ref. 5067-4626).   Tagmentation and sequencing: Successful cDNA libraries were tagmented using the transposase Tn5 (Picelli et al., 2014). 1ng of cDNA in 5µl water was mixed with 15µl tagmentation mix (1µl of Tn5; 2µl 10x TAPS MgCl2 Tagmentation buffer; 5µl 40% PEG8000; 7µl water, per reaction) and incubated 8 min at 55°C in a thermal cycler. Tn5 was inactivated and released from the DNA by the addition of 5µl 0.2% SDS and 5 min incubation at room temperature. Sequence library amplification was performed using 5µl Nextera XT Index primers (Illumina, Ref. 15032356) and 15µl PCR mix (1µl KAPA HiFi DNA polymerase (KAPA Biosystems Ref. KK202); 10µl 5x KAPA HiFi buffer; 1.5 µl 10mM dNTPs; 2.5µl water, per reaction), and incubation (3 min 72°C; 30 s 72°C; 10 cycles of (10 s 72°C; 30 s 55°C; 30 s 72°C); 5 min 72°C; 4°C) in a thermal cycler. Sequencing libraries were purified using 1:1 volume of AMPure XP beads (Beckman Coulter, Ref. A63882) according to the manufacturer’s protocol (No. PT5163-1, version PR0X3693), inspected on an Agilent 2100 Bioanalyser, using Agilent High Sensitivity DNA chips (Ref. 5067-4626), and the DNA concentration was measured using a Qubit 2.0 Fluorometer (Invitrogen) with the Qubit dsDNA High Sensitivity Assay kit (Molecular Probes, Ref. Q32854). Pools of samples for multiplexing, with unique Illumina barcode for each cell, were prepared according to the Nextera XT DNA Sample Preparation Guide (No. 15031942 page 46, llumina). DNA sequencing was performed on an Illumina HiSeq2000 (43bp single-end) and on Illumina NextSeq500 (75bp single-end).

treatment_protocol: Manual isolation

tag: weeks of gestation

tag: Sex

value: female

tag: donor


title: single cell mRNA d5_25_af

source_name: adrenal gland


title: single cell mRNA d5_20_gf


title: single cell mRNA d5_22_gf


title: single cell mRNA d5_21_gf


title: single cell mRNA d5_26_af


title: single cell mRNA d5_17_gf


title: Mirlet7d_LOF_PRO-seq_MLE_12

description: Addgene (Plasmid #29766)

data_processing:
Visualization of raw reads was done using FastQC to check the quality of raw reads.
Raw reads were sub-set by using seqtk sample to  22300000 millions reads per sample
Trimmomatic was used to trim the raw reads. (java -jar trimmomatic-0.32.jar PE -threads 4 -phred33  ILLUMINACLIP:adapters/TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:20 CROP:70 HEADCROP:5)
BWA was used to map the trimmed reads with the following parameters( bwa aln -n 2  -l 32 -k2 -t 8) followed by (bwa sampe -n1)
The ouput mapped files were converted to bam files using samtools view -Sb and samtools sort.
Unmapped reads were obtained using samtools view (-f 4) from the  bam file obtained after mapping the samples to mm9. Then they were converted to bam files and from bam files later conterted to fastq file with bamToFastq (default)
the mapping to the Drosophila genome (dm39 was performed with the same parameters than used for mm9 mapping.
Quantification of the PRO-seq libraries was performed by using analyzeRepeats.pl rna mm9 -count genes -d for the coing genes and for the ncRNAs, using analyzeRepeats.pl NONCODEv4.gtf mm9 -count genes -d
The mapped files in bed format were used to create a Taq library using makeTagDirectory (-unique -sspe -mapq30).
The makeUCSCfile command (norm to spiking, (mapped reads on the drosophila genome (dm3)
genome build: mm9
processed data files format and content: Bedgraph_UCSC files to load in the UCSC genome Browser

growth_protocol: Mouse lung epithelial cell MLE-12 (ATCC CRL-2110) was kept at 37°c in DMEM: F12 medium containing 5 % Fetal Calf Serum, and 1% P/S (penicillin/Streptomycin). Schneider’s Drosophila Line 2 (S2 cell line, ATCC CRL-1963) was cultured in complete Schneider’ Drosophila medium (10% heat inactivated FCS, 1% Penn-strep) at 26 deg C.

extract_protocol:
MLE-12 cells were harvested and spike-in control (Drosophila S2 cells) were added just before cell permeabilization. Then cells were permeabilized. Precision nuclear run-on was performed. Biotinylated nascent RNAs were  enriched and purified using Trizol (Invitrogen #15596026).
Library preparation of nuclear RNA was performed using Lib-Prep: SMARTer Stranded Total RNA Sample Prep Kit - HI Mammalian (Clontech) following the manufacturer’s instructions.

treatment_protocol: MLE-12 cells were transfected with 2.5ug of empty vector of Mirlet7 sponge construct and harsvested after 48 h.

value: Mirlet7d sponge


title: single cell mRNA d5_19_gf


title: single cell mRNA d5_15_gf


title: single cell mRNA d5_16_gf


title: Ctrl_PRO-seq_MLE_12


title: single cell mRNA d5_14_gf


title: single cell mRNA d4_07_gf


title: single cell mRNA d4_08_gf


title: single cell mRNA d4_12_af


title: single cell mRNA d4_11_af


title: single cell mRNA d4_10_gf


title: single cell mRNA d4_06_gf


title: single cell mRNA d4_09_gf


title: single cell mRNA d4_05_gf


title: single cell mRNA d4_13_af


title: single cell mRNA d4_04_gf


title: single cell mRNA d5_18_gf


title: single cell mRNA d4_03_gf


title: single cell mRNA d3_40_gm

value: male


title: single cell mRNA d4_01_gf


title: single cell mRNA d3_38_gm


title: single cell mRNA d4_02_gf


title: single cell mRNA d5_24_af


title: single cell mRNA d3_24_gm


title: single cell mRNA d3_23_gm


title: single cell mRNA d3_27_am


title: single cell mRNA d3_39_gm


title: single cell mRNA d3_21_gm


title: single cell mRNA d3_26_am


title: single cell mRNA d3_25_gm


title: single cell mRNA d2_36_af


title: single cell mRNA d2_37_af


title: single cell mRNA d2_34_gf


title: single cell mRNA d3_20_gm


title: single cell mRNA d2_35_gf


title: single cell mRNA d2_33_gf


title: single cell mRNA d3_22_gm


title: single cell mRNA d2_18_af


title: single cell mRNA d2_14_gf


title: single cell mRNA d2_13_gf


title: single cell mRNA d2_15_gf


title: single cell mRNA d1_31_af


title: single cell mRNA d1_28_gf


title: single cell mRNA d1_08_af


title: single cell mRNA d1_07_af


title: single cell mRNA d1_27_gf


title: single cell mRNA d1_06_gf


title: single cell mRNA d1_04_gf


title: single cell mRNA d1_02_gf


title: single cell mRNA d5_71_gf


title: single cell mRNA d1_29_gf


title: single cell mRNA d5_72_gf


title: single cell mRNA d2_19_af


title: single cell mRNA d5_73_af


title: single cell mRNA d5_70_gf


title: single cell mRNA d2_32_gf


title: single cell mRNA d2_17_gf


title: single cell mRNA d5_69_gf


title: single cell mRNA d2_16_gf


title: single cell mRNA d5_67_gf


title: single cell mRNA d2_12_gf


title: single cell mRNA d5_66_gf


title: single cell mRNA d1_01_gf


title: single cell mRNA d5_64_gf


title: single cell mRNA d5_74_af


title: single cell mRNA d5_63_gf


title: single cell mRNA d5_65_gf


title: single cell mRNA d5_68_gf


title: single cell mRNA d1_05_gf


title: single cell mRNA d4_48_af


title: single cell mRNA d4_47_af


title: single cell mRNA d4_49_af


title: single cell mRNA d5_75_af


title: single cell mRNA d5_76_af


title: single cell mRNA d1_03_gf


title: single cell mRNA d4_45_af


title: single cell mRNA d4_46_af


title: single cell mRNA d4_44_af


title: single cell mRNA d4_42_af


title: single cell mRNA d4_33_gf


title: single cell mRNA d4_37_gf


title: single cell mRNA d4_43_af


title: single cell mRNA d4_36_gf


title: single cell mRNA d4_38_gf


title: single cell mRNA d4_40_af


title: single cell mRNA d4_39_af


title: single cell mRNA d4_32_gf


title: single cell mRNA d4_41_af


title: single cell mRNA d4_34_gf


title: single cell mRNA d4_35_gf


title: single cell mRNA d4_50_af


title: single cell mRNA d3_61_am


title: single cell mRNA d3_60_am


title: single cell mRNA d4_31_gf


title: single cell mRNA d3_59_am


title: single cell mRNA d3_62_am


title: single cell mRNA d2_58_gf


title: TDP-43 (siMyolinc)

city: Copenhagen SV

first: Shizuka

last: Uchida

email: heart.lncrna@gmail.com, suc@dcm.aau.dk

address: Frederikskaj 10B, 2. (building C)

department: Department of Clinical Medicine

institute: Aalborg University

data_processing:
The sequencing reads were analyzed and mapped to the mouse genome assembly mm10 via Ion PGM Torrent Server (Life Technologies).
The BAM files were used as inputs to HOMER (Heinz et al., 2010) for peak calling and further analysis for motif discoveries.
Genome_build: mm10
Supplementary_files_format_and_content: Text files generated by HOMER.

source_name: C2C12 cells, TDP-43 (siMyolinc)

growth_protocol: Murine myoblast cell line C2C12 cells were cultured in the growth medium containing 20% FBS (Life Technologies, #10270106) in DMEM with high glucose, pyruvate (Life Technologies, # 41966-029) supplemented with antibiotics (penicillin and streptomycin, Sigma-Aldrich, #P4333) at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol:
After two days of differentiation, C2C12 cells were detached with trypsin-EDTA and fixed with 1% formaldehyde. Shearing of chromatin was carried out through Bioruptor Plus (Diagenode) using the following sonication steps: 20 cycles at the low intensity for 30 sec ON / 30 sec OFF; 40 cycles at the high intensity for 30 sec ON / 30 sec OFF; and 50 cycles at the high intensity for 30 sec ON / 30 sec OFF. The efficiency of shearing was assessed by running the sheared chromatin on an 2% agarose gel. Using this sheared chromation, ChIP was performing with EZ-Magna ChIP A/G Kit (Millipore, #17-10086) following manufacturer’s protocol. For each ChIP experiment, 10 μg of an antibody were used.
For each library preparation, 100 ng of immunoprecipitated DNA were used as a starting template following manufacturer’s protocol. Briefly, immunoprecipitated DNA was end-repaired, adapter-ligated and amplified using Ion Plus Fragment Library Kit (Life Technologies, #4471252). The adapter-ligated DNA was size selected through E-Gel Electrophoresis System (Life Technologies) to obtain the optimal size for 200bp read sequencing. Then, size selected DNA was amplified for 18 cycles of PCR. After amplification, the fragments size of the library was assessed through High Sensitivity DNA Analysis Kit (Agilent, # 5067-4626). To calculate a dilution factor, Ion Library Quantitation Kit (Life Technologies, #4468802) was used. Using this dilution factor, template-positive Ion-Sphere particles were prepared using Ion PGM™ Template OT2 200 Kit (Life Technologies,  #4480974) via Ion OneTouch 2 System (Life Technologies). The quality of template-positive Ion-Sphere particles was assessed via Ion-Sphere™ Quality Control Assay (Life Technologies, #4468656). Particles were subsequently enriched according to manufacturer’s protocols. The enriched template-positive Ion-Sphere particles were sequenced using Ion 318™ Chip Kit v2 (Life Technologies, #4484355) and Ion PGM™ Hi-Q™ Sequencing Kit (Life Technologies, #A25592) via Ion PGM™ System (Life Technologies).

treatment_protocol: Transient siRNA transfection (10nM final concentration) was carried out using RNAiMax (Life Technologies) according to the manufacturer’s protocol. To induce the differentiation process (initiated 24 hours after the transfection), C2C12 cells were cultured in the differentiation medium containing 2% horse serum (Sigma-Aldrich, #H1270) in DMEM with low glucose, pyruvate (Life Technologies, #31885-023) supplemented with antibiotics (penicillin and streptomycin, Sigma-Aldrich, #P4333).

value: myoblast cell line C2C12

tag: transfection

value: siRNA-mediated knockdown of Myolinc

tag: time

value: Day 2 of differentiation

tag: chip antibody

value: TDP-43 (Abcam, catalog# ab41972; lot# GR200025-1)


title: single cell mRNA d2_57_gf


title: single cell mRNA d2_55_gf


title: Myog (siMyolinc)

source_name: C2C12 cells, Myog (siMyolinc)

tag: cell line

value: Myogenin (Santa Cruz, catalog# sc-12732; lot# J0813)


title: IgG (siMyolinc)

source_name: C2C12 cells, IgG (siMyolinc)

value: normal mouse IgG (Millipore, catalog# 12-371B; lot# 2017312)


title: single cell mRNA d2_56_gf


title: input DNA (siMyolinc)

source_name: C2C12 cells, input DNA (siMyolinc)


title: single cell mRNA d2_54_gf


title: cis output 3

city: Barcelona

first: Guillaume

last: Diss

address: C/ Dr. aiguader, 88

country: Spain

institute: CRG

description:
from plasmid library
TableS4.xslx

data_processing:
trans library filtering (sample 1-6): Paired reads for which one of the two variable regions had an average Phred score below or equal to 20 were also discarded. Additionally, paired reads were also filtered-out if they had i) one or more non-resolved bases (Ns) in the variable or UMI regions, ii) more than one mutated codon in each gene’s variable region or iii) if the mutated codon ended in an A or T (since these were not encoded by the NNS mutagenic primers). (custom perl script)
cis library (sample 7-12): Paired-end reads, which were overlapping over the full length of the variable region, were assembled using PEAR version 0.9.6 38 with a p-value threshold for correct assembly of 0.05, a maximum and minimum fragment length of 150 nt, and a minimum overlap size of 100 nt. These parameters force the assembly of sequences of the unique expected length. An average of 30% and 20% of the paired end reads from the three input and output libraries, respectively, were not assembled and filtered out. These included the adapter sequences and indels (resulting from the <100% coupling efficiency inherent to DNA synthesis). Additionally, assembled reads with Ns in any part of the sequence were filtered out.
variant calling (custom perl script)
UMIs counting (custom perl script)
Supplementary_files_format_and_content: Excel file with read count for each variants in each sample

molecule: other

organism: synthetic construct

source_name: deep mutational scanning

growth_protocol: Yeast was grown in synthetic complete media -HIS at 30ºC (for input samples) and SC -HIS 1M NaCl at 37ºC (output samples). Cells were harvest, centrifuged and pellets saved at -20ºC for DNA extraction

extract_protocol: The sequencing libraries were constructed by two consecutive PCR reactions using a method adapted from Levy et al 35. The first PCR was designed to amplify the region of interest, i.e. from directly upstream of the first mutated codon in FOS to directly upstream of the first mutated codon in JUN (the two genes are in head-to-tail orientation). The first PCR also added Unique Molecular Barcodes (UMIs) and the first half of the illumina adapter sequences. A small number of cycles of the first PCR would limit the number of differently barcoded molecules that derive from the same template molecule. The second PCR would then add the remainder of the Illumina adapter sequences. Plasmid concentrations in the total DNA extractions were first quantified by qPCR using primer pair OGD241-OGD242 that bind in ori region of the plasmid. For each six samples of each of the cis and trans libraries, respectively 4 and 48 PCRs were performed using Q5 Hot Start High-Fidelity DNA Polymerase (New England Biolabs) according to manufacturer’s protocol in 50 μL reactions with 4.2 x 107 molecules of plasmid from the DNA extraction, 25 pmol of primers OGD237 and OGD238, and a melting temperature of 66˚C (previously determined by temperature gradient), an extension time of 30 sec or 1 min, respectively, for 4 cycles. A total of 2 x 109 molecules of plasmids were then used to prepare the sequencing libraries from each sample. Excess primers were removed by adding 2 μL of ExoSAP-IT (Affymetrix) and incubating for 20 min at 37˚C followed by an inactivation for 15 min at 80˚C. This step was necessary because these 60 nt primers are not efficiently removed by the following column purification step. The 48 PCRs of each sample of the trans library were then pooled and purified using eight Qiagen PCR purification kit (Qiagen) columns per sample. According to manufacturer’s protocol, one column is able to bind 10 μg of DNA, which corresponds to ~8 x 108 genomes. Eight columns were then used to ensure that they are not saturated by the genomic DNA carried over from the DNA extraction. The DNA was eluted in 2 x 50 μL of EB buffer (provided by the manufacturer) and pooled for each sample. The eluted DNA was then split into 24 PCR reactions per, which were performed using Kapa HiFi HotStart DNA polymerase (Kapa Biosystems) according to manufacturer’s protocol in 50 μL with 15 pmol of illumina adapter primers. The reverse primers carried a different index for each of the six samples of the same library. For this PCR step, Kapa was chosen over Q5 because it was less efficient in the first PCR reactions (higher optimal melting temperature) and thus would lead to a lower re-barcoding of amplicons with new UMIs present on primers from the first PCR reaction that would have been carried over. Each sample was loaded on an agarose gel to check for correct amplification. A strong non-specific band of lower size was observed, which seemed to gradually disappear as the number of cycles in the first PCR was increased. However, increasing the number of cycles would increase the probability of producing amplicons with different UMIs that derived from the same original template molecule. The number of cycles in the first PCR was thus kept to four and the band of correct size was extracted by gel purification from each sample. To this end, the 24 PCRs of each sample were pooled, concentrated on four Qiagen PCR purification kit (Qiagen) columns per sample and each eluted with 2 x 50 μL of EB buffer (provided by the manufacturer). The bands of correct size were then purified on 2% agarose gel starting from 100 μL of each sample using 10 μL QIAEX II beads (Qiagen) according to manufacturer’s protocol and eluted in 20 μL EB buffer. DNA concentration was determined by picogreen in triplicates and the six samples were pooled at equimolar ratio. The pooled sample was sequenced in a single lane of an Illumina HiSeq2500 with 125 bp paired-end reads at the EMBL Genomics Core Facilities in Heidelberg, Germany.

tag: molecule

value: PCR amplicon


title: single cell mRNA d2_53_gf


title: TDP-43_3

source_name: C2C12 cells, TDP-43


title: single cell mRNA d2_52_gf


title: TDP-43_2


title: cis input 2

description:
from plasmid library
TableS4.xslx


title: cis input 3

description:
from plasmid library
TableS4.xslx


title: cis output 1

description:
from plasmid library
TableS4.xslx


title: trans output 3

description:
from plasmid library
TableS1.xlsx


title: MyoD (siMyolinc)

source_name: C2C12 cells, MyoD (siMyolinc)

value: MyoD (Santa Cruz, catalog# sc-304; lot# C0812)


title: trans output 2

description:
from plasmid library
TableS1.xlsx


title: cis output 2

description:
from plasmid library
TableS4.xslx


title: cis input 1

description:
from plasmid library
TableS4.xslx


title: Myog

source_name: C2C12 cells, Myog


title: IgG

source_name: C2C12 cells, IgG


title: TDP-43


title: trans output 1

description:
from plasmid library
TableS1.xlsx


title: Pol2 (siMyolinc)

source_name: C2C12 cells, Pol2 (siMyolinc)

value: RNA polymerase II CTD repeat YSPTSPS (phospho S2) (Abcam, catalog# ab5095; lot# GR193165-1)


title: trans input 2

description:
from plasmid library
TableS1.xlsx


title: Pol2

source_name: C2C12 cells, Pol2


title: trans input 3

description:
from plasmid library
TableS1.xlsx


title: Nuclear_RNA_seq_Random_GOF

data_processing:
Raw reads was done using FastQC, trimmed of the raw reads using Trimmomatic (Bolger et al. 2014) with the following parameters( ILLUMINACLIP:adapters/TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:17 CROP:60 HEADCROP:6)
RNA_seq reads were aligned to the mm9 genome.
 After mapping, the sam files were converted to bam format by using samtools view (-Sb) followed by samtools sort. Mapping was performed using bowtie2 following the Parameters (bowtie2 -D 15 -R 3 -N 0 -L 20 -i S,1,0.56 -p8). For the
MakeTaqlibrary -format sam; was used to create the taq library
to quantify the libraries ;
 analyzeRepeats.pl mm9 -count genes -strand both was used for the Protein-coding whereas for the ncRNAs (analyzeRepeats.pl  NONCODE_v4.gtf mm9 -count genes -strand both and -rpkm) was used.
homer makeUCSC (normalized to 10 millions) was used to obtain bedgraph files to Visualize in UCSC genome browser
Genome_build: Mouse mm9
Supplementary_files_format_and_content: Bedgraph_UCSC files to load in the UCSC genome Browser

growth_protocol: MLE-12 cells were kept at 37°c in DMEM medium containing 10 % Fetal Calf Serum, and 1% P/S/G (penicillin/Streptomycin/L-glutamine)

extract_protocol:
Total RNA was isolated with TRIzol(R)  (Invitrogen)
[Nuclear_RNA_seq] Libraries were prepared according to SMARTer Stranded Total RNA Sample Prep Kit - HI Mammalian (including rRNA depletion RiboGone)
[Pull_Down_Input_Mirlet7d] Libraries were treated the Kit  for rRNA depletion by RiboGone™ - Mammalian and Pre-amplification step was performed with pre-amplification using SMARTer® Universal Low Input RNA Kit for Sequencing

treatment_protocol: MLE-12 cells were transfected with 25nM of Biotinylated microRNA (Random or Mirlet7d) and harsvested after 48 h

tag: genotype/variation