title: Sterile2.3

source_name: Line T295H_Sterile2

value: 35 days after planting


title: S. pombe Set2D cells_BRL110

status: Public on Jul 20 2017

type: SRA

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

country: USA

institute: St Jude Children's Research Hospital

library_source: transcriptomic

data_processing:
2 X100 bp paired end stranded sequencing was performed on an Illumina HiSeq 2500. Basecalling was performed using Illumina Casava 1.7
FASTQ sequences adapter trimmed (cutadapt) and mapped to the S. Pombe  genome by STAR
Bams are sorted by samtools by name and mapped reads were counted with HTSEQ
Genome_build: Schizosaccharomyces_pombe. ASM294v2.29
Supplementary_files_format_and_content: count files are txt format files that contain raw read counts that map  to  transcripts for each defined gene.

molecule: total RNA

organism: Schizosaccharomyces pombe

source_name: S. pombe Set2D cells

growth_protocol: Cultures were grown overnight in YES at 25°C to a density of 2.5 x 106 cells/ml in a 25mL culture.

extract_protocol:
The cells were pelleted by centrifugation and washed in DEPC H2O. The pellet was resuspended in 750ul TES Buffer [50mM Tris-HCl pH 7.5, 10mM EDTA, 100mM NaCl, 0.5% SDS made in DEPC H2O] along with an equal volume of 5:1 phenol:chloroform pH 4.7 and incubated at 65°C for one hour with vortexing for 10 seconds every 10 minutes. The samples were then cooled on ice and centrifuged for five minutes at 13,000 RPM. The aqueous phase was transferred to a 2mL phase lock tube and an additional phenol:chloroform extraction was performed. After centrifugation, the aqueous phase was transferred to a new tube and an equal volume of chloroform was added. To precipitate the RNA, the aqueous phase was transferred to a 2mL microcentrifuge tube and three volumes of ice cold ethanol and 3M NaOAc pH 5.2 were added and the samples were kept at -20°C to precipitate the RNA. The next day, samples were centrifuged at 14,000 RPM and 4°C for 15 minutes to pellet the RNA. The pellet was washed with ice cold 70% ethanol and air dried for 30 minutes. A Turbo DNAse (Ambion) reaction was set up with 100ug of RNA in a 150ul reaction containing 5ul of Turbo DNAse. The reaction was incubated at 37°C for 30 minutes and another 5ul of Turbo DNAse was added and incubated for an additional 30 minutes prior to the removal of the DNAse using 50ul of inactivation beads. An RNeasy Mini kit (Sigma) was used to further clean up and concentrate the RNA which was eluted in a final volume of 30ul of DEPC H2O.
Libraries were prepared from 2ug of RNA. Ribosomal RNA was removed from the samples using Ribo-Zero Gold rRNA Removal Kit (Yeast) following manufacturer instructions (Illumina). Libraries were prepared using the TruSeq Strand Total RNA Library Prep Kit, beginning at Elution 2 – Fragment – Prime step immediately preceding cDNA synthesis according to the manufacturer instructions (Illumina) with the following modifications; the 94 C Elution 2 – Fragment – Prime incubation was reduced to five minutes and the PCR was reduced to 11 cycles.

treatment_protocol: Not applicable

tag: genotype/variation

value: H3 WT Set2D mutant


title: T55ExoP_S2

city: Wako

first: Itoshi

last: NIKAIDO

state: Saitama

address: 2-1 Hirosawa

department: Center for Biosystems Dynamics Research

country: Japan

institute: RIKEN

description: We analyzed 384 wells with 10 pg total RNA.

data_processing:
BCL files generated by Illumina NextSeq500 were converted to fastq files by bcl2fastq2 (v2.17.1.14) with demultiplexing pool barcodes.
Data for Quartz-Seq2 was processed by Quartz-Seq2 pipeline. Data for Drop-seq was processed by Drop-seq pipeline.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include UMI counts for each gene for each cell

organism: Mus musculus

source_name: Purified total RNA from ES cells

extract_protocol:
We performed two single-cell RNA-seq methods (Drop-seq and Quartz-Seq2). Drop-seq was performed as reported previously [Cell. 2015;161:1202–14]. Moreover, we established Quartz-Seq2 (a high-throughput single-cell RNA-sequencing method that effectively uses limited sequence reads). We used two sets of RT primer for Quartz-Seq2. The set of v3.1 RT primers has 384 kinds of unique cell barcodes, with a length of 14 nucleotides (OPC purification, FASMAC). The set of v3.2 RT primers has 1,536 kinds of unique cell barcodes, with a length of 15 nucleotides (OPC purification, Sigma). The set of v3.1 RT primers corresponds to one set of the 384-well PCR plate with lysis buffer, the wells of which have unique barcodes. The set of v3.2 RT primers corresponds to four sets of the 384-well PCR plate with lysis buffer. Single cells were isolated in the 384-well PCR plate with 1 µL of lysis buffer (0.1111 µM respective RT primers, 0.12 mM dNTP mix, 0.3% NP-40, 1 unit/µL RNasin plus) containing ERCC spike mix I.
For Quartz-Seq2, cryopreserved 384-well plates with single-cell lysate were centrifuged at 10,000 g and 4ºC for 1 min. Subsequently, we denatured total RNA in each 384 plate at 70ºC for 90 s and hybridized the RT primer to poly-adenylated RNA at 35ºC for 15 s using the C1000/S1000 thermal cycler. The resulting plates were again centrifuged at 10,000 g and 4ºC for 1 min. Next, the plates were placed on the 384 aluminum plate at 0ºC. We peeled away the seal and added 1 µL of RT premix (2x Thermopol buffer, 5 units/µL SuperScript III, 0.55 units/µL RNasin plus) to 1 µL of lysis buffer for each well using a Mantis microfluidic dispensing system (Formulatrix) or a 384 Transfer Plate system (1859-384S, Watson). The above RT solution was used for the RT25 condition. For the RT100 condition, we used the following RT solution: 2x Thermopol buffer, 20 units/µL SuperScript III, and 2.2 units/µL RNasin plus. We sealed the plates again and agitated them at 2,600 rpm and 4ºC for 1 min. The plates were then centrifuged at 10,000 g and 4ºC for 1 min. We then performed reverse transcription at 35ºC for 5 min and 50ºC for 50 min. The reverse transcription was stopped at 70ºC for 15 min. Then, the plates were placed on a prechilled aluminum block, after which we peeled off their seals. Subsequently, we turned the plates upside down on the assembled collector type A or type B (supplemental figure). We mainly used type A. We centrifuged the plates with an assemble collector at 3,010 g and 4ºC for 3 min with swing-bucket rotors. Subsequently, we collected the cDNA solution into a disposable reservoir. Typically, we obtained 650–700 µL of cDNA solution from one 384-well PCR plate. We purified and concentrated the cDNA solution using the DNA Clean & Concentrator™-5 kit (Zymo Research). We used three purification columns for one 384-well PCR plate in the case of the v3.1 RT primer system (384-cell barcode). Purified cDNA was extracted into 20 µL of nuclease-free water from one column purification and transferred into an eight-linked PCR tube (TaKaRa). The PCR tubes were placed on an aluminum PCR stand at 0ºC. We added 25 µL of TdT solution [1x Thermopol buffer, 2.4 mM dATP, 0.0384 units/µL RNase H (Invitrogen), 26.88 units/µL terminal transferase (Roche)] into 20 µL of extracted cDNA using a pipette at 0ºC. The resulting 45 µL of TdT solution was mixed with a pipette at 0ºC or ThermoMixer at 2,000 g and 0ºC for 1 min. Immediately thereafter, the PCR tubes were centrifuged at 10,000 g and 0ºC for 1 min. We used a C1000/S1000 thermal cycler equipped with the 96-Deep Well Reaction Module for the following steps. The PCR tubes were placed on the block of the thermal cycler, which had been prechilled to 0ºC. We then performed a poly-A tailing reaction at 37ºC for 75 s. The solution was inactivated at 65ºC for 10 min. The PCR tubes were placed on an aluminum PCR stand at 0ºC. We then dispensed approximately 11 µL of solution into four wells from 45 µL of TdT solution. We added 46.16 µL of PCR I premix (1.08492x MightyAmp Buffer version 2, 0.06932 µM Tagging primer, 0.05415 units/µL MightyAmp DNA polymerase) to 11 µL of TdT solution for the respective wells of the PCR tube. We performed gentle inversion mixing on the resulting solution in the PCR tube. The tubes were then centrifuged at 10,000 g and 4ºC for 1 min. Subsequently, the solution was mixed with ThermoMixer at 2,000 rpm and 4ºC for 2 min. Then, we spun down the tube again. Next, we denatured the solution at 98ºC for 130 s and hybridized Tagging primer to poly-A-tailed cDNA at 40ºC for 1 min. After that, we performed the “Increment step” by heating to 68ºC at 0.2ºC every second and performed second-strand synthesis at 68ºC for 5 min. The tubes were placed on an aluminum PCR stand at 0ºC. We added 50.232 µL of PCR II premix (0.99697x MightyAmp Buffer version.2, 1.8952 µM gM primer) to 56.16 µL of PCR I solution. We performed gentle inversion mixing on the resulting solution in the PCR tube. The tubes were then centrifuged at 10,000 g and 4ºC for 1 min. Subsequently, the solution was mixed with ThermoMixer at 2,000 rpm and 4ºC for 2 min, after which we spun down the tube again. We then placed it on the block of the thermal cycler at 68ºC. Subsequently, we amplified the cDNA for 11 cycles under the following conditions: 98ºC for 10 s, 65ºC for 15 s, and 68ºC 5 min. We then incubated the tube at 68ºC for an additional 5 min. Finally, we transferred all of the PCR solution, derived from one 384-well PCR plate, to a 50-mL Polypropylene Centrifuge Tube (Watson). Typically, we obtained approximately 1.2 mL of PCR solution per 384-well PCR plate. We added 32 µL of 3 M sodium acetate (pH 5.2) and 6420 µL PB-Buffer (Qiagen) to the PCR solution. The mixture was then purified using a MinElute Spin Column (Qiagen). Purified cDNA was extracted into 40 µL of nuclease-free water. We additionally purified the cDNA with 32 µL of Ampure XP beads. Finally, we obtained 32 µL of purified cDNA. We checked the length distribution of amplified cDNA with an Agilent High Sensitivity DNA Kit (Agilent). The typical average size of the amplified cDNA in Quartz-Seq2 was approximately 1,400 bp.   In the case of the usage of the v3.2 RT primer in Quartz-Seq2, we modified the above steps as follows. After reverse transcription, we collected cDNA solution into a disposable reservoir from four sets of 384-well plates, which corresponded to 1,536 wells. We purified and concentrated the cDNA solution using eight purification columns for four 384-well PCR plates in the case of the v3.2 RT primer system. In the PCR step, we amplified cDNA for nine cycles with the following conditions: 98ºC for 10 s, 65ºC for 15 s, and 68ºC for 5 min. Finally, we transferred all of the PCR solution derived from four 384-well plates to a 50-mL Polypropylene Centrifuge Tube (Watson). Typically, we obtained approximately 3.5 mL of PCR solution per four 384-well PCR plates. We added 88 µL of 3 M sodium acetate (pH 5.2) and 17.6 mL of PB-Buffer (Qiagen) to the PCR solution. The mixture was purified using the MinElute Spin Column (Qiagen). Subsequently, cDNA was again purified using Ampure XP magnetic beads.   For the Quartz-Seq1-like reaction, we performed the following procedure in accordance with our previous study. We added 1 µL of RT premix (2x PCR buffer, 5 units/µL SuperScript III, 0.55 units/µL RNasin plus) to 1 µL of lysis buffer. We then performed reverse transcription at 35ºC for 5 min and 45ºC for 20 min. This reverse transcription was stopped at 70ºC for 15 min. We added 5 µL of ExoIB solution (1.6x Exonuclease I buffer, 3.2x PCR buffer, 16 mM DTT) and 20 µL of TdT solution [1x PCR buffer, 3 mM dATP, 0.0384 units/µL RNase H (Invitrogen), 33.6 units/µL terminal transferase (Roche)] into 20 µL of extracted cDNA using a pipette at 0ºC. The PCR tubes were placed on the block of the thermal cycle

tag: cell type

value: 10pg total RNA from ES cells

tag: strain

tag: cell line

tag: Sex

value: male

tag: the number of single-cell/well contained in each data

tag: method name of single-cell rna-seq

value: prototypes 4 of Quartz-Seq2

tag: type of sequence library preparation

value: Ligation

tag: sequencer

tag: the number of fastq reads for dge-matrix (in million)

tag: read2 length for dge-matrix (nt)


title: Sterile2.2

city: West Lafayette

first: Karen

middle: A

last: Hudson

state: IN

address: 915 West State Street

department: Crop Production and Pest Control

institute: USDA-ARS

data_processing:
Aligned to Gmax275 primary transcriptome using Bowtie2
removed reads that aligned multiple transcripts
removed genes with <10 hits per stage/experiment
Normalization using DESeq2.0
Genome_build: Glycine max 275
Supplementary_files_format_and_content: .csv files with RPKM values for each sample

organism: Glycine max

extract_protocol:
RNA was extracted from trifoliate leaves using Phenol-cholorform method.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: line

value: Line T295H

tag: time point

tag: tissue

value: Leaf

tag: sample group

value: Sterile


title: Depodding2.2

source_name: Line Williams 82_Depodding2

value: Line Williams 82

value: 45 days after planting

value: Depodded


title: S. pombe G34R cells_BRL109

source_name: S. pombe G34R cells

value: H3 G34R mutation


title: T55ExoM_S1

value: Quartz-Seq2 (v3.1, RT100)


title: S. pombe G34R cells_BRL108


title: Sterile_Control2.2

source_name: Line T295H_Sterile_Control2

value: Control


title: Sterile_Control2.3


title: Sterile_Control2.1


title: S. pombe WT cells_BRL103

source_name: S. pombe WT cells

value: H3 WT


title: SterileAP1.2

source_name: Line T295H_SterileAP1

value: 28 Days after planting (R2 growth stage)

value: Initial timepoint


title: SterileAP1.3


title: SterileAP1.1


title: S. pombe WT cells_BRL102


title: S. pombe WT cells_BRL101


title: Sterile_Control3.1

source_name: Line T295H_Sterile_Control3

value: 63 days after planting


title: OR2W5_K562

city: Cambridge

first: Nicolas

last: Erard

address: Robinson Way

country: United Kingdom

institute: CRUK Cambridge Institute

library_source: genomic

data_processing:
Remove adapters using cutadapt (v. 1.11), options:  -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT --minimum-length 75
Map reads to olfactory receptor sequence using bwa (v. 0.7.10-r789), default parameter
Merge r1 and r2 mapping patterns using awk
Count similar mapping patterns using awk
Supplementary_files_format_and_content: Counts of CRISPR/Cas9 induced genomic scars at each olfactory receptor locus

molecule: genomic DNA

organism: Homo sapiens

source_name: K562-Cas9 cells

growth_protocol: A375 and K562 cell lines were grown at 37C with 5% CO2 according to ATCC guidelines

extract_protocol:
Genomic DNA was extracting using the QIAamp Blood DNA Midi Kit (Qiagen). For each sample, the targeted olfactory receptor sequence was extracted from genomic DNA in 8 separate 30-cycle PCR reactions where 2 ug of input DNA was included in each reaction.
Illumina adapters where subsequently added in a second PCR.
Samples were sequenced on the Illumina MiSeq platform.

treatment_protocol: Cells were infected with lentivirus harboring sgRNAs targeting olfactory receptors], with an MOI of 0.3, and were kept in culture for 12 doublings

tag: targeted olfactory receptor


title: OR10A4_K562


title: cdc15 releaseNOC

city: Paris

first: Vittore

middle: Ferdinando

last: Scolari

address: 28, rue du Dr. Roux

department: Genomics and Genetics & C3BI

country: France

institute: Institut Pasteur

data_processing:
Iterative alignment, Min-leght=20, step=20, bowtie2 --very-sensitive --rdg 500,3 --rfg 500,3
Filtering, Mapping quality=30, no ambiguous reads
Assignment to restriction fragment
Filter cis contacts according to read orientation if distance in rst fragment is less then 7
Rebinning at 5000 bp resolution
Genome_build: S288C reference genome R64
Supplementary_files_format_and_content: CSV file containing the contact matrix

organism: Saccharomyces cerevisiae

source_name: Cell culture

growth_protocol: Cells were grown in either rich medium (YPD: 1% bacto peptone (Difco), 1% bacto yeast extract (Difco) and 2% glucose) or synthetic complete (SC: 0.67% yeast nitrogen base without amino acids (Difco), supplemented with a mix of amino-acids, uracil and adenine, 2% glucose), at either 30°C or 23-25°C (corresponding to the permissive temperature of the conditional TS mutations cdc6-1, cdc14-3 and cdc15-2).

extract_protocol:
For each Hi-C experiment aliquots of 1-3 x 10e9 cells in 150 ml YPD/SC were fixed in 3% formaldehyde (Sigma) for 20 min at room temperature and quenched with 25 ml glycine 2.5 M for 20 min at 4°C. Cross-linked cells were recovered through centrifugation, washed with YPD and incubated for 30 min in 10 ml of sorbitol 1M, DTT 5mM and Zymolyase 100T (CFinal=1 mg/ml; Armsbio). Spheroplasts were washed once with 5 ml sorbitol 1M, once with 5 ml 1X RE buffer (DpnII NEB buffer) and finally suspended in 3.5 ml of 1X RE buffer. The spheroplasts were treated with 3% SDS for 20 min at 65°C and the lysate was digested overnight with DpnII (CFinal=450 U/pellet; NEB) at 37°C. The digestion was centrifuged for 20 min at 18000 g, the supernatant discarded and the pellet suspended in 400 μl of water. The 5’ overhangs from DpnII digestion were filled in using dNTP 30 μM (biotin-14-dCTP, dATP, dGTP and dTTP; Invitrogen), at 37°C for 45 min. The biotinylated DNA fragments were ligated by T4 DNA ligase (CFinal=250 Weiss U/pellet; Thermo Scientific) for 4 h at 16°C. DNA purification was achieved through an overnight incubation at 65°C in presence of proteinase K 250 μg/ml and EDTA 6.2 mM, followed by a phenol/chloroform extraction on the precipitated DNA and an RNAse A DNase-free 500 μg/ml treatment.
Hi-C DNA libraries were 500 bp sheared, using CovarisS220 apparatus and were used as template for the paired-end llumina sample preparation method. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase (NEB), DNA Pol I large fragment (Klenow polymerase; NEB) and T4 polynucleotide kinase (NEB). The blunt, phosphorylated ends were treated with Klenow fragment (exo minus; NEB) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters. After adapter ligation library fragments of ~500 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified biotin-labeled DNA fragments were selectively captured by Dynabeads Myone Streptavidin C1 (Invitrogen) and PCR amplified with Illumina primers for 12 cycles.

treatment_protocol: Cell cycle synchronizations: mechanic (elutriation), genetic (TS mutations) and chemic (nocodazole, nutrient deprivation).

tag: genotype

value: MAT-alpha his3{delta} leu2{delta} ura3{delta} trp1{delta} can1{delta} ade2{delta} cdc15-2(Ts)

tag: cell phase

value: M

tag: synchronization

value: release from cdc15-2 TS block in nocodazole


title: Sterile2.1

value: 35 days after planting


title: cdc15 release20 NOC

tag: strain

value: release 20 minutes from cdc15-2 TS block and add nocodazole


title: anaphase cdc15 III

value: M (late anaphase)

value: release from G1 elutriation and block in anaphase with cdc15-2 TS


title: OR6C74_A375

source_name: A375-Cas9 cells

tag: cell line


title: OR10A4_A375


title: Croatan_single_screen_K562_T6_R1

data_processing:
Trim reads to 20bp using fastx_trimmer (-l20) (FASTX Toolkit 0.0.13.2)
Map reads to relevant sgRNA index using bowtie v1.1.0 (options: -v0 --norc)
Count total mapped reads per sgRNA using awk
Join total counts from samples for each library and cell line using join
Supplementary_files_format_and_content: Counts of sgRNAs for different timepoints

organism: synthetic construct

extract_protocol:
Genomic DNA was extracted 2 days after infection (T0) and after 12 doublings (T6) using the QIAamp Blood DNA Midi Kit (Qiagen).
For each sample, sgRNA sequences were extracted from genomic DNA in 8 separate 30-cycle PCR reactions where 2 ug of input DNA was included in each reaction. Illumina adapters where included on the PCR primers for this PCR.
Samples were sequenced on the Illumina MiSeq platform.

treatment_protocol: Cells were infected with lentivirus harboring sgRNA libraries, with an MOI of 0.3, and were kept in culture for 12 doublings

tag: timepoint

value: T6 (12 doublings)

tag: library

value: Croatan single sgRNA screen library


title: v32ESPrE_S1

description: We analyzed single-cells, which were sorted to 1,536-wells in total.

source_name: a mixture of ES cells and the ES-derived primitive endoderm (PrE) cells

tag: cell type

value: ES single-cells and PrE single-cells

tag: Sex

value: male

tag: the number of single-cell/well contained in each data

tag: method name of single-cell rna-seq

value: Quartz-Seq2 (v3.2, RT25)

value: Ligation


title: Croatan_single_screen_K562_T6_R2


title: Croatan_single_screen_K562_T0_R3


title: Croatan_single_screen_K562_T0_R2


title: anaphase cdc15smc2

value: MATa cdc15-2(Ts) smc2-AID-9myc::NAT TIR1-9myc::URA3 SPO2051-91-GFP::TRP1 HTA1-mCherry::HPH  2xpGAL1-CEN6::HIS3::KAN


title: anaphase cdc15 NOC

value: release from G1 elutriation and block in anaphase with cdc15-2 TS and nocodazole


title: G2 scc1

value: MATa (rad5?) pADH1-OsTIR1-myc9::TRP1 GPD-TK(x7)::URA3 scc1-AID::KANr

value: release from G1 elutriation


title: S-G2 scc1


title: Croatan_dual_screen_K562_T6_R2

value: Croatan dual sgRNA screen library


title: Croatan_dual_screen_K562_T0_R3


title: Croatan_dual_screen_K562_T6_R1


title: Croatan_dual_screen_K562_T0_R2


title: both_116nt

value: 10pg total RNA from ES cells

value: Quartz-Seq2 (v3.1, RT100)

tag: type of sequence library preparation

value: Ligation&Nextera

tag: sequencer

tag: the number of fastq reads for dge-matrix (in million)

tag: read2 length for dge-matrix (nt)


title: GPP_WP_screen_K562_T6_R3

value: GPP Wep Portal screen library


title: HTXLigation01_S1_ds074


title: S. pombe G34R cells_BRL107

tag: genotype/variation

value: H3 G34R mutation


title: GPP_WP_screen_K562_T6_R2


title: G1 III

value: exponential G1

value: elutriation


title: G1 II


title: HTXLigation02_S1_ds074


title: Croatan_single_screen_K562_T6_R3

value: T6 (12 doublings)

value: Croatan single sgRNA screen library


title: Croatan_dual_screen_K562_T0_R1


title: asynchronous 2

value: all

value: asynchronous


title: Croatan_dual_screen_K562_T6_R3


title: Sterile_Control3.2

tag: line

value: Line T295H

tag: time point

value: 63 days after planting

tag: tissue

value: Leaf

tag: sample group

value: Control


title: HTXLigation03_S1_ds074

tag: strain

value: male

value: Ligation


title: GPP_WP_screen_K562_T0_R3


title: anaphase cdc6

tag: genotype

value: MATa his3{delta} ura3{delta}0 trp1{delta} can1{delta} ade2{delta} DBF4-Myc18::LEU2 cdc6-1(Ts)

tag: cell phase

value: M

tag: synchronization

value: release 3 h from cdc6-1 TS block


title: AP1.2

source_name: Line Williams 82_AP1

value: Line Williams 82

value: 38 days after planting (R2 growth stage)

value: Initial timepoint


title: S. pombe Set2D cells_BRL111

value: H3 WT Set2D mutant


title: GPP_WP_screen_K562_T0_R2

tag: timepoint

tag: library

value: GPP Wep Portal screen library


title: GPP_WP_screen_K562_T6_R1

value: T6 (12 doublings)


title: sgRNAScorer_screen_K562_T6_R3

value: sgRNAScorer screen library


title: Ligation_116nt

tag: cell type

value: 10pg total RNA from ES cells

tag: cell line

tag: Sex

tag: the number of single-cell/well contained in each data

value: Quartz-Seq2 (v3.1, RT100)


title: G1 cdc6

value: release from G1 elutriation and block at G1/S checkpoint with cdc6-1 TS


title: sgRNAScorer_screen_K562_T6_R2


title: HTXMerged01_S1_ds074

tag: method name of single-cell rna-seq

tag: type of sequence library preparation

value: Ligation&Nextera

tag: sequencer

tag: the number of fastq reads for dge-matrix (in million)


title: sgRNAScorer_screen_K562_T6_R1


title: GPP_WP_screen_K562_T0_R1


title: sgRNAScorer_screen_K562_T0_R2


title: sgRNAScorer_screen_K562_T0_R1


title: cdc15 release60

value: MAT-alpha his3{delta} leu2{delta} ura3{delta} trp1{delta} can1{delta} ade2{delta} cdc15-2(Ts)

value: release 60 minutes from cdc15-2 TS block


title: HTXMerged03_S1_ds074

value: male

tag: read2 length for dge-matrix (nt)


title: cdc15 release40

value: release 40 minutes from cdc15-2 TS block


title: Edit-R_screen_K562_T6_R1

value: Edit-R screen library


title: Edit-R_screen_K562_T0_R3


title: HTXNextera02_S1_ds074

value: Nextera


title: Edit-R_screen_K562_T6_R3


title: Edit-R_screen_K562_T6_R2


title: cdc15 release20

value: M

value: release 20 minutes from cdc15-2 TS block


title: sgRNAScorer_screen_K562_T0_R3


title: OR6C74_K562

tag: targeted olfactory receptor


title: HTXMerged02_S1_ds074


title: HTXNextera01_S1_ds074


title: cdc20 release40

value: MATa his3{delta} leu2{delta} ura3{delta}0 can1{delta} ade2{delta} cdc20::MET-HA3-CDC20::TRP1

value: release 40 minutes from cdc20::MET block


title: NOC release90

value: release 90 minutes from G2/M nocodazole block


title: Nextera_116nt


title: NOC release60

value: S

value: release 60 minutes from G2/M nocodazole block


title: cdc20 release20

value: release 20 minutes from cdc20::MET block


title: anaphase cdc15 II

value: M (late anaphase)

value: release from G1 elutriation and block in anaphase with cdc15-2 TS


title: HTXNextera03_S1_ds074

value: 10pg total RNA from ES cells

value: Quartz-Seq2 (v3.1, RT100)


title: Edit-R_screen_K562_T0_R1


title: NOC release45 II

value: release 45 minutes from G2/M nocodazole block


title: Croatan_single_screen_A375_T6_R3

value: T6 (12 doublings)

value: Croatan single sgRNA screen library


title: metaphase cdc20

value: M (metaphase)

value: release from G1 elutriation and block in metaphase with cdc20::MET


title: OR2W5_A375


title: Depodding_Control2.2

source_name: Line Williams 82_Depodding_Control2

tag: line

value: Line Williams 82

tag: time point

value: 45 days after planting

tag: tissue

value: Leaf

tag: sample group

value: Control


title: Croatan_single_screen_A375_T6_R2


title: anaphase cdc14

tag: strain

tag: genotype

value: MATa his3{delta} leu2{delta} ura3{delta}0 trp1{delta} can1{delta} ade2{delta} cdc14-3(Ts)

tag: cell phase

value: M (early anaphase)

tag: synchronization

value: release from G1 elutriation and block in anaphase with cdc14-3 TS


title: NOC release20 II

value: M

value: release 20 minutes from G2/M nocodazole block


title: RT100p01_S1

tag: cell type

tag: cell line

value: male

value: Ligation


title: Croatan_single_screen_A375_T0_R3

tag: timepoint

tag: library


title: RT100p02_S1

value: 10pg total RNA from ES cells

tag: Sex

tag: the number of single-cell/well contained in each data

tag: method name of single-cell rna-seq

value: Quartz-Seq2 (v3.1, RT100)

tag: type of sequence library preparation


title: G2 NOC II

value: release from G1 elutriation and block in G2/M with nocodazole


title: RT100RNAp06_S1

tag: sequencer

tag: the number of fastq reads for dge-matrix (in million)

tag: read2 length for dge-matrix (nt)


title: G2

value: release from G1 elutriation


title: Croatan_single_screen_A375_T0_R2

value: Croatan single sgRNA screen library


title: midS II

value: mid S


title: earlyS I

value: early S


title: RT25p01_S2

value: Quartz-Seq2 (v3.1, RT25)


title: Croatan_dual_screen_A375_T6_R3

value: T6 (12 doublings)

value: Croatan dual sgRNA screen library


title: Croatan_single_screen_A375_T0_R1


title: earlyS III


title: G1 I

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0

value: exponential G1

value: elutriation


title: RT100Cellp03_S1

description: We analyzed single-cells, which were sorted to 384-wells in total.

source_name: a mixture of mouse ES cells and the ES-derived primitive endoderm (PrE) cells

value: ES single-cells and PrE single-cells


title: Croatan_dual_screen_A375_T6_R2


title: G0

value: quiescent G0

value: carbon source deprivation


title: Croatan_single_screen_A375_T6_R1


title: asynchronous I

value: all

value: asynchronous


title: cdc14 release30

value: MATa his3{delta} leu2{delta} ura3{delta}0 trp1{delta} can1{delta} ade2{delta} cdc14-3(Ts)

value: M

value: release 30 minutes from cdc14-3 TS block


title: NOC release45 I

value: release 45 minutes from G2/M nocodazole block


title: RT25p02_S1

value: 10pg total RNA from ES cells

value: male

value: Ligation


title: WT  flies grown in 29C replica 3

city: Waltham

first: Sebastian

last: Kadener

state: MA

address: 415 South Street

institute: Brandeis University

data_processing:
Alignment to the drosophila genome (dm3)  using tophat
Counting number of reads for each gene at the 3' end using ESAT tool  (Derr A. et al 2016)
Genome_build: dm3
Supplementary_files_format_and_content: Table with reads counts for each gene.

organism: Drosophila melanogaster

source_name: fly heads

extract_protocol:
Total RNA was extracted using Trizol reagent (Sigma) and treated with DNase I (NEB) following the manufacturer's protocol.
Libraries preparation was based on a method previously described (Engreitz et al., 2013). The protocol was modified to get only 3' ends of the genes by applying polyA selection step after fragmentation and first linker ligation.

tag: genotype/variation

value: wild type

tag: temperature


title: WT  flies grown in 29C replica 2


title: NOC release20 I

tag: strain

value: release 20 minutes from G2/M nocodazole block


title: RT25RNAp07_S2

value: Quartz-Seq2 (v3.1, RT25)


title: WT  flies grown in 29C replica 1


title: Croatan_dual_screen_A375_T0_R3

value: Croatan dual sgRNA screen library


title: Croatan_dual_screen_A375_T0_R2


title: lateS

tag: genotype

value: late S

value: release from G1 elutriation


title: ADAR hypomorph flies grown in 29C replica 3

value: ADAR hypomorph


title: small_RNA_seq: spermatogonia, biological replicate 2, technical replicate 1

city: Fukuoka

first: Kota

last: Inoue

address: 3-1-1 Maidashi, Higashiku

department: Medical Institute of Bioregulation

institute: Kyushu University

data_processing:
The same libraries were sequenced twice (technical replicates 1 and 2)
The sequencing methods for technical replicate 1 ; sequenced by HiSeq2500 (Rapid mode for 50-bp single-end sequencing, yielding 4-8 million reads per sample)
The sequencing methods for technical replicate 2 ; sequenced by HiSeq1500 (High-output mode for 100-bp single-end sequencing, yielding 4-8 million reads per sample)
The adaptor sequence was trimed by cutadapt, and read numbers for each insert sequence were counted
The sequences were mapped to the consensus sequences of mouse retrotransposons using Seqmap allowing 2-bp missmatches.
Genome_build: repeatmaskerlibraries-20130422
Supplementary_files_format_and_content: tab-divided text files for sequence read numbers and comma-divided text files for rpm values for each retrotransposon.

source_name: male germ cells

extract_protocol:
standard procedure involving phenol/chloroform extraction, and isopropanol precipitation
The libraries were prepared using TruSeq Small RNA Sample Prep kit (Illumina)

treatment_protocol: Total RNA was isolated by acid phenol extraction using Isogene (Nippon Gene) from FACS-purified spermatogonia and spermatocytes (L/Z)

tag: isolation

value: FACS with Hoechst-33342 staining

tag: Stage

value: spermatogonia

tag: age

value: postnatal 3-4wks


title: small_RNA_seq: spermatogonia, biological replicate 1, technical replicate 1


title: RT25Cellp06_S1

tag: cell type

value: ES single-cells and PrE single-cells

tag: cell line


title: anaphase cdc15 I

value: MAT-alpha his3{delta} leu2{delta} ura3{delta} trp1{delta} can1{delta} ade2{delta} cdc15-2(Ts)

tag: cell phase

value: M (late anaphase)

tag: synchronization

value: release from G1 elutriation and block in anaphase with cdc15-2 TS


title: small_RNA_seq: leptotene/zygotene, biological replicate 2, technical replicate 1

value: leptotene/zygotene


title: small_RNA_seq: leptotene/zygotene, biological replicate 1, technical replicate 1


title: ADAR hypomorph flies grown in 29C replica 2


title: midS I

value: mid S


title: GPP_WP_screen_A375_T6_R3

tag: timepoint

value: T6 (12 doublings)

tag: library

value: GPP Wep Portal screen library


title: Croatan_dual_screen_A375_T0_R1


title: Croatan_dual_screen_A375_T6_R1


title: ADAR hypomorph flies grown in 29C replica 1


title: G2 NOC I

value: release from G1 elutriation and block in G2/M with nocodazole


title: GPP_WP_screen_A375_T6_R1


title: BS_seq: Dnmt3L KO

data_processing:
Sequenced using HiSeq2500 (Illumina) by single-end 100-bp sequencing (High output mode, one lane per sample). Softwares used to generate bcl files were RTA 1.71.21.3 and HCS 2.0.12.0
Approximately 130 to 140 million reads were obtained for each sample, with an average sequencing depth of about 1.7.
The sequence reads were mapped to the mouse genome by Bismark.
Only data for CpG sites are included in the processed data  files.
For each CpG site,  data of both strands are combined
Genome_build: mm10
Supplementary_files_format_and_content: tab-divided text files including (1) chromosome name, (2) position start, (3) position end, (4) methylation level (0-1), (5) number of methylated reads, (6) number of unmethylated reads, (7) strand, and (8) dinucleotide.

source_name: Spermatogonia

extract_protocol:
Genomic DNAs were extracted by the standard procedure involving Proteinase K digestion, phenol/chloroform extraction, and ethanol precipitation.  After bisulfite treatment, DNA was used for the PBAT library preparation.
the PBAT method

treatment_protocol: Spermatogonia at postnatal day 7 were isolated by fluorescence-activated cell sorting (FACS) using FACS Aria II (BD Biosciences) with an anti-EpCAM antibody and a secondary antibody labeled with Alexa488

tag: cell

value: FACS-purified spermatogonia

value: Dnmt3L KO

value: postnatal day 7


title: Dmel_S2_LPHS

city: Irapuato

first: NESTOR

middle: OCTAVIO

last: NAZARIO-YEPIZ

state: Guanajuato

address: Km 9.6 Libramiento Norte Carretera León

country: Mexico

institute: LANGEBIO-CINVESTAV Irapuato

description:
100bp of insert
Dmel_Diet_counts.txt
Dmel2r_gene_exp.diff

data_processing:
Transcriptome analysis was performed using the TopHat-Cufflinks pipeline (Trapnell et al., 2013).
Two replicates of each treatment (species/diets) were done, and paired-end reads were mapped with “bowtie2/tophat2”.
For D. arizonae, “cufflinks” and “cuffmerge” were applied to generate a GTF file, containing the locations of predicted transcripts.
Differential expression was calculated with “cuffdiff2”, using the BAM files that TopHat generated, with default settings and FDR ≤ 0.05 (Trapnell et al., 2013).
Genome_build: Reference genomes were indexed with “bowtie2-build”, using genome versions: r6.04 for D. melanogaster (FlyBase), first release for D. arizonae (Sanchez-Flores et al., 2016) and r1.3 for D. mojavensis (FlyBase).
Supplementary_files_format_and_content: There are two different processed files: "Diet_counts.txt" and "gene_exp.diff". "Diet_counts.txt" are tab-delimited text files that include count values of each samples (by species). "gene_exp.diff" are output files from cuffdiff2: this are tab delimited files that list the results of differential expression testing between samples for genes (comparisons between diets by species)(http://cole-trapnell-lab.github.io/cufflinks/cuffdiff/#cuffdiff-output-files).

source_name: Whole larvae

growth_protocol: All stocks, prior to use in experiments, were grown at room temperature (~25°C) in standard banana-opuntia media. To obtain larvae for development or transcriptomic studies, sexually mature adults were placed in yeasted egg collecting chambers (Genesee Scientific) and the embryos were allowed to develop to early third instar at which time they were transferred to the experimental diets for 24 hours.

extract_protocol:
Frozen samples were homogenized with Tri-Reagent using Teflon homogenizers and extracted using Direct-zolTM RNA MiniPrep extraction kit (Zymo Research) according to the manufacturer’s protocol. Three aliquots of each sample were taken, one to measure RNA concentration in NanoDrop (Thermo Scientific), another for analyses in a 1% agarose gel, and one for the sequencing core facility at LANGEBIO.
Libraries were prepared with TruSeq® RNA Sample Preparation Kit v2 (Illumina), selecting only polyA mRNAs and synthetizing double stranded cDNAs to attach to the Illumina adapters.

treatment_protocol: Third instar larvae were exposed for 24 hours to diets either high in protein relative to sugar (HPLS), diets with equal amounts of protein and sugar (EPS) , and diets low in protein but high in sugar (LPHS).

tag: developmental stage

value: Third instar

tag: diet

value: low protein-high sugar


title: WT  flies grown in 18C replica 3

value: wild type


title: GPP_WP_screen_A375_T6_R2


title: Dmel_S2_EPS

value: equal protein-sugar


title: GPP_WP_screen_A375_T0_R3


title: WT  flies grown in 18C replica 1


title: WT  flies grown in 18C replica 2


title: ADAR hypomorph flies grown in 18C replica 3

value: ADAR hypomorph


title: Dmel_S1_LPHS


title: AZA non-responder PD7169_EOT

city: Sydney

first: Ashwin

last: Unnikrishnan

state: NSW

address: Room 217, Level 2, Adult Cancer Program, Lowy Cancer Research Centre, University of New South Wales

department: Lowy Cancer Research Centre

country: Australia

institute: University of New South Wales

data_processing:
Base-calling was done by Illumina Real Time Analysis, scoring metric v1.5.
Raw reads were prefiltered to remove all reads that have 3 or more bases with a quality score of less than Q13
All provided cleaned data have had adaptors clipped
Alignments were all made against hg19. mRNA-seq: tophat (version 1.3.1) -g 25 -r 20 --segment-length 45 -G "hg19_refseq.gtf" --solexa1.3-quals
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each sample.

source_name: Bone marrow

extract_protocol:
Bone marrow CD34+ cells were isolated from mononuclear cells from MDS or CMML patients. RNA was then isolated from 100,000 CD34+ cells using Qiagen Rneasy Mini kits as per manufacturer's recommendations. 30ng of RNA was amplified using NuGEN Ovation RNA-seq v2 kits and the resulting amplified ds cDNA was used for library preparation following standard Illumina protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: phenotype

value: AZA Non-Responder

tag: treatment stage

value: Cycle 6 day 28 (C6d28)

tag: tissue

value: bone marrow


title: GPP_WP_screen_A375_T0_R1


title: Dmel_S1_EPS


title: ADAR hypomorph flies grown in 18C replica 2

tag: genotype/variation

tag: temperature


title: sgRNAScorer_screen_A375_T6_R3

value: sgRNAScorer screen library


title: AZA non-responder PD7167_EOT


title: ADAR hypomorph flies grown in 18C replica 1


title: earlyS II

tag: strain

tag: genotype

value: early S

value: release from G1 elutriation


title: AZA non-responder PD7166_EOT


title: Dmel_S1_HPLS

value: high protein-low sugar


title: AZA non-responder PD7158_EOT


title: sgRNAScorer_screen_A375_T6_R2

value: T6 (12 doublings)


title: GPP_WP_screen_A375_T0_R2

value: GPP Wep Portal screen library


title: BS_seq: Pld6 KO

value: FACS-purified spermatogonia

value: Pld6 KO

tag: age


title: BS_seq: WT

value: WT

value: postnatal day 7


title: AZA non-responder PD7152_EOT

tag: cell type


title: sgRNAScorer_screen_A375_T6_R1


title: tmg3

city: Kansas City

first: Stefan

middle: Hannes

last: Graw

address: 3901 Rainbow Blvd

department: Biostatistics

institute: University of Kansas Medical Center

data_processing:
Alignment and calculate expression values using RSEM with the following parameters
rsem-calculate-expression --bowtie2 --output-genome-bam --paired-end
Differential expression analysis of RNA-seq expression profiles using EdgeR
Genome_build: HG38
Supplementary_files_format_and_content: Tab delimited gene expression file including gene_id, transcript_id(s), length, effective_length, expected_count, TPM, FPKM

source_name: SH-SY5Y_ OGA inhibitor Thiamet-G (tmg)

growth_protocol: SY5Y cells were adapted to 5mM galactose DMEM for at least one week prior to adding the treatment. Cells were maintained at a 75% confluency and media were replaced on a daily basis.

extract_protocol:
Cells were pelleted, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 800ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 10uM Thiamet-G or .35mM glucosamine was added to the cells on a daily basis. Cells were subjected to treatments for at least three weeks prior to RNA isolation.

tag: cell line

tag: passages

value: Neuroblastoma cells


title: Dmel_S2_HPLS

value: Third instar


title: ATACseq_Adult_mut_Lckcre

city: Yokohama

first: Takaho

middle: A.

last: Endo

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

department: IMS

description: Bcl11b fl/HM Lck-cre pre-selection DP thymocytes

data_processing:
Basecalls performed using Illumina offline basecaller (OLB) version 1.9.4
ChIP-seq sequences were aligned on mm9 using bowtie2 (version 2.1.0) with default parameters.
Accumulated reads were mapped on mouse genome and reads per kilobase is recorded in processed files.
Genome_build: mm9
Supplementary_files_format_and_content: wiggle file format of mapped reads per kilobase

source_name: adult pre-selection DP thymocyte

growth_protocol: TCRb low CD24 high CD4+CD8+ pre-selection thymocytes were prepared from newborn mice or 4-6 week old mice.

extract_protocol:
Nuclei were prepared from 25,000-sorted cells. The transposase reactions were carried using Nextera DNA Library Preparation Kit (Illumina).
Purified DNA fragments were amplified by PCR. The purified library was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: adult

value: Bcl11b fl/HM Lck-cre

value: thymocyte


title: tmg2


title: ATACseq_Adult_mut_Cd4cre

description: Bcl11b fl/HM Cd4-cre pre-selection DP thymocytes

value: Bcl11b fl/HM Cd4-cre


title: tmg1


title: ATACseq_Fetus_mut_rep2

description: Bcl11-mutant thymocyte rep2

source_name: newborn pre-selection DP thymocyte

value: newborn


title: glcn3


title: ATACseq_Adult_control_WT

description: Bcl11b +/+ adult thymocyte


title: AZA Responder_PD7163_EOT

source_name: AZA Responder

value: AZA Responder

value: Cycle 6 day 28 (C6d28)

value: bone marrow


title: AZA Responder_PD7168_EOT


title: Croatan_single_screen_K562_T0_R1

value: Croatan single sgRNA screen library


title: AZA Responder_PD7156_EOT


title: Edit-R_screen_A375_T6_R3

value: T6 (12 doublings)

value: Edit-R screen library


title: Edit-R_screen_A375_T6_R2


title: cnt2


title: ATACseq_Fetus_mut_rep1

description: Bcl11-mutant thymocyte rep1


title: Edit-R_screen_A375_T0_R3


title: AZA Responder_PD7153_EOT


title: AZA Responder_PD7157_EOT


title: Bcl11b_ThPOKgfpTESPE

description:
S07459
Bcl11b ChIP-seq of total thymocytes from Thpok gfp:dTESPE mouse

source_name: total thymocyte

growth_protocol: Thymus were derived from 4-6 wk old mice.

extract_protocol:
Cells were subjected to crosslinking and nuclei were lysed. Nuclei sample was sonicated using a model XL2000 ultrasonic cell disruptor (MICROSON). Sonicated chromatin was incubated overnight at 4 °C with anti-Bcl11b antibody (Bethyl Laboratories, A300383A) that was preconjugated with magnetic beads (Dynabeads). Immunoprecipitated DNA was then purified.
Libraries were prepared according to NEB's instructions accompanying the NEBNext ChIP-seq Library prep Kit (E6240). The purified library was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 1500 following the manufacturer's protocols.

value: Thpok gfp:dTESPE

tag: chip antibody


title: ATACseq_Fetus_WT_rep1

description: Control fetus thymocyte rep1

value: control


title: AZA Responder_PD7151_EOT


title: glcn1


title: glcn2


title: sgRNAScorer_screen_A375_T0_R1

tag: timepoint

value: sgRNAScorer screen library


title: Edit-R_screen_A375_T6_R1

tag: library


title: AZA Responder_PD7164_EOT


title: ATACseq_Fetus_WT_rep2

description: Control fetus thymocyte rep2


title: ATACseq_Adult_WT

description: Control adult thymocyte


title: sgRNAScorer_screen_A375_T0_R2


title: sgRNAScorer_screen_A375_T0_R3


title: Edit-R_screen_A375_T0_R2


title: Bcl11b_ThPOKgfp

description:
S07458
Bcl11b ChIP-seq of total thymocytes from Thpok gfp mouse

value: Thpok gfp

value: anti-Bcl11b antibody (Bethyl Laboratories, A300383A)


title: AZA Responder_PD7160_EOT


title: AZA Responder_PD7155_EOT


title: Edit-R_screen_A375_T0_R1


title: cnt3

value: Neuroblastoma cells


title: AZA Responder_PD7168

value: Pre-treatment


title: cnt1


title: cKO4

description: RNA-seq of Bcl11b+/+ CD24hiTCRblo pre-selection DP thymocytes

data_processing:
Basecalls performed using Illumina offline basecaller (OLB) version 1.9.4
Sequences were aligned to mm9 genome using tophat2 (version 2.8.0) with default parameters.
Aligned seqeunces were converted relative expression using cufflinks (version 2.1.1).
Genome_build: mm9
Supplementary_files_format_and_content: plain text containig FPKM (fragments per kilobase exon per million reads) values.

source_name: pre-selection DP thymocytes

extract_protocol:
Before FACS staining, DN thymocytes were highly purified by depletion of CD4+ and CD8+ and DP thymocytes with AutoMACS. Then, DN NKT cells were FACS sorted using BD FACS Aria, and RNA was prepared using RNeasy Micro Plus kit containing gDNA eliminator columns (Qiagen). RNA was analyzed for quantity and quality using Agilent Bioanalyzer 2100 or Agilent 2200 TapeStation equipment, and 10 ng of total RNA was used with SMARTer Ultra Low Input RNA Kit v3 for Illumina Sequencing (Clontech) for cDNA synthesis.
Libraries were prepared according to NEB's instructions accompanying the NEBNext® ChIP-seq Library Prep Reagent set for Illumina.  Adapter ligated DNA was PCR amplified with Illumina primers for 15 cycles. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Hi-Seq 1500 following the manufacturer's protocols.

value: thymus


title: C3

city: London

first: Shiva

middle: M

last: Singh

state: ON

address: 1151 Richmond Street

department: Biology

country: Canada

institute: Western University

data_processing:
After passing Solexa CHASTITY quality filter, clean reads were aligned to mouse genome (UCSC MM10) using BOWTIE software (V2.1.0).
MeDIP enriched regions (peaks) with statistical significance were identified for each sample, using a q-value threshold of 10-4 by MACS v2.
Genome_build: mm10
Supplementary_files_format_and_content: xlsx Excel files include peak annotations for each sample, including a peak identifier assigned by MASC2, chromosome, start/end position of peak, length of peak region, fold enrichment against input, q-value, and peak-associated gene information.

source_name: Hippocampus

extract_protocol:
Mice were sacrificed via carbon dioxide asphyxiation and cervical spinal dislocation. Hippocampus was dissected, snap-frozen in liquid nitrogen, and stored at -80°C. DNA was isolated using AllPrep DNA/RNA Mini Kit (Qiagen) and stored at -80°C.
MeDIP-Seq was performed by ArrayStar Inc. Genomic DNA was sonicated with a Bioruptor sonicator, then end-repaired, A-tailed, and ligated to single-end adapters following standard Illumina genomic DNA protocol. After agarose size-selection to remove un-ligated adapters, adaptor-ligated DNA was used for immunoprecipitation using a Mouse monoclonal anti-5-methylcytosine antibody. A nonspecific Mouse IgG immunoprecipitation was performed in parallel to methyl DNA immunoprecipitation as a negative control. MeDIP and supernatant DNA were purified using Qiagen MinElute columns. Immunoprecipitated DNA was PCR amplified using single-end Illumina PCR primers. Reactions were purified with Qiagen MinElute columns, then final size selection was performed by electrophoresis in 2% agarose. Libraries were quality controlled by Agilent 2100 Bioanalyzer. An aliquot of each library was diluted and used in qPCR reactions to verify methylated fragment enrichment. Sequencing was carried out by running 150 cycles on Illumina HiSeq 2000 according to manufacturer’s instructions.

treatment_protocol: Male pups were given two subcutaneous dorsal injections at 9 AM and 11 AM on both PND4 and PND7. Ethanol treated mice were injected with 2.5 g/kg of ethanol in 0.15 M NaCl. Control mice were injected with 0.15 M saline.

tag: Sex

value: male

value: Hippocampus

value: postnatal day 21

tag: treatment

value: saline


title: cKO3


title: C2


title: C1


title: AZA Responder_PD7157

value: AZA Responder


title: AZA Responder_PD7151

value: bone marrow


title: cKO1


title: cKO2


title: AZA Responder_PD7156


title: HM2

description: RNA-seq of Bcl11bm/m CD24hiTCRblo pre-selection DP thymocytes


title: WT4


title: HM3


title: PD7161-2


title: WT5


title: BM Macrophage Day 12 Yes 2

first: Bernett

last: Lee

address: 8A Biomedical Grove #03-06 Immunos

country: Singapore

institute: Singapore Immunology Network

description:
RMM432
BM Macrophage Day 12 Yes
Processed data file: gene_counts.txt

data_processing:
FASTQ files were mapped to the mouse genome mm10 using STAR.
Gene counts were computed using featureCounts using GENCODE m9 annotations.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: gene_counts.txt: Tab-delimited featureCounts gene counts text file.

source_name: Bone marrow-derived macrophages, cocultured, day 12

extract_protocol:
Total RNA was extracted using Arcturus PicoPure RNA Isolation kit (Thermofisher, KIT0204) according to manufacturer's protocol. All mouse RNAs were analyzed on Labchip GX system (Perkin Elmer, United States) for quality assessment with median RNA Quality Score of 9.15.
cDNA libraries were prepared using 2ng of total RNA and 1ul of a 1:50,000 dilution of Ambion ERCC RNA Spike-in Controls (Thermofisher, 4456740) using the SMARTSeq v2 protocol described (Picelli S et al., 2014) with the following modifications: 1. Use of 20µM TSO, 2. Use of 250pg of cDNA with 1/5 reaction of Nextera XT kit (Illumina, FC-131). The length distribution of the cDNA libraries was monitored using DNA High Sensitivity Reagent Kit (Perkin Elmer, CLS60672) on the Labchip GX system (Perkin Elmer). All samples were subjected to an indexed PE sequencing run of 2x51 cycles on HiSeq 2000 (Illumina) at 16 samples per lane.

value: Bone marrow-derived macrophage

tag: coculture

value: Yes

tag: time point

value: day 12


title: BM Macrophage Day 12 Yes 3

description:
RMM433
BM Macrophage Day 12 Yes
Processed data file: gene_counts.txt


title: E1

value: ethanol


title: PD7164

tag: treatment stage

tag: phenotype


title: PD7167

tag: tissue

value: AZA Non-Responder


title: E3


title: Edit-R_screen_K562_T0_R2

source_name: K562-Cas9 cells

value: Edit-R screen library


title: BM Macrophage Day 12 Yes 1

description:
RMM431
BM Macrophage Day 12 Yes
Processed data file: gene_counts.txt


title: WT2


title: PD7153


title: AZA Responder_PD7163


title: E2


title: BM Macrophage Day 06 Yes 3

description:
RMM426
BM Macrophage Day 06 Yes
Processed data file: gene_counts.txt

source_name: Bone marrow-derived macrophages, cocultured, day 6

value: day 6


title: PD7160


title: WT1


title: WT3


title: BM Macrophage Day 06 Yes 2

description:
RMM425
BM Macrophage Day 06 Yes
Processed data file: gene_counts.txt


title: BM Macrophage Day 06 Yes 1

description:
RMM424
BM Macrophage Day 06 Yes
Processed data file: gene_counts.txt


title: Pld6 KO_mRNA_seq

data_processing:
Sequences were obtained by using HiSeq1500 (Rapid mode, yielding 55-92 million reads per sample)
Sequencing reads were mapped onto whole transcriptome (using a gtf file from iGenome) and whole genome by Tophat.
The resulting bam files were used to calculate gene expression levels by Cuffdiff.
SNPSplit was used to discriminate the derived alleles.
Cuffdiff was used to calculate the allele frequencies.
Genome_build: mm10
Supplementary_files_format_and_content: tab-divided text files including (1) gene name, (2) genotype, (3) replicate ID, (4) raw flags, (5) internal scaled frags, (6) external scaled frags, (7) FPKM, (8) effective length, and (9) status.

molecule: polyA RNA

source_name: Spermatocyte

extract_protocol:
Total RNA was isolated by acid phenol extraction using Isogene (Nippon Gene) from FACS-purified L/Z spermatocytes at 3-4 weeks afetr birth
The libraries for polyA(+) RNA sequencing were prepared using TruSeq stranded mRNA LT Sample Prep kit (Illumina)

treatment_protocol: For spermatocyte samples, the leptotene/zygotene-stage germ cells were purified by FACS.

value: F1 hybrid between C57BL6/J and MSM/Ms

tag: cell/tissue

value: FACS-purified L/Z spermatocytes

value: Pld6 KO

value: postnatal 3-4wks


title: BM Macrophage Day 03 Yes 2

description:
RMM418
BM Macrophage Day 03 Yes
Processed data file: gene_counts.txt

source_name: Bone marrow-derived macrophages, cocultured, day 3

value: day 3


title: PD7169

value: Pre-treatment


title: PD7165


title: PD7152


title: BM Macrophage Day 03 Yes 1

description:
RMM417
BM Macrophage Day 03 Yes
Processed data file: gene_counts.txt


title: small_RNA_seq: spermatogonia, biological replicate 2, technical replicate 2

tag: strain

tag: isolation

value: FACS with Hoechst-33342 staining

tag: Stage

value: spermatogonia


title: Dnmt3L_Het_mRNA_seq

tag: genotype

tag: age


title: PD7166

tag: cell type


title: small_RNA_seq: spermatogonia, biological replicate 1, technical replicate 2


title: BM Macrophage Day 00 No 2

description:
RMM410
BM Macrophage Day 00 No
Processed data file: gene_counts.txt

source_name: Bone marrow-derived macrophages, non-cocultured, day 0

value: No

value: day 0


title: Dnmt3L_KO_mRNA_seq


title: SCZ51D

city: Rochester

first: Steven

last: Goldman

state: NY

address: 601 Elmwood Ave

department: Center for Translational Neuromedicine

institute: University of Rochester Medical Center

data_processing:
mRNA sequencing in Illumina HiSeq 2500 platform for approximately 45 million 1x100 bp reads per sample
Trimming of adapter sequences and low-quality bases with Trimmomatic (version 0.32), parameters: "SLIDINGWINDOW:4:20 TRAILING:13 LEADING:13 ILLUMINACLIP:adapters.fasta:2:30:10 MINLEN:15"
Read alignment to human genome build GRCh38 with Subread (version 1.4.6-p3), parameters: "-T 12 --gzFASTQinput --BAMoutput -H"
Feature counting with featureCounts (version 1.4.6-p3) with grouping exons into genes, parameters: "-t exon -g gene"
Genome_build: GRCh38

source_name: Glial Progenitor Cell

growth_protocol: The GPC differentiation from human iPS cells is published in Wang et al. "Human iPSC-Derived Oligodendrocyte Progenitor Cells Can Myelinate and Rescue a Mouse Model of Congenital Hypomyelination" in Cell Stem Cell Volume 12, Issue 2, 2013

extract_protocol:
Human iPS cells were derived from fibroblasts obtained from schizophrenic patients and controls. The iPS cells were then differentiated into Glial Progenitor Cells (GPCs) which were than purified by FACS with PDGFRa (aka CD140a) as cell surface marker. The PDGFRa-positive GPC population was used in RNA isolation and sequencing.
RNA libraries were prepared for sequencing using Illumina's TruSeq RNA V2 library preparation kit.

value: Brain

tag: facs marker

value: hPDGFRa

tag: subject

value: Schizophrenic Patient

tag: subject age

tag: subject ethnicity

value: Caucasian

tag: subject gender

value: Male

tag: source

value: hiPSC

value: GPC


title: BM Macrophage Day 03 Yes 3

description:
RMM419
BM Macrophage Day 03 Yes
Processed data file: gene_counts.txt

value: Bone marrow-derived macrophage

tag: coculture

value: Yes

tag: time point


title: HM1

value: thymus


title: BM Macrophage Day 00 No 3

description:
RMM411
BM Macrophage Day 00 No
Processed data file: gene_counts.txt


title: BM Macrophage Day 00 No 1

description:
RMM409
BM Macrophage Day 00 No
Processed data file: gene_counts.txt


title: SCZ29C


title: PD7158

tag: treatment stage

value: bone marrow

tag: phenotype

value: AZA Non-Responder


title: iPSC Macrophage Day 12 Yes 3

description:
RMM407
iPSC Macrophage Day 12 Yes
Processed data file: gene_counts.txt

source_name: iPSC-derived macrophages, cocultured, day 12

value: iPSC-derived macrophage

value: day 12


title: small_RNA_seq: leptotene/zygotene, biological replicate 2, technical replicate 2

source_name: male germ cells

value: FACS with Hoechst-33342 staining

value: leptotene/zygotene

value: postnatal 3-4wks


title: small_RNA_seq: leptotene/zygotene, biological replicate 1, technical replicate 2


title: PD7161

source_name: Bone marrow

value: Pre-treatment

tag: tissue

value: AZA Responder


title: PD7154


title: Pld6 WT_mRNA_seq

tag: strain

value: F1 hybrid between C57BL6/J and MSM/Ms

tag: cell/tissue

value: FACS-purified L/Z spermatocytes

value: Pld6 WT


title: iPSC Macrophage Day 06 Yes 3

description:
RMM403
iPSC Macrophage Day 06 Yes
Processed data file: gene_counts.txt

source_name: iPSC-derived macrophages, cocultured, day 6

value: day 6


title: small_RNA_seq: spermatogonia

data_processing:
The sequencing methods ; sequenced by HiSeq1500 (rapid mode for 50-bp single-end sequencing, yielding 14–40 million reads per sample)
The adaptor sequence was trimed by cutadapt, and read numbers for each insert sequence were counted
The sequences were mapped to the consensus sequences of mouse retrotransposons using Seqmap allowing 2-bp missmatches.
Genome_build: repeatmaskerlibraries-20130422
Supplementary_files_format_and_content: tab-divided text files for sequence read numbers and comma-divided text files for rpm values for each retrotransposon.

treatment_protocol: Total RNA was isolated by acid phenol extraction using Isogene (Nippon Gene) from FACS-purified spermatogonia, spermatocytes (L/Z and P/D) and round spermatids

tag: isolation

tag: Stage

value: spermatogonia


title: Dmoj_S2_EPS

description:
100bp of insert
Dmoj_Diet_counts.txt
Dmoj2r_gene_exp.diff

organism: Drosophila mojavensis

source_name: Whole larvae

tag: developmental stage

value: Third instar

tag: diet

value: equal protein-sugar


title: iPSC Macrophage Day 03 Yes 3

description:
RMM399
iPSC Macrophage Day 03 Yes
Processed data file: gene_counts.txt

source_name: iPSC-derived macrophages, cocultured, day 3

tag: cell type

value: Yes

value: day 3


title: iPSC Macrophage Day 00 No 3

description:
RMM395
iPSC Macrophage Day 00 No
Processed data file: gene_counts.txt

source_name: iPSC-derived macrophages, non-cocultured, day 0

value: No

value: day 0


title: Dmoj_S2_HPLS

value: high protein-low sugar


title: small_RNA_seq: round spermatids

value: FACS with Hoechst-33342 staining

value: round spermatids

tag: age


title: small_RNA_seq: leptotene/zygotene, biological replicate 2

value: leptotene/zygotene

value: postnatal 3-4wks


title: Dmoj_S1_EPS


title: iPSC Macrophage Day 06 Yes 2

description:
RMM389
iPSC Macrophage Day 06 Yes
Processed data file: gene_counts.txt

value: iPSC-derived macrophage


title: iPSC Macrophage Day 12 Yes 2

description:
RMM393
iPSC Macrophage Day 12 Yes
Processed data file: gene_counts.txt

value: day 12


title: small_RNA_seq: pachytene/diptotene

value: pachytene/diptotene


title: Dmoj_S1_LPHS

value: low protein-high sugar


title: Dmoj_S1_HPLS


title: iPSC Macrophage Day 03 Yes 2

description:
RMM385
iPSC Macrophage Day 03 Yes
Processed data file: gene_counts.txt


title: iPSC Macrophage Day 00 No 2

description:
RMM381
iPSC Macrophage Day 00 No
Processed data file: gene_counts.txt


title: small_RNA_seq: leptotene/zygotene, biological replicate 1


title: PD7155

value: Pre-treatment

value: bone marrow

value: AZA Responder


title: Combinatorial_screen_A375_T6_R3

data_processing:
Trim reads to 20bp using fastx_trimmer (FASTX Toolkit 0.0.13.2)
Map reads to barcode index using bowtie2, with default parameters (version 2.2.3)
Count total mapped reads per barcode using awk
Join total counts from samples using join
Supplementary_files_format_and_content: Counts of sgRNA pairs at different timepoints

source_name: A375-Cas9 cells

growth_protocol: A375 cells were grown at 37C with 5% CO2 according to ATCC guidelines

extract_protocol:
Genomic DNA was extracted 2 days after infection (T0) and after 12 doublings (T6) using the QIAamp Blood DNA Midi Kit (Qiagen).
For each sample, barcodes identifying sgRNA pairs were extracted from genomic DNA in 24 separate 30-cycle PCR reactions where 2 ug of input DNA was included in each reaction. Illumina adapters where included on the PCR primers for this PCR.
Samples were sequenced on the Illumina MiSeq platform.

treatment_protocol: Cells were infected with lentivirus harboring a combinatorial sgRNA library, with an MOI of 0.3, and were kept in culture for 12 doublings

tag: timepoint

value: T6 (12 doublings)

tag: library

value: Combinatorial screen library


title: P0testis_mRNA_seq: DKO, biological replicate 2

data_processing:
Sequences were obtained by using HiSeq1500 (Rapid mode, yielding 9-40 million reads per sample)
Sequencing reads were mapped onto whole transcriptome (using a gtf file from iGenome) and whoke genome by Tophat.
The resulting bam files were used to calculate gene expression levels by Cuffdiff.
For the spematocyte data, reads mapped to a region overlapping a repeat sequence (Repeatmasker table from UCSC genome browser) were removed for the calculation.
Genome_build: mm10
Supplementary_files_format_and_content: tab-divided text files including (1) gene name, (2) genotype, (3) replicate ID, (4) raw flags, (5) internal scaled frags, (6) external scaled frags, (7) FPKM, (8) effective length, and (9) status.

extract_protocol:
Total RNA was isolated by acid phenol extraction using Isogene (Nippon Gene) from new born testes (at P0) and FACS-purified L/Z spermatocytes at 3-4 weeks afetr birth
The libraries for polyA(+) RNA sequencing were prepared using TruSeq stranded mRNA LT Sample Prep kit (Illumina)

value: whole testes

tag: genotype

value: DKO, biological replicate 2, read1

value: postnatal day 0


title: P0testis_mRNA_seq: DKO, biological replicate 1

value: DKO, biological replicate 1, read1


title: P0testis_mRNA_seq: DKO, biological replicate 3

value: DKO, biological replicate 3, read1


title: Combinatorial_screen_A375_T6_R1


title: iPSC Macrophage Day 12 Yes 1

description:
RMM379
iPSC Macrophage Day 12 Yes
Processed data file: gene_counts.txt

value: Yes


title: Combinatorial_screen_A375_T6_R2


title: P0testis_mRNA_seq: Dnmt3L KO, biological replicate 2

value: Dnmt3L KO, biological replicate 2, read1


title: SCZ29A

value: Brain

tag: facs marker

value: hPDGFRa

tag: subject

value: Schizophrenic Patient

tag: subject age

tag: subject ethnicity

value: Caucasian

tag: subject gender

value: Male

tag: source

value: hiPSC

value: GPC


title: Dmoj_S2_LPHS

value: Third instar

value: low protein-high sugar


title: iPSC Macrophage Day 06 Yes 1

description:
RMM375
iPSC Macrophage Day 06 Yes
Processed data file: gene_counts.txt

value: iPSC-derived macrophage

tag: coculture

tag: time point

value: day 6


title: iPSC Macrophage Day 03 Yes 1

description:
RMM371
iPSC Macrophage Day 03 Yes
Processed data file: gene_counts.txt

value: day 3


title: P0testis_mRNA_seq: Pld6 KO, biological replicate 4

tag: strain

tag: cell/tissue

value: whole testes

value: Pld6 KO, biological replicate 4, read1

value: postnatal day 0


title: Combinatorial_screen_A375_T0

value: Combinatorial screen library


title: DO8_2

city: Qingdao

first: Da

last: HUO

address: No. 7 Nanhai Road, Qingdao, China

country: China

institute: Institute of Oceanology,Chinese Academy of Science

data_processing:
The original image data was transferred into sequence data by base calling(using CASAVA version 1.5+), (defined as ‘raw reads’) and saved as fastq files that include the detailed reads sequences and the reads quality information.
The raw reads obtained from Illumina sequencing were processed by trimming poor quality reads, 5’ adapter pollution reads, reads without 3’ adapters, reads without insert fragments, reads containing poly(A) stretches, and reads less than 18nt. rRNA, tRNA, snRNA and snoRNA were removed by blasting against the GenBank database (http://blast.ncbi.nlm.nih.gov) and the Rfram database (http://sanger.ac.uk/software/Rfam).
Considering that no miRNA information of the sea cucumber was in miRBase19.0, the remaining clean reads were aligned to search all known precursor/mature miRNAs of all animal species in miRBase 19.0 with perfect matches.
Chose the highest expression miRNA for each mature miRNA family which was regarded as a temporary miRNA database. Clean data was aligned to the above temporary miRNA database and the expression of miRNA is generated by summing the count of reads which can align to the temporary miRNA database without mismatches.
Potentially novel miRNAs were identified using MIREAP (http://sourceforge.net/projects/mireap/) with stem-loop structure prediction
Supplementary_files_format_and_content: miRNA sequence and read counts

organism: Apostichopus japonicus

source_name: DO8, Apostihopus japonicus respiratory tree

extract_protocol:
Total RNA was extracted from an individual respiratory tree using the Animal Tissue RNA Purification Kit (LC Sciences, Houston, TX) according to the manufacturer’s instructions.
The quality and concentration of RNA were measured by Bioanalyzer 2100 (Agilent, CA, USA) after which the mRNA in total RNA was enriched by using the oligo(dT) magnetic beads. After the addition of fragmentation buffer, the mRNA was interrupted and formed short fragments (~200 bp). The first strand cDNA was then synthesized by the random hexamer-primer, using the mRNA fragments as templates. Buffer, dNTPs, RNase H and DNA polymerase I were added to synthesize the second strand. The double strand cDNA was purified using the QiaQuick PCR extraction kit, and washed with EB buffer so as to facilitate end repair and the addition of a single nucleotide A (adenine). Finally, sequencing adaptors were ligated to the fragments. The required fragments were purified by means of agarose gel electrophoresis and enriched by PCR amplification.

tag: stress

value: control

tag: tissue

value: Apostihopus japonicus respiratory tree


title: P0testis_mRNA_seq: Dnmt3L KO, biological replicate 1

value: Dnmt3L KO, biological replicate 1, read1


title: PD7162

tag: treatment stage

value: Pre-treatment

value: bone marrow

tag: cell type

tag: phenotype

value: AZA Non-Responder


title: P0testis_mRNA_seq: Pld6 KO, biological replicate 3

value: Pld6 KO, biological replicate 3, read1

tag: age


title: DO8_1


title: CMC with NNV-infected DLB-1 fish 2

city: MURCIA

first: ALBERTO

last: CUESTA

state: MURCIA

address: CAMPUS UNIVERSITARIO ESPINARDO, FACULTAD BIOLOGIA

department: CELL BIOLOGY AND HISTOLOGY

country: Spain

institute: UNIVERSITY OF MURCIA

data_processing:
Images analysis, base calling and quality scoring of the run were processed using the manufacturer’s software Real Time Analysis (RTA 1.13.48) and followed by generation of FASTQ sequence files by CASAVA 1.8
RNA-seq data were aligned to the Dicentrarchus labrax assembly with GEM v1.7
RNA-seq reads were re-aligned with the GEMtools RNA-seq pipeline v1.7
Differentially expressed genes (DEGs) were determined with the DESeq2 R package
Genome_build: Dicentrarchus labrax assembly with GEM v1.7

organism: Dicentrarchus labrax

source_name: CMC with NNV-infected DLB-1 fish 2

extract_protocol:
Total RNA from cells was isolated by PureLink® RNA Mini Kit
Libraries from the total RNA were prepared using the TruSeq®Stranded mRNA LT Sample Prep Kit from 0,5 µg of RNA
RNA-seq. Each library was sequenced using TruSeq SBS Kit v3-HS, in paired end mode with the read length 2x76bp

value: Head-kidney leucocytes

tag: sample type

value: DLB-1 cell line infected with nodavirus


title: CMC with NNV-infected DLB-1 fish 1

source_name: CMC with NNV-infected DLB-1 fish 1


title: DO4_3

source_name: DO4, Apostihopus japonicus respiratory tree

value: slight hypoxia


title: iPSC Macrophage Day 00 No 1

description:
RMM367
iPSC Macrophage Day 00 No
Processed data file: gene_counts.txt

value: iPSC-derived macrophage

value: No

value: day 0


title: P0testis_mRNA_seq: Pld6 KO, biological replicate 2

value: whole testes

tag: genotype

value: Pld6 KO, biological replicate 2, read1


title: P0testis_mRNA_seq: Pld6 KO, biological replicate 1

value: Pld6 KO, biological replicate 1, read1

value: postnatal day 0


title: DO4_1


title: DO4_2


title: CMC with DLB-1 fish 3

source_name: CMC with DLB-1 fish 3

value: DLB-1 cell line mock


title: CMC with DLB-1 fish 2

source_name: CMC with DLB-1 fish 2


title: P0testis_mRNA_seq: WT, biological replicate 1

value: WT, biological replicate 1, read1


title: DO2_3

source_name: DO2, Apostihopus japonicus respiratory tree

value: hypoxia

value: Apostihopus japonicus respiratory tree


title: CMC with DLB-1 fish 1

source_name: CMC with DLB-1 fish 1


title: P0testis_mRNA_seq: WT, biological replicate 2

value: WT, biological replicate 2, read1


title: Spermatocyte_mRNA_seq: Dnmt3L KO, biological replicate 2

source_name: Spermatocyte

value: FACS-purified L/Z spermatocytes

value: Dnmt3L KO, biological replicate 2

value: postnatal 3-4wks


title: Spermatocyte_mRNA_seq: Dnmt3L KO, biological replicate 1

value: Dnmt3L KO, biological replicate 1


title: DO2_2


title: CMC control fish 3

source_name: CMC control fish 3

value: Head-kidney leucocytes

value: DLB-1 cell line


title: DO8_3

value: control


title: Pvi_sRNA

city: Shanghai

first: Chenjiang

last: You

state: Shanghai

address: 2005 Songhu Rd

institute: Fudan University

description: small RNA

data_processing:
Basecalls performed using Illumina CASAVA
Sequence reads were trimmed and size selected (18-42nt for sRNA data and 19-21nt for degradome data) using cutadapt v1.9.1, and then filtered to remove rRNA, tRNA, snoRNA, etc. against the annotation of Selaginella moellendorffii using bowtie with parameters -v 2 -k1.
Genome_build: None
Supplementary_files_format_and_content: filtered small reads in fasta format with read counts after understrike

organism: Pteris vittata

source_name: leaves

growth_protocol: native plant in Shenzhen, Guangdong, China. grow on stonewall

extract_protocol:
Total RNA extraction:  1g fresh wight plant material were ground in liquid nitrogen, and the powder were resuspended in 15ml 2%CTAB(2% CTAB, 2% PVP, 100mM Tris, 25mM EDTA, 2M NaCl, 5% β-mercaptoethanol).  Incubated the homogenized sample at 65˚C for 10 min. Cooled the sample to the room temperature, added 3ml chloroform,mixed thoroughly, then centrifuged the sample at  4˚C,12,000 g for 10 min. Transferred the supernantant to a new tube, added 1/4 volume of 10 M LiCl, mixed gently, then stored the sample in a 4˚C refrigerator overnight. Centrifuged the sample at 12,000 g for 30 min, discarded the aqueous. The pellet was washed  with 5ml  70% EtOH twice and discarded the supernantant, air dry the pellet and dissolved the total RNA using RNase-free water.
For sample 1-25, sRNA libraries were constructed with NEBNext® Multiplex Small RNA Library kit (NEB, #E7300S). Briefly, 30ug total RNA was resolved on 15% Ura PAGE, and 15-40nt small RNAs were recovered by gel purification. 3' and 5' adaptors were ligated to the small RNAs, and reverse transcription was conducted with the RT primer complementary to the 3' adaptor. Finally, the libraries were amplified with the primers complementary to the 5' and 3' adaptor sequences. For sample 26, the dedgradome library was constructed according to Zhai et.,al (2014). Briefly, polyA-RNA was purified from 75ug total RNA with Dynabeads® mRNA Purification Kit (Thermo Fisher, #61006). 5' adaptors was ligated to polyA RNA, reverse transcription and double-stranded cDNA synthesis were performed. The product was purified with Agencourt AMPure XP (Beckman Coulter, #A63881). The double-strand DNA was digested  with MmeI followed by 3' adaptor ligation. PAGE purification and recovery of ligated dsDNA products (50-75bp). Finally, the library was amplified with the primers complementary to the 5' and 3' adaptor sequences using purified dsDNA products as the template. Final PCR products with the length of 128bp was obtained and recovered from the gel.

value: leaves


title: CMC with NNV-infected DLB-1 fish 3

source_name: CMC with NNV-infected DLB-1 fish 3

value: DLB-1 cell line infected with nodavirus


title: CMC control fish 2

source_name: CMC control fish 2


title: DO2_1


title: CMC control fish 1

source_name: CMC control fish 1


title: Dch_sRNA

description: small RNA

organism: Diplopterygium chinense

growth_protocol: native plant in Shenzhen, Guangdong, China. grow under forest


title: Spermatocyte_mRNA_seq: Pld6 KO, biological replicate 2

value: Pld6 KO, biological replicate 2


title: Vst_sRNA

description: small RNA

organism: Trichomanes striatum

growth_protocol: introduced from Hainan, China and cultivated in greenhouse, temperature controlled at 15~25 ˚C


title: Smo_degradome

description: total RNA

organism: Selaginella moellendorffii

growth_protocol: introduced from Shenzhen, Guandong, China and cultivated in greenhouse, temperature controlled at 15~25 ˚C


title: Cfo_sRNA

description: small RNA

organism: Cyrtomium fortunei

growth_protocol: introduced from Guiyang, Guizhou, China and cultivated in greenhouse, temperature controlled at 15~25 ˚C


title: Des_sRNA

description: small RNA

organism: Diplazium esculentum

growth_protocol: native plant in Shenzhen, Guangdong, China. grow on lawn


title: Spermatocyte_mRNA_seq: Pld6 KO, biological replicate 1

value: Pld6 KO, biological replicate 1


title: Isi_sRNA

description: small RNA

organism: Isoetes sinensis

growth_protocol: introduced from Zhejiang, China and cultivated in greenhouse, temperature controlled at 15~25 ˚C


title: Spermatocyte_mRNA_seq: WT, biological replicate 2

value: WT, biological replicate 2


title: Pcu_sRNA

description: small RNA

organism: Microsorum cuspidatum

growth_protocol: introduced from Baoshan, Yunnan, China and cultivated in greenhouse, temperature controlled at 15~25 ˚C


title: Smo_sRNA

description: small RNA


title: Sch_sRNA

description: small RNA

organism: Odontosoria chinensis

growth_protocol: native plant in Shenzhen, Guangdong, China. grow on mountain slope, under forest edge


title: Darz_S2_LPHS

description:
100bp of insert
Darz_Diet_counts.txt
Darz2r_gene_exp.diff

organism: Drosophila arizonae

source_name: Whole larvae

tag: developmental stage

value: Third instar

tag: diet

value: low protein-high sugar


title: Spermatocyte_mRNA_seq: WT, biological replicate 1

organism: Mus musculus

value: WT, biological replicate 1


title: Ani_sRNA

description: small RNA

organism: Asplenium nidus


title: Darz_S2_EPS

value: equal protein-sugar


title: Mpl_sRNA

description: small RNA

organism: Microlepia platyphylla

growth_protocol: introduced from Wenshan, Yunnan, China and cultivated in greenhouse, temperature controlled at 15~25 ˚C


title: Cba_sRNA

description: small RNA

organism: Cibotium barometz


title: Afo_sRNA

description: small RNA

organism: Angiopteris fokiensis

growth_protocol: introduced from Shenzhen, Guandong, China and cultivated in shadehouse, grow under 75% shade net


title: Pnu_sRNA

description: small RNA

organism: Psilotum nudum

growth_protocol: native plant in Shenzhen, Guangdong, China. epiphyte on tree trunk


title: Darz_S2_HPLS

growth_protocol: All stocks, prior to use in experiments, were grown at room temperature (~25°C) in standard banana-opuntia media. To obtain larvae for development or transcriptomic studies, sexually mature adults were placed in yeasted egg collecting chambers (Genesee Scientific) and the embryos were allowed to develop to early third instar at which time they were transferred to the experimental diets for 24 hours.

value: high protein-low sugar


title: Asp_sRNA

description: small RNA

organism: Alsophila spinulosa


title: Dpe_sRNA

description: small RNA

organism: Dicranopteris pedata


title: Darz_S1_LPHS


title: Sml_sRNA

description: small RNA

organism: Salvinia molesta

source_name: floating leaves

growth_protocol: introduced from Malaysia and cultivated in greenhouse, temperature controlled at 15~25 ˚C

value: floating leaves


title: Aca_sRNA

description: small RNA

organism: Azolla caroliniana

growth_protocol: naturalized to Guiyang, Guizhou, China. grow in fishpond


title: Darz_S1_EPS


title: Ova_sRNA

description: small RNA

organism: Plenasium vachellii


title: Sun_sRNA

description: small RNA

organism: Selaginella uncinata


title: Ovu_sRNA

description: small RNA

organism: Ophioglossum vulgatum


title: Lce_sRNA

description: small RNA

organism: Palhinhaea cernua


title: Era_sRNA

description: small RNA

organism: Equisetum ramosissimum


title: 75538_female_liver

status: Public on Jul 19 2017

city: Darlinghurst

first: Paul

middle: E

last: Young

address: 405 Liverpool Street

institute: Victor Chang Cardiac Research Institute

data_processing:
alignment and methylation calling - Bismark
Trimming - proprietary scripts by Zymo Research
files converted to methylKit input format prior to constructing tiles
filtered for 10X coverage and above and below the 99.8th coverage percentile
Genome_build: mm10
Supplementary_files_format_and_content: txt files of 100bp tiles

source_name: liver

extract_protocol:
Phenol:Chloroform
methyl miniseq by Zymo Research

value: liver

value: 24 weeks

tag: gender

value: female


title: Scu_sRNA

description: small RNA

organism: Salvinia cucullata

growth_protocol: introduced from Taiwan and cultivated in greenhouse, temperature controlled at 15~25 ˚C


title: Darz_S1_HPLS

organism: Drosophila arizonae


title: 75541_male_liver

organism: Mus musculus

value: male


title: Lja_sRNA

description: small RNA

organism: Lygodium japonicum


title: 75536_male_liver


title: 75539_female_liver


title: 75535_male_liver


title: 69829_female_liver


title: 69828_male_liver


title: 72364_male_liver


title: 69827_male_liver


title: 69830_female_liver


title: 75542_8_female_heart

source_name: heart

value: heart


title: 72365_female_liver


title: 75538_5_male_heart


title: 75541_7_female_heart


title: 75542_14_female_brain

source_name: brain

value: brain


title: 75541_13_female_brain


title: 75539_6_female_heart


title: 75535_3_male_heart


title: 75539_12_female_brain


title: 75535_9_male_brain


title: 75536_4_male_heart


title: 75542_female_liver


title: 75536_10_male_brain


title: 75538_11_male_brain


title: rnpB SPET-seq (in vitro)

city: Groningen

first: Danny

last: Incarnato

state: Netherlands

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: University of Groningen

description:
In vitro SPET-seq on RNase P RNA (rnpB)
rnpB SPET-seq (in vitro)

data_processing:
library strategy: SPET-seq
FastQ files were examined using the FastQC tool. All the relevant SPET-seq data (nascent RNA) analysis and normalization steps were performed using a custom wrapper built on top of the RNA Framework13. Briefly, reads were clipped from 3’ adapter sequences using Cutadapt v1.10, discarding reads shorter than 15 nucleotides. Forward and reverse reads were independently mapped to the RNase P (rnpB) gene using Bowtie v1.1.2, by allowing up to 7 mapping positions to enable mapping to the 7 E. coli rRNA genes (parameters: -n 2 -m 7 -a --best --strata -5 5 [--norc for forward reads, --nofw for reverse reads]). Forward and reverse mapped reads were then re-paired. Using reverse read mapping positions (corresponding to RNA Polymerase positions along gene), forward reads were split into separate SAM files for each transcription intermediate. SAM files were then passed to the rf-count tool of the RNA Framework to generate RT-stop counts (RC) files, that were then normalized using the rf-norm tool.
Genome_build: U00096.2
Supplementary_files_format_and_content: Mapped reads were rescaled to a size of 10 bp, and BEDGraph files were generated using the genomeCoverageBed utility of the BEDTools suite.
Supplementary_files_format_and_content: DMS-seq data (pooled Total and Ribo- RNA) is provided in the form of RNA Framework's (http://www.rnaframework.com) RNA Count (RC) files. For a detailed description of the RC format, please refer to: http://rnaframework.readthedocs.io/en/latest/rf-count/#rc-rna-count-format
Supplementary_files_format_and_content: SPET-seq data (pooled Total and Ribo- RNA from both replicates) is provided in the form of RNA Framework's (http://www.rnaframework.com) RNA Count (RC) files. For each analyzed transcript, 10 files corresponding to SPET-seq data for the 10 transcription deciles are provided. For a detailed description of the RC format, please refer to: http://rnaframework.readthedocs.io/en/latest/rf-count/#rc-rna-count-format
Supplementary_files_format_and_content: SPET-seq data is provided in the form of RNA Framework's (http://www.rnaframework.com) RNA Count (RC) files. A file corresponding to each transcription intermediate is provided. For a detailed description of the RC format, please refer to: http://rnaframework.readthedocs.io/en/latest/rf-count/#rc-rna-count-format

organism: Escherichia coli

source_name: rnpB SPET-seq (in vitro)

extract_protocol:
RNA was purified on RNA Clean & Concentrator™-5 columns following manufacturer’s instructions, and eluted in 6 μl of nuclease-free water. 6 μl of 2X RNA Loading Dye (ThermoScientific, cat. R0641) were added to purified RNA. Both DMS treated and untreated samples were heated at 95°C for 2 minutes, and immediately placed on ice. Samples were resolved on a 10% TBE-Urea polyacrylamide gel, and a gel slice ranging from 50 nt to the full-length product was cut. Gel slices were crushed by centrifugation through a punctured 0.5 ml tube, and resuspended in 500 μl of Diffusion buffer [500 mM Ammonium acetate; 0.05% SDS] supplemented with 60 U SUPERase• In™ RNase Inhibitor, then rotated at 4°C for 16 hours to allow passive diffusion of RNA fragments into buffer. RNA was precipitated by addition of 1 ml Isopropanol, and 2 μl Glycogen (20 μg/μl), and resuspended in 6 μl nuclease-free water.
10 pmol of a pre-adenylated (rApp) adapter were ligated to rnpB nascent RNA in a reaction volume of 20 μl, using 400 U T4 RNA Ligase 2, Deletion Mutant in the presence of 20% PEG-8000, by incubation at 25°C for 2 hours. Reaction clean-up was performed using RNA Clean & Concentrator™-5 columns, and RNA was eluted in 5.5 μl nuclease-free water. RNA was heat-denatured at 70°C for 5 minutes, and reverse transcription was carried out in a final volume of 10 μl, in the presence of 0.5 mM dNTPs, 5 pmol of RT primer, 20 U RNaseOUT™ Recombinant Ribonuclease Inhibitor, and 100 U SuperScript® III Reverse Transcriptase, by incubation at 50°C for 50 minutes. Template RNA was degraded by adding 1 μl of 1 M NaOH, and incubating at 95°C for 5 minutes. Reaction clean-up was performed using RNA Clean & Concentrator™-5 columns, and cDNA was eluted in 6 μl nuclease-free water. cDNA fragments were resolved on a 10% TBE-Urea polyacrylamide gel, and a gel slice corresponding to fragments in the range of 40-300 nt was cut. DNA was recovered by passive diffusion in Diffusion buffer for 16 hours at 37°C with moderate shaking. cDNA was precipitated by addition of 1 ml Isopropanol, and 2 μl Glycogen (20 μg/μl), and resuspended in 8.25 μl nuclease-free water. 10 pmol of a 5’-phosphorilated adapter were ligated to the 3’-OH of cDNA fragments in a final reaction volume of 25 μl, in the presence of 0.05 mM ATP, 20% PEG-4000, and 100 U CircLigase™ II ssDNA Ligase, by incubation at 60°C for 4 hours, and 68°C for 2 hours. Adapter-ligated cDNA fragments were purified from excess adapter using 1.8 volumes of Agencourt AMPure XP beads, following manufacturer’s instructions. cDNA was eluted in 20 μl of nuclease-free water, and indexed sequencing adapters were introduced by 15 cycles of PCR in the presence of 25 pmol of each primer, and 25 μl NEBNext® High-Fidelity 2X PCR Master Mix.

treatment_protocol: In vitro transcription reactions were performed in a final volume of 50 µl. Each reaction contained 2 µl E. coli RNA Polymerase Holoenzyme (NEB, cat. M0551S), 5 µl E. coli RNA Polymerase Buffer (10X), 1 µl SUPERase• In™ RNase Inhibitor (Ambion, cat. AM2696), and 500 ng template DNA. Reactions were incubated at 37°C for 5 minutes to allow formation of the RNA Polymerase-DNA binary complex. Transcription was started by addition of 1 µl NTPs (25 mM each), and incubated at 37°C for 5 minutes. Transcription was stopped by addition of 1 µl DNase I (50 U/µl) and Actinomycin D (Sigma Aldrich, cat. A1410, dissolved in DMSO to 5 μg/μl) to a final concentration of 25 ng/μl. Reactions were diluted by addition of 50 μl E. coli RNA Polymerase Buffer 1X. DMS (Sigma Aldrich, cat. D186309) was diluted 1:6 in 100% Ethanol to a final concentration of 1.76 M. Diluted DMS was added to reactions to a final concentration of 100 mM. For control samples, an equal volume of a 1:6 dilution of nuclease-free water in 100% Ethanol was added. Samples were incubated with moderate shaking (800 RPM) at 25°C for 2 minutes, after which reactions were immediately transferred to ice. Two volumes of ice-cold RNA Binding Buffer from RNA Clean & Concentrator™-5 kit (Zymo Research, cat. R1014) supplemented with DTT (Sigma Aldrich, cat. 43815) to a final concentration of 0.7 M, were added to quench DMS, and samples were vigorously vortexed for 10 seconds.

tag: substr

tag: molecule subtype

value: In vitro synthesized RNase P (rnpB) RNA


title: RNA-seq from young mouse 2 STs; treatment: LPS+PAM at 0h; technical replicate 2.

first: Carl

middle: G

last: de Boer

address: 415 Main St

institute: The Broad Institute

data_processing:
Mapping reads to transcriptome with RSEM
Combine reads from technical replicates
Calculate TPMs
Genome_build: mm9
Supplementary_files_format_and_content: TPM and raw counts for all samples (technical replicates separate)

source_name: HSCs identified by cell surface markers, isolated from mouse bone marrow.

growth_protocol: All cells were grown at 37C and 5%CO2 in HSPC media.

extract_protocol:
PrepEase RNA Spin Kit (usb®).
SMART-seq2

treatment_protocol: Where applicable, treated HSCs were grown in HSPC media with 100ng/ml LPS (SIGMA CAT: L2880-100MG), and 1ug/ml Pam3csk4 (Invivogen CAT: 41-11-60-10)

tag: mouse age

value: young

value: ST

tag: treatment

value: LPS+PAM

tag: time point (h)

tag: biological replicate

tag: technical replicate


title: RNA-seq from old mouse 2 STs; treatment: LPS+PAM at 1h; technical replicate 1.

value: old


title: RNA-seq from old mouse 2 STs; treatment: LPS+PAM at 0h; technical replicate 2.


title: RNA-seq from young mouse 1 STs; treatment: LPS+PAM at 0.5h; technical replicate 1.


title: RNA-seq from old mouse 2 STs; treatment: LPS+PAM at 4h; technical replicate 1.


title: RNA-seq from young mouse 1 STs; treatment: LPS+PAM at 1h; technical replicate 1.


title: RNA-seq from young mouse 2 STs; treatment: LPS+PAM at 1h; technical replicate 1.


title: RNA-seq from young mouse 2 STs; treatment: LPS+PAM at 12h; technical replicate 1.


title: RNA-seq from young mouse 2 STs; treatment: LPS+PAM at 2h; technical replicate 1.


title: RNA-seq from old mouse 2 MPPs; treatment: LPS+PAM at 8h; technical replicate 1.

value: MPP


title: RNA-seq from young mouse 1 MPPs; treatment: LPS+PAM at 8h; technical replicate 1.


title: RNA-seq from old mouse 2 STs; treatment: LPS+PAM at 0h; technical replicate 1.


title: RNA-seq from young mouse 1 STs; treatment: LPS+PAM at 0h; technical replicate 2.


title: RNA-seq from old mouse 2 STs; treatment: LPS+PAM at 12h; technical replicate 1.


title: RNA-seq from young mouse 1 STs; treatment: LPS+PAM at 12h; technical replicate 1.


title: RNA-seq from young mouse 2 STs; treatment: LPS+PAM at 0.5h; technical replicate 1.


title: RNA-seq from young mouse 1 STs; treatment: LPS+PAM at 0h; technical replicate 1.


title: RNA-seq from old mouse 2 STs; treatment: LPS+PAM at 0.5h; technical replicate 1.


title: RNA-seq from old mouse 2 STs; treatment: LPS+PAM at 8h; technical replicate 1.


title: RNA-seq from young mouse 2 STs; treatment: LPS+PAM at 8h; technical replicate 1.


title: RNA-seq from young mouse 1 STs; treatment: LPS+PAM at 2h; technical replicate 1.


title: RNA-seq from young mouse 1 STs; treatment: LPS+PAM at 8h; technical replicate 1.


title: RNA-seq from young mouse 1 STs; treatment: LPS+PAM at 4h; technical replicate 1.


title: RNA-seq from young mouse 2 MPPs; treatment: LPS+PAM at 4h; technical replicate 1.


title: RNA-seq from young mouse 2 STs; treatment: LPS+PAM at 4h; technical replicate 1.


title: RNA-seq from old mouse 2 STs; treatment: LPS+PAM at 2h; technical replicate 1.


title: RNA-seq from young mouse 2 STs; treatment: LPS+PAM at 0h; technical replicate 1.


title: RNA-seq from young mouse 1 MPPs; treatment: LPS+PAM at 4h; technical replicate 1.


title: RNA-seq from old mouse 2 MPPs; treatment: LPS+PAM at 4h; technical replicate 1.


title: RNA-seq from young mouse 1 MPPs; treatment: LPS+PAM at 2h; technical replicate 1.


title: RNA-seq from young mouse 2 MPPs; treatment: LPS+PAM at 8h; technical replicate 1.


title: RNA-seq from old mouse 2 MPPs; treatment: LPS+PAM at 12h; technical replicate 1.


title: RNA-seq from old mouse 2 MPPs; treatment: LPS+PAM at 2h; technical replicate 1.


title: RNA-seq from young mouse 2 MPPs; treatment: LPS+PAM at 2h; technical replicate 1.


title: RNA-seq from young mouse 2 MPPs; treatment: LPS+PAM at 12h; technical replicate 1.


title: RNA-seq from old mouse 2 MPPs; treatment: LPS+PAM at 1h; technical replicate 1.


title: RNA-seq from young mouse 1 MPPs; treatment: LPS+PAM at 0h; technical replicate 1.


title: RNA-seq from young mouse 2 MPPs; treatment: LPS+PAM at 0.5h; technical replicate 1.


title: RNA-seq from old mouse 2 MPPs; treatment: LPS+PAM at 0h; technical replicate 1.


title: RNA-seq from young mouse 2 MPPs; treatment: LPS+PAM at 0h; technical replicate 2.


title: RNA-seq from young mouse 2 MPPs; treatment: LPS+PAM at 0h; technical replicate 1.


title: RNA-seq from old mouse 2 LTs; treatment: LPS+PAM at 4h; technical replicate 1.

value: LT


title: RNA-seq from old mouse 2 MPPs; treatment: LPS+PAM at 0.5h; technical replicate 1.


title: RNA-seq from old mouse 2 MPPs; treatment: LPS+PAM at 0h; technical replicate 2.


title: RNA-seq from young mouse 2 MPPs; treatment: LPS+PAM at 1h; technical replicate 1.


title: RNA-seq from young mouse 2 LTs; treatment: LPS+PAM at 8h; technical replicate 1.


title: RNA-seq from old mouse 2 LTs; treatment: LPS+PAM at 2h; technical replicate 1.


title: RNA-seq from young mouse 2 LTs; treatment: LPS+PAM at 2h; technical replicate 1.


title: RNA-seq from young mouse 1 MPPs; treatment: LPS+PAM at 0h; technical replicate 2.


title: RNA-seq from young mouse 1 MPPs; treatment: LPS+PAM at 0.5h; technical replicate 1.


title: RNA-seq from young mouse 1 LTs; treatment: LPS+PAM at 8h; technical replicate 1.


title: RNA-seq from young mouse 1 LTs; treatment: LPS+PAM at 4h; technical replicate 1.


title: RNA-seq from young mouse 1 LTs; treatment: LPS+PAM at 2h; technical replicate 1.


title: RNA-seq from old mouse 2 LTs; treatment: LPS+PAM at 12h; technical replicate 1.


title: RNA-seq from old mouse 2 LTs; treatment: LPS+PAM at 1h; technical replicate 1.


title: RNA-seq from young mouse 2 LTs; treatment: LPS+PAM at 1h; technical replicate 1.


title: RNA-seq from young mouse 1 LTs; treatment: LPS+PAM at 1h; technical replicate 1.


title: RNA-seq from old mouse 2 LTs; treatment: LPS+PAM at 0.5h; technical replicate 1.


title: RNA-seq from old mouse 2 LTs; treatment: LPS+PAM at 8h; technical replicate 1.


title: RNA-seq from young mouse 1 MPPs; treatment: LPS+PAM at 1h; technical replicate 1.


title: RNA-seq from young mouse 2 LTs; treatment: LPS+PAM at 4h; technical replicate 1.


title: RNA-seq from young mouse 1 LTs; treatment: LPS+PAM at 0.5h; technical replicate 1.


title: RNA-seq from young mouse 2 LTs; treatment: LPS+PAM at 12h; technical replicate 1.


title: RNA-seq from young mouse 1 MPPs; treatment: LPS+PAM at 12h; technical replicate 1.


title: RNA-seq from young mouse 1 LTs; treatment: LPS+PAM at 0h; technical replicate 2.


title: RNA-seq from young mouse 2 LTs; treatment: LPS+PAM at 0h; technical replicate 1.


title: RNA-seq from young mouse 1 LTs; treatment: LPS+PAM at 0h; technical replicate 1.


title: RNA-seq from young mouse 4 STs; treatment: None at 2h; technical replicate 1.


title: RNA-seq from young mouse 4 STs; treatment: None at 4h; technical replicate 1.


title: RNA-seq from young mouse 4 STs; treatment: None at 0h; technical replicate 1.


title: RNA-seq from old mouse 2 LTs; treatment: LPS+PAM at 0h; technical replicate 1.


title: RNA-seq from young mouse 4 MPPs; treatment: None at 4h; technical replicate 1.


title: RNA-seq from old mouse 4 STs; treatment: None at 8h; technical replicate 1.


title: RNA-seq from young mouse 4 MPPs; treatment: None at 8h; technical replicate 1.


title: RNA-seq from young mouse 4 STs; treatment: None at 8h; technical replicate 1.


title: RNA-seq from young mouse 4 MPPs; treatment: None at 2h; technical replicate 1.


title: RNA-seq from young mouse 4 MPPs; treatment: None at 0h; technical replicate 1.


title: RNA-seq from young mouse 2 LTs; treatment: LPS+PAM at 0h; technical replicate 2.


title: RNA-seq from old mouse 2 LTs; treatment: LPS+PAM at 0h; technical replicate 2.


title: RNA-seq from old mouse 4 STs; treatment: None at 4h; technical replicate 1.


title: RNA-seq from old mouse 4 MPPs; treatment: None at 4h; technical replicate 1.


title: RNA-seq from young mouse 4 LTs; treatment: None at 8h; technical replicate 1.


title: RNA-seq from young mouse 4 LTs; treatment: None at 2h; technical replicate 1.


title: RNA-seq from young mouse 2 LTs; treatment: LPS+PAM at 0.5h; technical replicate 1.


title: RNA-seq from young mouse 4 LTs; treatment: None at 0h; technical replicate 1.


title: RNA-seq from young mouse 4 LTs; treatment: None at 4h; technical replicate 1.


title: RNA-seq from old mouse 4 MPPs; treatment: None at 0h; technical replicate 1.


title: RNA-seq from old mouse 4 LTs; treatment: None at 8h; technical replicate 1.


title: RNA-seq from old mouse 4 LTs; treatment: None at 4h; technical replicate 1.


title: RNA-seq from old mouse 4 STs; treatment: None at 2h; technical replicate 1.


title: RNA-seq from old mouse 4 STs; treatment: None at 0h; technical replicate 1.


title: RNA-seq from young mouse 3 STs; treatment: LPS+PAM at 8h; technical replicate 1.


title: RNA-seq from old mouse 4 LTs; treatment: None at 2h; technical replicate 1.


title: RNA-seq from young mouse 3 STs; treatment: LPS+PAM at 0.5h; technical replicate 1.


title: RNA-seq from young mouse 3 STs; treatment: LPS+PAM at 1h; technical replicate 1.


title: RNA-seq from young mouse 3 STs; treatment: LPS+PAM at 2h; technical replicate 1.


title: RNA-seq from young mouse 3 STs; treatment: None at 0h; technical replicate 1.


title: RNA-seq from young mouse 1 STs; treatment: LPS+PAM at 1h; technical replicate 3.


title: RNA-seq from young mouse 3 STs; treatment: LPS+PAM at 12h; technical replicate 1.


title: RNA-seq from young mouse 3 STs; treatment: LPS+PAM at 4h; technical replicate 1.


title: RNA-seq from young mouse 3 MPPs; treatment: LPS+PAM at 4h; technical replicate 1.


title: RNA-seq from old mouse 4 MPPs; treatment: None at 8h; technical replicate 1.


title: RNA-seq from young mouse 3 MPPs; treatment: LPS+PAM at 0.5h; technical replicate 1.


title: RNA-seq from old mouse 4 MPPs; treatment: None at 2h; technical replicate 1.


title: RNA-seq from old mouse 4 LTs; treatment: None at 0h; technical replicate 1.


title: RNA-seq from young mouse 3 MPPs; treatment: LPS+PAM at 1h; technical replicate 1.


title: RNA-seq from young mouse 3 MPPs; treatment: LPS+PAM at 12h; technical replicate 1.


title: RNA-seq from young mouse 3 MPPs; treatment: None at 0h; technical replicate 1.


title: RNA-seq from young mouse 1 STs; treatment: LPS+PAM at 1h; technical replicate 2.


title: RNA-seq from young mouse 3 MPPs; treatment: LPS+PAM at 2h; technical replicate 1.


title: RNA-seq from young mouse 3 LTs; treatment: LPS+PAM at 0.5h; technical replicate 1.


title: RNA-seq from young mouse 3 LTs; treatment: LPS+PAM at 4h; technical replicate 1.


title: RNA-seq from young mouse 3 LTs; treatment: LPS+PAM at 2h; technical replicate 1.


title: RNA-seq from young mouse 3 LTs; treatment: LPS+PAM at 12h; technical replicate 1.


title: RNA-seq from young mouse 1 LTs; treatment: LPS+PAM at 12h; technical replicate 1.


title: RNA-seq from young mouse 3 LTs; treatment: None at 0h; technical replicate 1.


title: RNA-seq from young mouse 3 MPPs; treatment: LPS+PAM at 8h; technical replicate 1.


title: RNA-seq from old mouse 2 LTs; treatment: LPS+PAM at 0.5h; technical replicate 2.


title: RNA-seq from young mouse 3 LTs; treatment: LPS+PAM at 1h; technical replicate 1.


title: RNA-seq from old mouse 2 LTs; treatment: LPS+PAM at 2h; technical replicate 2.


title: RNA-seq from old mouse 2 LTs; treatment: LPS+PAM at 12h; technical replicate 2.


title: RNA-seq from old mouse 2 LTs; treatment: LPS+PAM at 8h; technical replicate 2.


title: RNA-seq from old mouse 2 LTs; treatment: LPS+PAM at 1h; technical replicate 2.


title: RNA-seq from old mouse 2 LTs; treatment: None at 0h; technical replicate 4.