title: B.ovis bcaA1 mutant in 0.04 percent CO2 replicate 2

city: East Lansing

first: Sean

last: Crosson

state: Michigan

address: 567 Wilson Rd

department: Dept. Microbiology and Molecular Genetics

institute: Michigan State University

data_processing:
data were processed using the RNA-seq workflow in CLC Genomics Workbench 11.0 (Qiagen) for alignment (Mismatch cost: 2; insertion cost: 3; deletion cost: 3; length fraction; 0.8, similarity fraction: 0.8) and calculation of differential gene expression
Genome_build: NC_009505
Supplementary_files_format_and_content: Total counts, RPKM, TPM, CPM

organism: Brucella ovis

source_name: bacterial cells

growth_protocol: Six independent cultures each of B. ovis wild-type and B. ovis bcaA1 strains were inoculated into brucella broth and allowed to grow to saturation overnight in a roller in a 5% CO2 incubator. Cells were back diluted to an OD600 of 0.05 and monitored until they reached OD600 of 0.1. Three tubes of B. ovis bcaA1 were transferred to a roller in an atmospheric incubator (i.e. 0.04% CO2), while three tubes of bcaA1 remained in the 5% CO2 incubator. Both sets of bcaA1 cultures were harvested after an additional 2.5 hours of growth. Cells from three tubes of wild-type B. ovis were harvested at this same time, while the last three tubes of wild-type B. ovis were transferred to the atmospheric incubator and rolled for an additional 2.5 hours. The wild-type B. ovis cultures showed no signs of growth over this period in 0.04% CO2. The remaining three wild-type B. ovis tubes incubated in the atmospheric (0.04%) CO2 incubator were then harvested. RNA was prepped from all harvested cell samples.

extract_protocol:
Each individual culture sample was aliquoted into 6 1.5ml Eppendorf tubes (for a total of 9ml) and spun for 60 seconds at 14,500 x g. Pelleted cells were re-suspended in 1ml of Trizol (Ambion) and stored at -80 C.  Samples were then thawed at 65 C for 10 minutes. Once thawed, 200 microliters of cold chloroform was added, cells were vortexted for 15 seconds and incubated at room temperature (RT) for 5 minutes. Samples were centrifuged at 4 C (17000 x g) for 4 minutes and 500 microliters of 100% cold isopropanol was added to the clear supernatant (SN) in fresh tube, then frozen for at least 1hr at -80 C.  After 30 minutes, samples were centrifuged at 4 C (17000 x g), the supernatant was removed, and 1ml of 70% ethanol was added to wash the pellet. After an additional 5 minute centrifuge (at 4 °C, 17000 xg), residual ethanol was removed and the RNA pellet was resuspended in RNAse free water (50 microliters). RNA was treated with DNAse and further purified with RNA purification kit (Qiagen).
Standard Illumina directional RNA-seq library construction with ribozero rRNA depletion.

treatment_protocol: cultures were incubated in atmopsheres containing either 5% CO2 or 0.04% CO2 to assess the effects of atmospheric CO2 levels on transcription

tag: co2 level

value: 0.04 percent


title: Lymphocyte-ERG009_T1_CCR7HI_D10

status: Public on May 04 2019

type: RNA

city: Memphis

first: Jeremy

middle: Chase

last: Crawford

state: TN

address: MS 221, 262 Danny Thomas Place

department: Department of Host-Microbe Interactions

country: USA

institute: St. Jude Children's Research Hospital

scan_protocol: The chips were then loaded using the IFC Controller HX (Fluidigm) and transferred to the Biomark HD real-time PCR reader to analyze using the GE Fast 96x96 PCR+Melt v2 protocol.

data_processing: Ct values were recovered from the BioMark HD. Single-cell qPCR data Ct values are non-normalized.  The value 999 is reported by the Fluidigm software and we consider these zero values.

molecule: total RNA

organism: Homo sapiens

source_name: Tumor infiltrating lymphocyte

label_protocol: The remaining components of the RT reaction were added to each well, including 0.15 μL 10X SuperScript Enzyme Mix (Thermo Fisher), 0.12 μL T4 Gene 32 Protein (NEB), and nuclease free water (Teknova). Thermal cycling conditions for the reverse transcription of single-cell mRNA into cDNA was 25°C for 5 min, 50°C for 30 min, 55°C for 25 min, 60°C for 5 min, 70°C for 10 min, and then hold at 4°C. After reverse transcription, the cDNA was amplified using 1.5 μL of a pool of the designed primers (STA mix; Fluidigm), 7.5 μL TaqMan PreAmp Master Mix (Thermo Fisher), and 0.075 μL 0.5M EDTA (Thermo Fisher). The thermal cycling conditions were 95°C for 10 min, 20 cycles of 96° for 5 sec and 60°C for 4 min, and then hold at 4°C. Amplified cDNA was then treated with Exonuclease I (NEB) to remove any unincorporated primers by adding 6 μL of 4 U/μL Exonuclease I (20 U/μL Exonuclease I diluted with water and 10X Exonuclease I Reaction buffer). Thermal cycling conditions were 37°C for 30 min, 80°C for 15 min, and then hold at 4°C. The cDNA was then diluted 5-fold for loading onto the chip. The sample mix to be loaded onto the chip included 2.5 μL 2X Sso Fast EvaGreen Supermix with low ROX (Bio-Rad), 0.25 μL 20S DNA Binding Dye Sample Loading Reagent (Fluidigm), and 2.25 μL of the prepared cDNA. The assay mix loaded onto the chip included 2.5 μL 2X Assay Loading Reagent (Fluidigm), 1X DNA Suspension Buffer (Teknova), and 100 μM of each forward and reverse primer mix (Fluidigm).

extract_protocol: After successful sorting, the plates were incubated at 65°C for 90 seconds, and chilled on ice for 5 minutes for RNA denaturation.

treatment_protocol: Cells were stained with a variety of antibodies and tetramers prior to single-cell sorting into 386-well plates.

tag: tumor type

value: Pediatric leukemia

tag: cell type

value: Tumor infiltrating lymphocyte

tag: platewell id

tag: patient id

tag: tetname

tag: tetramer

tag: cell subtype

tag: tet type

value: TetPos


title: Sn12C pTripz YAPsh/pTripz TAZsh/GFP-luc +Dox 3

city: Washington

first: Chunling

last: Yi

state: DC

address: 3970 Reservoir Rd NW

institute: Georgetown University

hyb_protocol: Each labelled cRNA sample was hybridized to HumanHT-12 V4.0 Expression BeadChip (Illumina, USA) according to manufacturer's specifications

scan_protocol: Microarrays were scanned on a BeadArray Reader (Illumina, USA) at scan factor 1 according to manufacturer's specifications

data_processing: Normalized using neqc function from limma package in R. The data was filtered for features where the detection p value was <0.05 for at least 3 of the samples.

label: biotin

source_name: SN12C cell line

label_protocol: total RNA from each sample was reverse transcribed into cDNA and in-vitro transcribed into biotin-labeled cRNA using the Illumina TotalPrep RNA Amplification Kit (Ambion).

growth_protocol: Cell lines were grown in RPMI medium (containing glutamine) supplemented with 10% FBS and 1% penicillin/streptomycin.

extract_protocol: Medium was aspirated and cells were washed once with PBS, collected using a scraper, and centrifuged to produce a cell pellet. Then pellet was then frozen until RNA extraction. For RNA extraction, the RNAeasy Mini Kit (Qiagen, Cat#74106) was used according to manufacturers instructions.

treatment_protocol: Cells were treated with Doxycycline for at least 3 days to induce shRNA expression. 24 Hours prior to harvest cell culture medium was changed to medium without FBS.

tag: yap/taz status

value: KD


title: B.ovis bcaA1 mutant in 0.04 percent CO2 replicate 3

type: SRA

library_source: transcriptomic

tag: genotype


title: WT-IR leukemic bone marrow B cells, biological replicate 3

city: Salamanca

first: Isidro

last: Sánchez García

address: Campus Miguel de Unamuno

department: Centro de inv. del Cáncer (CIC).

country: Spain

institute: Inst. de Inv. Biomédica de Salamanca (IBSAL). H. U. de Salamanca. Inst. de Biología Molecular y Celular del Cáncer (IBMCC).

description: Gene expression data from leukemic WT-IR bone marrow cells

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Washing and scanning were performed using GeneChip System of Affymetrix (GeneChip Hybridization Oven 640, GeneChip Fluidics Station 450)

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: The RMA function provided by the package oligo from R/Bioconductor was applied to the raw expression data.

organism: Mus musculus

source_name: Leukemic WT-IR

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Ambion)

growth_protocol: Animals were housed in SPF facility after 2 Gy irradiation

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

treatment_protocol: Not applicable

tag: disease state

value: leukemic

value: WT

tag: tissue

value: Bone marrow

value: B cells

tag: treatment

value: three weeks of 2Gy irradiation


title: WT B. ovis in 0.04 percent CO2 replicate 3

value: wild-type


title: WT B. ovis in 0.04 percent CO2 replicate 2


title: WT-IR leukemic bone marrow B cells, biological replicate 2


title: Sn12C pTripz YAPsh/pTripz TAZsh/GFP-luc +Dox 1


title: Sn12C pTripz/GFP-luc +Dox 3


title: Sn12C pTripz/GFP-luc +Dox 2


title: WT-IR leukemic bone marrow B cells, biological replicate 1


title: Sn12C pTripz YAPsh/pTripz TAZsh/GFP-luc +Dox 2


title: WT B. ovis in 0.04 percent CO2 replicate 1


title: Lymphocyte-ERG009_T1_CCR7HI_C8


title: LysMcre G-CSF Untreated Replicate 3

city: Birmingham

first: Etty

last: Benveniste

state: AL

address: 510 20th Street South, 1220 Faculty Office Tower

department: Cell, Developmental and Integrative Biology

institute: University of Alabama at Birmingham

data_processing:
Genewiz took the sequenced reads and trimmed to remove possible adapter sequences and nucleotides with poor quality bases (error rate < 0.05) at the ends. After trimming, sequence reads shorter than 30 nucleotides were discarded.
Genewiz took the remaining sequence reads and aligned to the Mus musculsus genome with CLC Genomics Server program. Gene hit counts were measured and RPKM values were calculated.
Genome_build: mm10
Supplementary_files_format_and_content: Normalized counts of each genes for each samples

source_name: Neutrophils Isolated from Bone Marrow

growth_protocol: Bone marrow cells were isolated from the femurs of mice. CD11b+Ly6G+ Neutrophils were flow sorted

extract_protocol:
Neutrophils were collected, centrifuged and washed for 3 times. Then RNA was isolated using Trizol
RNA was sent to Genewiz for their standard library construction

treatment_protocol: Neutrophils were incubated with or without mouse recombinant G-CSF (10ng/ml) for 8h in RPMI medium containing 10% FBS

value: Neutrophils

tag: conditions

value: G-CSF (10 ng/ml) 8h

value: LysMCre Socs3fl/fl


title: B.ovis bcaA1 mutant in 5 percent CO2 replicate 2

value: 5 percent


title: B.ovis bcaA1 mutant in 5 percent CO2 replicate 1


title: B.ovis bcaA1 mutant in 5 percent CO2 replicate 3


title: LysMcre G-CSF Untreated Replicate 2


title: LysMcre G-CSF Untreated Replicate 1


title: WT B. ovis in 5 percent CO2 replicate 1


title: Lymphocyte-ERG009_T1_CCR7HI_C11


title: Socs3fl/fl G-CSF Replicate 2

value: Socs3 fl/fl


title: Socs3fl/fl G-CSF Replicate 3


title: SHR 4

city: Gainesville

first: tao

last: yang

state: Florida

address: McKnight Brain Institute, 1149 Newell Drive

institute: University of Florida

description:
8-S4
8-S4

data_processing:
The quality of the RNA-Seq sequence data was first evaluated using FastQC (13) prior to further downstream analysis. Low quality sequences were removed and the reads with lower quality were trimmed using Trimmomatic (3).
The Star Aligner (10) was used to map high quality paired-end reads to the latest rat genome, Rnor_6.04. Gene expression was obtained using RSEM5. The expected read counts and Fragments Per Kilobase of transcript per Million mapped reads (FPKM), were extracted for further analysis. The estimated read counts were taken as input for edgeR6 to perform differential expression analysis using generalized linear models. The thresholds for calling significantly differentially expressed genes were set at false discovery rate (FDR) 0.05, fold change 2, and the average FPKM of at least one for each comparison group higher than 0.
Supplementary_files_format_and_content: all_gene_expression: FPKM

organism: Rattus rattus

source_name: proximal colonic epithelium

growth_protocol: Colonic epithelia were isolated as previously described. Briefly, freshly obtained proximal colon tissue was sequentially incubated with: (1) HBSS (VWR, Radnor, PA) containing 1.5mM DTT and 3mM EDTA on ice for 20 min; (2) HBSS containing 1.5mM EDTA at 37oC for 10 min. Then the tissue was shaken for 3 min to separate the epithelium from the remaining tissue. The epithelium suspension was centrifuged at 1500 rpm at 4oC and washed with HBSS containing 10% FBS. The cells obtained were aliquoted and stored at -80oC until RNA was extracted.

extract_protocol:
The epithelium cell pellet was lysed and total RNA was extracted by using RNeasy plus mini kit (QIAGEN, Germantown, MD) according to manufacturer’s protocol. RNA concentration was determined on Qubit 2.0 Fluorometer (ThermoFisher, Waltham, MA) and RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). Total RNA with 28S/18S > 1 and RINs between 7.1 and 9.3 were used for RNAseq library construction.
Kit for Illumina (New England Biolabs, Ipswich, MA) following manufacturer’s instructions. Briefly, 500 ng of total RNA was used for mRNA isolation using NEBNext Poly(A) mRNA Magnetic Isolation module (New England Biolabs, Ipswich, MA). Purified mRNA was used to construct RNA library using NEBNext Ultra II Directional Library Prep kit (New England Biolabs, Ispwich, MA). Briefly, RNA was fragmented in NEBNext First Strand Synthesis Buffer by heating at 94 °C. This step was followed by first strand cDNA synthesis using reverse transcriptase and oligodT primers.  Subsequently, synthesis of double-stranded cDNA was performed, followed by end-repair and adaptor ligation.  At this point, Illumina adaptors were ligated to the sample.  Finally, the library with unique barcode was enriched by 10 cycles of amplification, and purified by Agencourt AMPure beads (Beckman Coulter, Brea, CA). The library was sized on the bioanalyzer and quantitated by Qubit.
In preparation for sequencing on the HiSeq3000 Illumina sequencer, uniquely barcoded libraries were normalized to 2.5 nM and equimolar amounts pooled. The RNA-seq library pool was spiked with 1% of PhiX library. Library pools were processed according to the Illumina HiSeq3000 protocol for clustering on the cBOT machine. After denaturation, neutralization and mixing with the ExAmp reagent, the final pool concentration for clustering was 0.25 nM. Sequencing was done using a 2x101 cycles format (paired-end configuration). A typical sequencing run in the HiSeq3000 produced 600-650 million paired-end reads per lane.

value: colon

value: SHR epithelium


title: WKY 1 epithelium RRBS

library_source: genomic

data_processing:
Obtained RRBS data were analyzed using Qiagen CLC Main Workbench V12 (Qiagen, Germantown, MD) with Bisulfite Sequencing Plugin according to manufacturer’s instruction. Critical parameters were set as below: (1) mapping options: match score 1; mismatch cost 2; linear gap cost: insertion 3 and deletion 3; length faction 0.5; similarity fraction 0.8; reads with equal mapping score were assigned randomly; enable automatic paired distance estimation. (2) Sample thresholds: minimum high confidence site coverage 1; minimum high site count 1; maximum mean site coverage 0.0. Specific sites were analyzed using Fisher exact test. (3) The first 5 bases on the 5’-end of each read were excluded from methylation analysis, due to the common technical bias introduced by end-repair steps in RRBS library preparation. (4) The reference genome of Rattus Norvegicus (ensembl_v91) was obtained from CLC benchwork 12 reference data library function. The CpG sites with more than 20 sequencing reads were included in the analysis.
Supplementary_files_format_and_content: clc

molecule: genomic DNA

extract_protocol:
Genomic DNA was isolated from colonic epithelia of WKY and SHR using the Quick DNA Miniprep Kit (Zymo Research, Irvine, CA).
RRBS libraries were constructed using the Diagenode premium RRBS kit C02030032 (Diagenode Inc. USA, Denville, NJ). Briefly, 100ng of genomic DNA was digested with Msp I enzyme at 37oC for 12 hours. End preparation (End repair and A-tailing) was conducted for TA-adaptor ligation in the following step. After ligation, the mixture was incubated with AMPure XP Beads (Beckman Coulter, Brea, CA) at room temperature for 15 min to allow DNA binding to the beads. The DNA bound to beads was washed prior to resuspension in buffer. After quantification of the resuspended DNA sample by real time PCR, equal amounts of each sample were pooled. The pooled library was treated with bisulfite and purified using columns according to the manufacturer’s protocol. Finally, the library was amplified by real time PCR and purified with AMPure XP beads.

value: WKY epithelium


title: SHR 3 epithelium RRBS


title: SHR 2 epithelium RRBS


title: WKY 2 epithelium RRBS


title: WKY 3 epithelium RRBS


title: Lymphocyte-ERG009_T1_CCR7HI_C10

value: Pediatric leukemia

value: Tumor infiltrating lymphocyte


title: Lymphocyte-ERG009_T1_CCR7HI_B9

value: TetPos


title: Lymphocyte-ERG009_T1_CCR7HI_B7


title: Socs3fl/fl G-CSF Replicate 1


title: SHR 1 epithelium RRBS


title: SHR 3

description:
7-S3
7-S3


title: Lymphocyte-ERG009_T1_CCR7HI_C7


title: LysMcre Socs3fl/fl Untreated Replicate 3

value: Untreated


title: WT B. ovis in 5 percent CO2 replicate 2


title: Lymphocyte-ERG009_T1_CCR7HI_C12


title: LysMcre Socs3fl/fl Untreated Replicate 2


title: Lymphocyte-ERG009_T1_CCR7HI_B11


title: Lymphocyte-ERG009_T1_CCR7HI_B12


title: SHR 2

description:
6-S2
6-S2


title: SHR 1

description:
5-S1
5-S1


title: Lymphocyte-ERG009_T1_CCR7HI_B10


title: Lymphocyte-ERG009_T1_CCR7HI_B8


title: WKY 4

description:
4-W4
4-W4


title: LysMcre Socs3fl/fl Untreated Replicate 1


title: Socs3fl/fl Untreated Replicate 3


title: Lymphocyte-ERG009_T1_CCR7HI_A9


title: Socs3fl/fl Untreated Replicate 1


title: Socs3fl/fl Untreated Replicate 2


title: WKY 1

description:
1-W1
1-W1


title: Single-nucleus from the sinus nodes of 8 mice (pooled) [H4_S1]

city: Copenhagen

first: Tune

middle: Hannes

last: Pers

address: Blegdamsvej 3B

department: Novo Nordisk Foundation Center for Basic Metabolic Research

country: Denmark

institute: University of Copenhagen

description:
H4_S1
processed data file: normdata.csv.gz
processed data file: metadata.csv.gz

data_processing:
Read alignment: The Cellranger 3.0 pipeline (10x Genomics, USA) was used to align reads, quantify unique molecular identifiers (UMI) and generate feature-barcode expression matrices. Read 1 consists of the 10x barcode (base pairs 1-16) and UMI (base pairs 17-28). The reads were mapped to an adapted reference from 10x mm10-premrna to include introns according to the procedure set out on the 10x Genomics website (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/advanced/references).
Quality Control: The raw expression matrices produced by the Cellranger count tool were subsequently analysed using the Seurat v.3.0.0.9000 R package. For each sample, based on an estimated 9000 cells loaded, the 5157 barcodes with the highest number of counts were initially selected for downstream analysis. In a further filtering step, based on visual inspection of QC plots, barcodes with at least 3000 UMI and proportions of mitochondrial and ribosomal RNA below 0.08 and 0.1, respectively, were retained. The DoubletFinder R package V2.0 was used to remove suspected doublets.
Normalization, scaling and dimensionality reduction: The data was log normalized with the LogNormalize() command, the FindVariableFeatures() command was used to find the top 2000 variable genes and the ScaleData() command was used to scale the expression data to Z-scores and regress out confounding variation associated with the number of UMI or with ribosomal or mitochondrial gene content. The RunPCA() command was used to compute 75 principal components (PCs).
Clustering and marker gene detection: The FindNeighbors() and FindClusters() commands were used with default parameters to identify cell clusters, and the FindMarkers() command was used with the MAST method from the MAST R package v1.8.2 to identify differentially expressed genes. These genes were used to manually add cell type annotations to the clusters.
Plotting: The RunTSNE() command was used to a perplexity of 30 to produce a 2-D T-distributed stochastic neighbor embedding (t-SNE). Clusters and gene expression panels were visualized using the ggplot2 R package v3.1.0.
Genome_build: mm10-premrna
Supplementary_files_format_and_content: normdata.csv.gz is a gene*cell matrix containing the filtered counts after running the Seurat NormalizeData() command with default settings. Comma-separated text file.
Supplementary_files_format_and_content: metadata.csv.gz contains columns "cell_ID", "nCount_RNA", "nFeature_RNA", "percent.mito", "percent.ribo", "sample_ID", "pANN", "pANNPredictions", "clust.res.0.8", "clustAnnot".  Comma-separated text file.

source_name: Heart sinus nodes

extract_protocol:
Sinus nodes were isolated from 16 mice. The hearts were quickly removed and the right atrium with the whole of the sinus node was dissected out in cold phosphate buffered saline (Sigma-Aldrich, UK). For the sinus node, the translucent intercaval region between the crista terminalis and the atrial septum (~1 by 1 mm) was dissected. Sinus nodes from four animals were pooled into a total of four samples, snap frozen in liquid nitrogen and stored at -80°C until processing. For nuclei isolation, samples were kept on dry ice prior to addition of 1 ml Nuclei EZ Lysis Buffer (Sigma-Aldrich). The tissue was triturated by pipetting 10x with a 1000 µl tip, followed by 10x with a 200 µl tip. The samples were incubated on ice for 5 min, with tube inversion every minute. After another trituration round (10x 1000 µl tip), a centrifugation at 800 g for 7 min was carried out. The supernatant was carefully removed and the nuclei and remaining tissue pieces were resuspended in 500 µl resuspension buffer (0.1 % BSA containing 0.2 U/µl Protector RNase inhibitor). The samples were filtered through a 70 µm nylon mesh that had been soaked in RNase away overnight and washed in MilliQ. Afterwards the filter was washed with 500 µl resuspension buffer and the samples were centrifuged at 800 g for 7 min. 990 µl of the supernatant was removed and 10 µl resuspension buffer added. The four samples were finally pooled again into two samples, H4_S1 and H5_S2, to ensure a sufficiently high cell count.
Chromium Single Cell 3' Reagent Kits (v3 Chemistry).

treatment_protocol: Euthanized by cervical dislocation in accordance with the United Kingdom Animals (Scientific Procedures) Act, 1986.

tag: strain/background

tag: Sex

value: Male

tag: age

value: 12-14 weeks

value: heart sinus node

tag: number of mice

value: 8 (pooled)


title: yeeA extopic expression

city: Ann Arbor

first: Taylor

last: Nye

address: 1105 N University Ave

department: MCDB

institute: University of Michigan

data_processing:
Data processing was performed using RS_Modification_and_Motif_analysis.1 version 2.3.0 from SMRT portal
Genome_build: Bacillus subtilis PY79, accession no  CP006881
Supplementary_files_format_and_content: csv file with the identified modified motifs

organism: Bacillus subtilis PY79

source_name: Bacillus subtilis PY79

growth_protocol: Cells were grown in S750 defined media at 30C with shaking to mid-log phase (OD600 of 0.5)

extract_protocol:
Genomic DNA was purified via CsCl gradient
Library construction was performed by the University of Michigan Sequencing Core, 5kb mean insert size

tag: strain

tag: genotype/variation

value: yeeA extopic expression


title: yeeA deletion

data_processing:
Library strategy: DNA-seq
Data processing was performed using RS_Modification_and_Motif_analysis.1 version 2.3.0 from SMRT portal
Genome_build: Bacillus subtilis NCIB 3610, accession no. CP020102
Supplementary_files_format_and_content: csv file with the identified modified motifs

organism: Bacillus subtilis

source_name: Bacillus subtilis NCIB 3610

growth_protocol: Cells were grown in LB at 30C with shaking to mid-log phase (OD600 of 0.5)

extract_protocol:
Genomic DNA was purified via phenol chlorofom extraction method
Library construction was performed by the University of Michigan Sequencing Core, 5kb mean insert size

value: yeeA deletion


title: WKY 2

description:
2-W2
2-W2

tag: cell type


title: WKY 3

description:
3-W3
3-W3


title: yabB, yeeA deletion

value: yabB, yeeA deletion


title: Sn12C pTripz/GFP-luc +Dox 1

value: WT


title: yeeA deletion


title: Single-nucleus from the sinus nodes of 8 mice (pooled) [H5_S2]

description:
H5_S2
processed data file: normdata.csv.gz
processed data file: metadata.csv.gz


title: yabB deletion

value: yabB deletion


title: Lymphocyte-ERG009_T1_CCR7HI_A7

tag: tumor type

tag: platewell id

tag: patient id

tag: tetname


title: Lymphocyte-ERG009_T1_CCR7HI_A10

tag: tetramer

tag: cell subtype

tag: tet type


title: Hi-C D7 EB [re-analyzed GSM3036558]

status: Public on May 03 2019

city: Boston

first: Chen-Yu

last: Wang

state: MA

address: 185 Cambridge Street

department: Molecular Biology

institute: Massachusetts General Hospital

data_processing:
Library strategy: Hi-C
RNA-seq: Reads were aligned allele-specifically to 129S1/SvJm (mus) and CAST/Eih (cas) genome using TopHat2.0.10. After removal of PCR duplicates, all unique reads mapped to the exons of each gene were quantified by Homer4.8 to generate a raw read count table. Strand-resolved fpm-normalized bigWig files from the raw RNA-seq reads for all reads (comp), mus-specific (mus) reads, and cas-specific (cas) reads were generated using custom scripts.
ChIP-seq: Reads were first trimmed to 50bp if performed using pair-end 69 cycles. Input and ChIP-seq reads were aligned allele-specifically to 129S1/SvJm (mus) and CAST/Eih (cas) genome using NovoAlign_v3-1.00.02. After removing PCR duplicates, uniquely mapped reads were used to generate fpm-normalized bigWig files from all reads (comp), mus-specific (mus) reads, and cas-specific (cas) reads. For the input sample of KO cells, libraries were sequenced twice to reach the desired depth, and the two sequencing files were combined to generate the fpm-normalized bigWig files. To quantify the difference in H3K27me3 and H2AK119ub enrichment between WT and KO cells, we subtracted the ChIP-seq profile of WT cells from that of KO cells using bigwigCompare.
CHART-seq: Input and CHART-seq reads were aligned allele-specifically to 129S1/SvJm (mus) and CAST/Eih (cas) genome using NovoAlign_v3-1.00.02. After removing PCR duplicates, uniquely mapped reads were used to generate input-subtracted coverage profiles using SPP. SPP-normalized profiles were then scaled between WT and KO cells so that they have equal total Xist coverage on the X chromosome. To quantify the difference in Xist enrichment between WT and KO cells, we subtracted the Xist CHART-seq profile of WT cells from that of KO cells using R.
In situ Hi-C: Each end of the read-pairs was aligned separately as single-end reads to 129S1/SvJm (mus) and CAST/Eih (cas) genome using NovoAlign_v3-1.00.02 and allele-specificity was assigned. The single-end alignments were joined to generate a Hi-C summary file. For the replicate 2 of KO cells treated with scramble siRNAs, libraries were sequenced twice to reach the desired depth, and the two sequencing files were combined to generate the Hi-C summary files.
Genome_build: mm9
Supplementary_files_format_and_content: RNA-seq: Uniquely mapped reads without PCR duplicates were used to generate strand-resolved fragment-per-million (fpm)-normalized RNA-seq coverage files (bigWig). WT1, WT clone 1. WT2, WT clone 2. KO1, Smchd1-/- clone 1. KO2, Smchd1-/- clone 2. DMSO, DMSO-treated. Aza, Aza-treated. cas, cas-specific reads. mus, mus-specific reads. comp, all reads. +, forward strand. -, reverse strand. Raw exonic reads in each RNA-seq library were quantified using Homer and summarized in RNAseq_raw_read_count_table.txt. In this table, purecas.TTF data were obtained by re-analyzing published pure cast tail-tip fibroblast RNA-seq data (GSM1412989) in Pinter et al., 2015.  Purecas.MEF data were from pure cas MEF RNA-seq data in this GEO entry.
Supplementary_files_format_and_content: ChIP-seq: Uniquely mapped reads without PCR duplicates were used to generate fragment-per-million (fpm)-normalized ChIP-seq coverage files (bigWig). WT, WT clone 1. KO, Smchd1-/- clone 1. cas, cas-specific reads. mus, mus-specific reads. comp, all reads. delta: KO minus WT. rep1, replicate 1. rep2, replicate 2.
Supplementary_files_format_and_content: CHART-seq: Uniquely mapped reads without PCR duplicates were used to generate fragment-per-million (fpm)-normalized CHART-seq coverage files (bigWig). WT, WT clone 1. KO, Smchd1-/- clone 1. cas, cas-specific reads. mus, mus-specific reads. comp, all reads. Uniquely mapped comp reads without PCR duplicates were then used to generate the input-subtracted Xist coverage profile by SPP as described in Simon et al., 2013 and scaled between WT and KO cells (files whose name starts with “SPP.normalized”). delta: KO minus WT. rep1, replicate 1. rep2, replicate 2.
Supplementary_files_format_and_content: In situ Hi-C: Allele-resolved Hi-C data were presented as Hi-C summary file (file names ending with “.summary.txt”), where the first 7 columns represent read names, chromosome for read 1, positions for read 1 (5’ end of read), strand of read 1 (+ or -), chromosome for read 2, positions for read 2 (5’ end of read), and strand of read 2 (+ or -), respectively. WT, WT clone 1. KO, Smchd1-/- clone 1. Scramble, scramble siRNA-treated. PRC1_KD, RING1A and RING1B siRNA-treated. HNRNPK_KD, HNRNPK siRNA-treated. cas, cas-specific reads. mus, mus-specific reads. comp, all reads. rep1, replicate 1. rep2, replicate 2. To match sequencing depths between samples, Hi-C summary files were randomly sampled to generate down-sampled Hi-summary files (file names starting with “Downsampled”). Principle component analysis was performed at 200-kb resolution using Homer. We also similarly re-analyzed published Hi-C data (GSE99991, GSE67516) of undifferentiated female ES cells (D0.ES, GSM3036556), day 4 embryoid bodies (D4.EB, GSM3036557), and day 7 embryoid bodies (D7.EB, GSM3036558) to derive the PC1 values of the X chromosome at 200-kb resolution using Homer. Principle component 1 or 2 were presented as bedGraph files (file names ending with “.PC1.200kb.bedGraph” or “.PC2.200kb.bedGraph”). Insulation scores were computed using iteratively corrected Hi-C contact matrices at 100-kb resolution and summarized in X_chromosome.insulation_score.txt. To investigate the relationships between TAD boundaries and borders of chromosome compartments, we additionally performed PCA at 100-kb resolution using Homer on the Hi-C data of WT and Smchd1-/- MEFs. Xa, comp (D0.ES) or cas (all others). Xi, mus.

source_name: mouse embryonic stem cells

growth_protocol: MEFs were grown in MEF media [DMEM, high glucose, GlutaMAX supplement, pyruvate (10569044, Thermo Fisher Scientific), 10% FBS, 25mM HEPES pH 7.2-7.5 (15630130, Thermo Fisher Scientific), 1X MEM non-essential amino acids (11140076, Thermo Fisher Scientific), 1X Pen/Strep (15140163, Thermo Fisher Scientific), and 0.1mM β-mercaptoethanol (21985023, Thermo Fisher Scientific)].

extract_protocol:
Total RNA was extracted using standard Trizol protocol. ChIP/CHART/Hi-C-enriched and input DNA were extracted with phenol:chloroform.
RNA-seq libraries were prepared by dUTP-mediated directional RNA-seq following NEBNext Ultra directional RNA library preparation protocol. ChIP-seq and Hi-C libraries were prepared by NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina. CHART-seq libraries were generated by NEBNext Ultra DNA Library Prep Kit for Illumina.
Paired-end 50 or 69-cycle with Illumina HiSeq

treatment_protocol: To treate cells with 5-aza-2'-deoxycytidine (Aza, A3656, Sigma), MEFs were grown in MEF media containing either DMSO (control) or Aza (0.3μM), with media changed daily for 5 days. To deplete PRC1, MEFs were transfected with either scramble siRNAs (siGENOME Non-Targeting siRNA #1, D-001210-01, Dharmacon) or a mixture of siRNAs targeting RING1A (D-062335-03, Dharmacon) and RING1B (D-042180-01, Dharmacon) using Lipofectamine® RNAiMAX Transfection Reagent (13778075, Thermo Fisher Scientific) according to manufacturer's instructions. Transfection of siRNAs was performed once a day for 4 days.

value: mouse embryonic stem cells

tag: genotype

tag: gender

value: female


title: Hi-C D0 ES [re-analyzed GSM3036556]


title: Hi-C Xist deletion

source_name: mouse dermal fibroblasts

value: mouse embryonic fibroblasts

value: post-XCI Xist deletion on the inactive X chromosome


title: Hi-C Smchd1-/- HNRNPK KD replicate2

source_name: mouse embryonic fibroblasts


title: Lymphocyte-ERG009_T1_CCR7HI_A8

value: Pediatric leukemia


title: Hi-C D4 EB [re-analyzed GSM3036557]


title: Hi-C WT HNRNPK KD replicate1


title: Hi-C Smchd1-/- PRC1 KD replicate2


title: CHART-seq Smchd1-/- clone 1 input replicate1

data_processing:
Library strategy: CHART-seq
RNA-seq: Reads were aligned allele-specifically to 129S1/SvJm (mus) and CAST/Eih (cas) genome using TopHat2.0.10. After removal of PCR duplicates, all unique reads mapped to the exons of each gene were quantified by Homer4.8 to generate a raw read count table. Strand-resolved fpm-normalized bigWig files from the raw RNA-seq reads for all reads (comp), mus-specific (mus) reads, and cas-specific (cas) reads were generated using custom scripts.
ChIP-seq: Reads were first trimmed to 50bp if performed using pair-end 69 cycles. Input and ChIP-seq reads were aligned allele-specifically to 129S1/SvJm (mus) and CAST/Eih (cas) genome using NovoAlign_v3-1.00.02. After removing PCR duplicates, uniquely mapped reads were used to generate fpm-normalized bigWig files from all reads (comp), mus-specific (mus) reads, and cas-specific (cas) reads. For the input sample of KO cells, libraries were sequenced twice to reach the desired depth, and the two sequencing files were combined to generate the fpm-normalized bigWig files. To quantify the difference in H3K27me3 and H2AK119ub enrichment between WT and KO cells, we subtracted the ChIP-seq profile of WT cells from that of KO cells using bigwigCompare.
CHART-seq: Input and CHART-seq reads were aligned allele-specifically to 129S1/SvJm (mus) and CAST/Eih (cas) genome using NovoAlign_v3-1.00.02. After removing PCR duplicates, uniquely mapped reads were used to generate input-subtracted coverage profiles using SPP. SPP-normalized profiles were then scaled between WT and KO cells so that they have equal total Xist coverage on the X chromosome. To quantify the difference in Xist enrichment between WT and KO cells, we subtracted the Xist CHART-seq profile of WT cells from that of KO cells using R.
In situ Hi-C: Each end of the read-pairs was aligned separately as single-end reads to 129S1/SvJm (mus) and CAST/Eih (cas) genome using NovoAlign_v3-1.00.02 and allele-specificity was assigned. The single-end alignments were joined to generate a Hi-C summary file. For the replicate 2 of KO cells treated with scramble siRNAs, libraries were sequenced twice to reach the desired depth, and the two sequencing files were combined to generate the Hi-C summary files.
Genome_build: mm9
Supplementary_files_format_and_content: RNA-seq: Uniquely mapped reads without PCR duplicates were used to generate strand-resolved fragment-per-million (fpm)-normalized RNA-seq coverage files (bigWig). WT1, WT clone 1. WT2, WT clone 2. KO1, Smchd1-/- clone 1. KO2, Smchd1-/- clone 2. DMSO, DMSO-treated. Aza, Aza-treated. cas, cas-specific reads. mus, mus-specific reads. comp, all reads. +, forward strand. -, reverse strand. Raw exonic reads in each RNA-seq library were quantified using Homer and summarized in RNAseq_raw_read_count_table.txt. In this table, purecas.TTF data were obtained by re-analyzing published pure cast tail-tip fibroblast RNA-seq data (GSM1412989) in Pinter et al., 2015.  Purecas.MEF data were from pure cas MEF RNA-seq data in this GEO entry.
Supplementary_files_format_and_content: ChIP-seq: Uniquely mapped reads without PCR duplicates were used to generate fragment-per-million (fpm)-normalized ChIP-seq coverage files (bigWig). WT, WT clone 1. KO, Smchd1-/- clone 1. cas, cas-specific reads. mus, mus-specific reads. comp, all reads. delta: KO minus WT. rep1, replicate 1. rep2, replicate 2.
Supplementary_files_format_and_content: CHART-seq: Uniquely mapped reads without PCR duplicates were used to generate fragment-per-million (fpm)-normalized CHART-seq coverage files (bigWig). WT, WT clone 1. KO, Smchd1-/- clone 1. cas, cas-specific reads. mus, mus-specific reads. comp, all reads. Uniquely mapped comp reads without PCR duplicates were then used to generate the input-subtracted Xist coverage profile by SPP as described in Simon et al., 2013 and scaled between WT and KO cells (files whose name starts with “SPP.normalized”). delta: KO minus WT. rep1, replicate 1. rep2, replicate 2.
Supplementary_files_format_and_content: In situ Hi-C: Allele-resolved Hi-C data were presented as Hi-C summary file (file names ending with “.summary.txt”), where the first 7 columns represent read names, chromosome for read 1, positions for read 1 (5’ end of read), strand of read 1 (+ or -), chromosome for read 2, positions for read 2 (5’ end of read), and strand of read 2 (+ or -), respectively. WT, WT clone 1. KO, Smchd1-/- clone 1. Scramble, scramble siRNA-treated. PRC1_KD, RING1A and RING1B siRNA-treated. HNRNPK_KD, HNRNPK siRNA-treated. cas, cas-specific reads. mus, mus-specific reads. comp, all reads. rep1, replicate 1. rep2, replicate 2. To match sequencing depths between samples, Hi-C summary files were randomly sampled to generate down-sampled Hi-summary files (file names starting with “Downsampled”). Principle component analysis was performed at 200-kb resolution using Homer. We also similarly re-analyzed published Hi-C data (GSE99991, GSE67516) of undifferentiated female ES cells (D0.ES, GSM3036556), day 4 embryoid bodies (D4.EB, GSM3036557), and day 7 embryoid bodies (D7.EB, GSM3036558) to derive the PC1 values of the X chromosome at 200-kb resolution using Homer. Principle component 1 or 2 were presented as bedGraph files (file names ending with “.PC1.200kb.bedGraph” or “.PC2.200kb.bedGraph”). Insulation scores were computed using iteratively corrected Hi-C contact matrices at 100-kb resolution and summarized in X_chromosome.insulation_score.txt. To investigate the relationships between TAD boundaries and borders of chromosome compartments, we additionally performed PCA at 100-kb resolution using Homer on the Hi-C data of WT and Smchd1-/- MEFs. Xa, comp (D0.ES) or cas (all others). Xi, mus.


title: CHART-seq WT clone 1 input replicate2


title: Hi-C WT Scramble


title: CHART-seq WT clone 1 Xist capture probes replicate2


title: CHART-seq WT clone 1 Xist capture probes replicate1


title: ChIP-seq Smchd1-/- clone 1 H2AK119ub

data_processing:
RNA-seq: Reads were aligned allele-specifically to 129S1/SvJm (mus) and CAST/Eih (cas) genome using TopHat2.0.10. After removal of PCR duplicates, all unique reads mapped to the exons of each gene were quantified by Homer4.8 to generate a raw read count table. Strand-resolved fpm-normalized bigWig files from the raw RNA-seq reads for all reads (comp), mus-specific (mus) reads, and cas-specific (cas) reads were generated using custom scripts.
ChIP-seq: Reads were first trimmed to 50bp if performed using pair-end 69 cycles. Input and ChIP-seq reads were aligned allele-specifically to 129S1/SvJm (mus) and CAST/Eih (cas) genome using NovoAlign_v3-1.00.02. After removing PCR duplicates, uniquely mapped reads were used to generate fpm-normalized bigWig files from all reads (comp), mus-specific (mus) reads, and cas-specific (cas) reads. For the input sample of KO cells, libraries were sequenced twice to reach the desired depth, and the two sequencing files were combined to generate the fpm-normalized bigWig files. To quantify the difference in H3K27me3 and H2AK119ub enrichment between WT and KO cells, we subtracted the ChIP-seq profile of WT cells from that of KO cells using bigwigCompare.
CHART-seq: Input and CHART-seq reads were aligned allele-specifically to 129S1/SvJm (mus) and CAST/Eih (cas) genome using NovoAlign_v3-1.00.02. After removing PCR duplicates, uniquely mapped reads were used to generate input-subtracted coverage profiles using SPP. SPP-normalized profiles were then scaled between WT and KO cells so that they have equal total Xist coverage on the X chromosome. To quantify the difference in Xist enrichment between WT and KO cells, we subtracted the Xist CHART-seq profile of WT cells from that of KO cells using R.
In situ Hi-C: Each end of the read-pairs was aligned separately as single-end reads to 129S1/SvJm (mus) and CAST/Eih (cas) genome using NovoAlign_v3-1.00.02 and allele-specificity was assigned. The single-end alignments were joined to generate a Hi-C summary file. For the replicate 2 of KO cells treated with scramble siRNAs, libraries were sequenced twice to reach the desired depth, and the two sequencing files were combined to generate the Hi-C summary files.
Genome_build: mm9
Supplementary_files_format_and_content: RNA-seq: Uniquely mapped reads without PCR duplicates were used to generate strand-resolved fragment-per-million (fpm)-normalized RNA-seq coverage files (bigWig). WT1, WT clone 1. WT2, WT clone 2. KO1, Smchd1-/- clone 1. KO2, Smchd1-/- clone 2. DMSO, DMSO-treated. Aza, Aza-treated. cas, cas-specific reads. mus, mus-specific reads. comp, all reads. +, forward strand. -, reverse strand. Raw exonic reads in each RNA-seq library were quantified using Homer and summarized in RNAseq_raw_read_count_table.txt. In this table, purecas.TTF data were obtained by re-analyzing published pure cast tail-tip fibroblast RNA-seq data (GSM1412989) in Pinter et al., 2015.  Purecas.MEF data were from pure cas MEF RNA-seq data in this GEO entry.
Supplementary_files_format_and_content: ChIP-seq: Uniquely mapped reads without PCR duplicates were used to generate fragment-per-million (fpm)-normalized ChIP-seq coverage files (bigWig). WT, WT clone 1. KO, Smchd1-/- clone 1. cas, cas-specific reads. mus, mus-specific reads. comp, all reads. delta: KO minus WT. rep1, replicate 1. rep2, replicate 2.
Supplementary_files_format_and_content: CHART-seq: Uniquely mapped reads without PCR duplicates were used to generate fragment-per-million (fpm)-normalized CHART-seq coverage files (bigWig). WT, WT clone 1. KO, Smchd1-/- clone 1. cas, cas-specific reads. mus, mus-specific reads. comp, all reads. Uniquely mapped comp reads without PCR duplicates were then used to generate the input-subtracted Xist coverage profile by SPP as described in Simon et al., 2013 and scaled between WT and KO cells (files whose name starts with “SPP.normalized”). delta: KO minus WT. rep1, replicate 1. rep2, replicate 2.
Supplementary_files_format_and_content: In situ Hi-C: Allele-resolved Hi-C data were presented as Hi-C summary file (file names ending with “.summary.txt”), where the first 7 columns represent read names, chromosome for read 1, positions for read 1 (5’ end of read), strand of read 1 (+ or -), chromosome for read 2, positions for read 2 (5’ end of read), and strand of read 2 (+ or -), respectively. WT, WT clone 1. KO, Smchd1-/- clone 1. Scramble, scramble siRNA-treated. PRC1_KD, RING1A and RING1B siRNA-treated. HNRNPK_KD, HNRNPK siRNA-treated. cas, cas-specific reads. mus, mus-specific reads. comp, all reads. rep1, replicate 1. rep2, replicate 2. To match sequencing depths between samples, Hi-C summary files were randomly sampled to generate down-sampled Hi-summary files (file names starting with “Downsampled”). Principle component analysis was performed at 200-kb resolution using Homer. We also similarly re-analyzed published Hi-C data (GSE99991, GSE67516) of undifferentiated female ES cells (D0.ES, GSM3036556), day 4 embryoid bodies (D4.EB, GSM3036557), and day 7 embryoid bodies (D7.EB, GSM3036558) to derive the PC1 values of the X chromosome at 200-kb resolution using Homer. Principle component 1 or 2 were presented as bedGraph files (file names ending with “.PC1.200kb.bedGraph” or “.PC2.200kb.bedGraph”). Insulation scores were computed using iteratively corrected Hi-C contact matrices at 100-kb resolution and summarized in X_chromosome.insulation_score.txt. To investigate the relationships between TAD boundaries and borders of chromosome compartments, we additionally performed PCA at 100-kb resolution using Homer on the Hi-C data of WT and Smchd1-/- MEFs. Xa, comp (D0.ES) or cas (all others). Xi, mus.

tag: chip antibody

value: H2AK119ub (#8240, Cell Signaling)


title: Hi-C Smchd1-/- Scramble replicate2


title: ChIP-seq WT clone 1 H2AK119ub


title: ChIP-seq Smchd1-/- clone 1 input


title: CHART-seq Smchd1-/- clone 1 Xist capture probes replicate2


title: ChIP-seq Smchd1-/- clone 1 H3K27me3 replicate1


title: ChIP-seq WT clone 1 H3K27me3 replicate2


title: ChIP-seq Smchd1-/- clone 1 H3K27me3 replicate2


title: Hi-C WT HNRNPK KD replicate2


title: CHART-seq WT clone 1 input replicate1


title: CHART-seq Smchd1-/- clone 1 Xist capture probes replicate1


title: Hi-C WT PRC1 KD


title: Hi-C Smchd1-/- HNRNPK KD replicate1


title: ChIP-seq WT clone 1 H3K27me3 replicate1


title: CHART-seq Smchd1-/- clone 1 input replicate2


title: ChIP-seq WT clone 1 input


title: Hi-C Smchd1-/- PRC1 KD replicate1


title: Lymphocyte-ERG009_T1_CCR7HI_C9

value: Tumor infiltrating lymphocyte

value: TetPos


title: Hi-C Smchd1-/- Scramble replicate1


title: Hi-C Smchd1-/-


title: Hi-C WT


title: RiboSeq_RPL12 S38D asynchronous cells rep2

city: Berlin

first: Markus

last: Landthaler

address: Hannoversche Str. 28

department: Berlin Institute for Medical Systems Biology

country: Germany

institute: Max Delbrueck Center

description: ribosome profiling reads

data_processing:
Library strategy: Ribosome profiling
Basecalls were converted to fastq files using Bcl2Fastq (2.16.0.10). Reads were demultiplexed and adapter sequences removed by Flexbar (2.5). Reads were then collapsed to remove PCR duplicates, followed by removal of random nucleotides (four on both 5’ and 3’ end of the reads) using fastx_trimmer (FASTX Toolkit 0.0.14). Reads aligning to rRNA sequences were removed by Bowtie2 (2.3.2) and the remaining sequences were aligned to the mouse genome (mm10) using STAR aligner (2.5.3a). The STAR genome index was built using annotation obtained from GENCODE (M14). Next, reads of 29 or 30 nucleotides in length were retained and counted in coding sequence (CDS) exons (-t CDS) using HTSeq-count (0.9.1).
To detect differences in translational efficacy, as well as in mRNA abundance and both effects (transcription and translation) we used DESeq2 (1.18.1) with an interaction term model. Briefly, RPF read counts were normalized using the DESeq2 estimateSizeFactors function by taking into account all read counts. For 3’ mRNA seq, ERCC spike-in read counts were used to obtain normalization factors using the same function. DESeq2 was run with default parameters. We considered genes with P-adjusted value <0.1 and log2-transformed fold change >0 to be differentially translated between wild-type mitotic vs wild-type asynchronous conditions. Log2-transformed fold changes for downstream comparisons were taken directly from the DESeq2 output.
Genome_build: mm10
Supplementary_files_format_and_content: text files (read counts from HTSeq-count output)

source_name: 19PP B cell lymphoma

growth_protocol: Murine B cell lymphoma line, 19PP, was established from Rag2-/-γC-/- mouse reconstituted with Cγ1-Cre; Myc/P110*flSTOP mouse BM cells (Sander et al., 2012). 19PP cells were transfected with Flp-expressing plasmid to delete GFP and hCD2 reporter genes. Reporter negative subline, 19DN, was established by FACS sorting of reporter double-negative 19PP cells. 19DN cells were maintained in DMEM medium (Gibco) containing 10% heat inactivated FBS, glutamax, sodium pyruvate, HEPES, non-essential amino acids, penicillin streptomycin (all 1%) and 52 μM β-mercaptoethanol.

extract_protocol:
Cell pellets were flash-frozen in liquid nitrogen, transferred to ice and lysed in mammalian polysome buffer (20 mM Tris-HCl, pH 7.4, 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 100 μg/ml CHX), supplemented with 1% (v/v) Triton X-100 and 25 U/ml TurboDNase (Thermo Fischer Scientific). Afterwards, lysates were triturated ten times through a 26-gauge needle, cleared by centrifugation (20.000 xg, 5 min, 4 C), flesh frozen in liquid nitrogen and stored at -80 C. To obtain ribosome-protected fragments, lysates (120-µl aliquots) were treated with 3 µl of RNase I (Ambion, AM2294, 100 U/µl) for 45 min at room temperature with slow agitation. RNase activity was inhibited by the addition of 4 µl of SUPERaseIn (Thermo Fischer Scientific, AM2696, 20 U/µl). Meanwhile, MicroSpin S-400 HR columns (GE Healthcare, 27-5140-01) were equilibrated with 3 ml of mammalian polysome buffer without DTT and CHX by gravity flow and emptied by centrifugation at 600 xg for 4 min. We then immediately loaded 100 μl of the digested lysate on the column and eluted the column by centrifugation at 600 xg for 2 min. We extracted RNA from the flow-through (approximately 125 μl) using Trizol LS (Life Technologies, 10296-010) in combination with the RNA Clean & Concentrator kit (Zymo Research).
We then depleted ribosomal RNA fragments using the RiboZero Kit (Illumina, MRZH11124) and separated the remaining RNA on a 17% denaturing urea-PAGE gel (National Diagnostics, EC-829). The size range from 27 nt to 30 nt, defined by loading with 20 pmol each of Marker-27 nt and Marker-30 nt, was cut out, and the RNA fragments were subjected to small RNA cloning and library generation (Hafner et al.,2012) using 3′ adaptor 4N-RA3, 5′ adaptor OR5-4N, RT primer RTP and PCR primers RP1 (forward primer) and RPI1-12 (reverse primer, containing barcodes, for sequences see Illumina Truseq small RNA oligonucleotides). All cDNA libraries were multiplexed at 12 samples per lane and sequenced on a HiSeq 2500 instrument using 1x51+7 cycles.

treatment_protocol: The mouse B cells were cultured in three 15 cm plates per condition until 60-70 % confluent and incubated with 100 ng/mL nocodazole (Sigma-Aldrich) for 8 hr to synchronize the cells in mitosis. Cellular DNA content before and after the nocodazole treatment was measured by flow cytometry. Nocodazole was then released by washing the cells twice in pre-warmed PBS and cells were incubated in fresh medium for 10 min. Cells were harvested by centrifugation in the presence of cycloheximide (100 µg/ml).

tag: cell line

value: cell line; lymphoma

tag: culture medium

value: DMEM

value: RPL12 S38D

tag: cell cycle phase

value: asynchronous


title: RiboSeq_RPL12 WT mitotic cells nocodazole rep2

description: ribosome profiling reads

value: mitotic cells nocodazole


title: RiboSeq_RPL12 S38A mitotic cells nocodazole rep2

description: ribosome profiling reads

value: RPL12 S38A


title: RiboSeq_RPL12 WT mitotic cells nocodazole rep1

description: ribosome profiling reads


title: RiboSeq_RPL12 S38D asynchronous cells rep1

description: ribosome profiling reads


title: RiboSeq_RPL12 S38A asynchronous cells rep2

description: ribosome profiling reads


title: RNA-seq Smchd1-/- clone 1 DMSO

data_processing:
RNA-seq: Reads were aligned allele-specifically to 129S1/SvJm (mus) and CAST/Eih (cas) genome using TopHat2.0.10. After removal of PCR duplicates, all unique reads mapped to the exons of each gene were quantified by Homer4.8 to generate a raw read count table. Strand-resolved fpm-normalized bigWig files from the raw RNA-seq reads for all reads (comp), mus-specific (mus) reads, and cas-specific (cas) reads were generated using custom scripts.
Genome_build: mm9
Supplementary_files_format_and_content: RNA-seq: Uniquely mapped reads without PCR duplicates were used to generate strand-resolved fragment-per-million (fpm)-normalized RNA-seq coverage files (bigWig). WT1, WT clone 1. WT2, WT clone 2. KO1, Smchd1-/- clone 1. KO2, Smchd1-/- clone 2. DMSO, DMSO-treated. Aza, Aza-treated. cas, cas-specific reads. mus, mus-specific reads. comp, all reads. +, forward strand. -, reverse strand. Raw exonic reads in each RNA-seq library were quantified using Homer and summarized in RNAseq_raw_read_count_table.txt. In this table, purecas.TTF data were obtained by re-analyzing published pure cast tail-tip fibroblast RNA-seq data (GSM1412989) in Pinter et al., 2015.  Purecas.MEF data were from pure cas MEF RNA-seq data in this GEO entry.

extract_protocol:
Total RNA was extracted using standard Trizol protocol.
RNA-seq libraries were prepared by dUTP-mediated directional RNA-seq following NEBNext Ultra directional RNA library preparation protocol.


title: RNA-seq Smchd1-/- clone 1 Aza


title: RiboSeq_RPL12 S38D mitotic cells nocodazole rep1

description: ribosome profiling reads


title: RPL12 S38D mitotic cells nocodazole rep2

description: 3'mRNAseq reads

data_processing:
Basecalls were converted to fastq files using Bcl2Fastq (2.16.0.10).Next, reads were demultiplexed by Flexbar (2.5) and adapter sequences removed by cutadapt (1.12). Reads were then aligned to the mm10 genome using the STAR aligner 2.5.3a with read counting mode enabled to directly obtain read count tables.
Genome_build: mm10
Supplementary_files_format_and_content: txt files (read counts from STAR output)

molecule: polyA RNA

extract_protocol:
Cell pellets were flash-frozen in liquid nitrogen, transferred to ice and lysed in mammalian polysome buffer (20 mM Tris-HCl, pH 7.4, 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 100 μg/ml CHX), supplemented with 1% (v/v) Triton X-100 and 25 U/ml TurboDNase (Thermo Fischer Scientific). Afterwards, lysates were triturated ten times through a 26-gauge needle, cleared by centrifugation (20.000 xg, 5 min, 4 C), flesh frozen in liquid nitrogen and stored at -80 C. To obtain 3’ mRNA-seq datasets for mRNA quantification, we isolated total RNA from mammalian polysome buffer lysates (120-µl aliquots) using Trizol LS.
Next, 1 µg of total RNA was mixed with 1 µl of 1:50 dilution of ERCC Spike-in Control Mix 1 (Thermo Fisher Scientific), TurboDNase-treated and input into QuantSeq 3’ mRNA-Seq Library Prep Kit FWD (Lexogen, Inc.). Subsequent steps were performed according to manufacturer’s instruction. All cDNA libraries were multiplexed at 12 samples per lane and sequenced on a HiSeq 2500 instrument using 1x51+7 cycles.


title: RNA-seq WT clone 2 Aza


title: RNA-seq Smchd1-/- clone 2 DMSO


title: RiboSeq_RPL12 S38A mitotic cells nocodazole rep1

description: ribosome profiling reads


title: RNA-seq WT clone 1 Aza


title: RNA-seq Smchd1-/- clone 2 Aza


title: RiboSeq_RPL12 S38A asynchronous cells rep1

description: ribosome profiling reads


title: RNA-seq WT clone 2 DMSO


title: RNA-seq pure cas MEF

value: CAST


title: RiboSeq_RPL12 WT asynchronous cells rep2

description: ribosome profiling reads

value: WT


title: RiboSeq_RPL12 WT asynchronous cells rep1

description: ribosome profiling reads


title: RPL12 S38D mitotic cells nocodazole rep1

description: 3'mRNAseq reads


title: RiboSeq_RPL12 S38D mitotic cells nocodazole rep2

description: ribosome profiling reads


title: RPL12 WT mitotic cells nocodazole rep2

description: 3'mRNAseq reads


title: RPL12 S38A mitotic cells nocodazole rep2

description: 3'mRNAseq reads


title: RPL12 S38A mitotic cells nocodazole rep1

description: 3'mRNAseq reads


title: RPL12 S38D asynchronous cells rep2

description: 3'mRNAseq reads


title: RPL12 WT mitotic cells nocodazole rep1

description: 3'mRNAseq reads


title: RPL12 S38D asynchronous cells rep1

description: 3'mRNAseq reads


title: RNA-seq WT clone 1 DMSO


title: Hi-C Xist deletion rep2

data_processing:
Library strategy: Hi-C
RNA-seq: Reads were aligned allele-specifically to 129S1/SvJm (mus) and CAST/Eih (cas) genome using TopHat2.0.10. After removal of PCR duplicates, all unique reads mapped to the exons of each gene were quantified by Homer4.8 to generate a raw read count table. Strand-resolved fpm-normalized bigWig files from the raw RNA-seq reads for all reads (comp), mus-specific (mus) reads, and cas-specific (cas) reads were generated using custom scripts.
ChIP-seq: Reads were first trimmed to 50bp if performed using pair-end 69 cycles. Input and ChIP-seq reads were aligned allele-specifically to 129S1/SvJm (mus) and CAST/Eih (cas) genome using NovoAlign_v3-1.00.02. After removing PCR duplicates, uniquely mapped reads were used to generate fpm-normalized bigWig files from all reads (comp), mus-specific (mus) reads, and cas-specific (cas) reads. For the input sample of KO cells, libraries were sequenced twice to reach the desired depth, and the two sequencing files were combined to generate the fpm-normalized bigWig files. To quantify the difference in H3K27me3 and H2AK119ub enrichment between WT and KO cells, we subtracted the ChIP-seq profile of WT cells from that of KO cells using bigwigCompare.
CHART-seq: Input and CHART-seq reads were aligned allele-specifically to 129S1/SvJm (mus) and CAST/Eih (cas) genome using NovoAlign_v3-1.00.02. After removing PCR duplicates, uniquely mapped reads were used to generate input-subtracted coverage profiles using SPP. SPP-normalized profiles were then scaled between WT and KO cells so that they have equal total Xist coverage on the X chromosome. To quantify the difference in Xist enrichment between WT and KO cells, we subtracted the Xist CHART-seq profile of WT cells from that of KO cells using R.
In situ Hi-C: Each end of the read-pairs was aligned separately as single-end reads to 129S1/SvJm (mus) and CAST/Eih (cas) genome using NovoAlign_v3-1.00.02 and allele-specificity was assigned. The single-end alignments were joined to generate a Hi-C summary file. For the replicate 2 of KO cells treated with scramble siRNAs, libraries were sequenced twice to reach the desired depth, and the two sequencing files were combined to generate the Hi-C summary files.
Genome_build: mm9
Supplementary_files_format_and_content: RNA-seq: Uniquely mapped reads without PCR duplicates were used to generate strand-resolved fragment-per-million (fpm)-normalized RNA-seq coverage files (bigWig). WT1, WT clone 1. WT2, WT clone 2. KO1, Smchd1-/- clone 1. KO2, Smchd1-/- clone 2. DMSO, DMSO-treated. Aza, Aza-treated. cas, cas-specific reads. mus, mus-specific reads. comp, all reads. +, forward strand. -, reverse strand. Raw exonic reads in each RNA-seq library were quantified using Homer and summarized in RNAseq_raw_read_count_table.txt. In this table, purecas.TTF data were obtained by re-analyzing published pure cast tail-tip fibroblast RNA-seq data (GSM1412989) in Pinter et al., 2015. Purecas.MEF data were from pure cas MEF RNA-seq data in this GEO entry.
Supplementary_files_format_and_content: ChIP-seq: Uniquely mapped reads without PCR duplicates were used to generate fragment-per-million (fpm)-normalized ChIP-seq coverage files (bigWig). WT, WT clone 1. KO, Smchd1-/- clone 1. cas, cas-specific reads. mus, mus-specific reads. comp, all reads. delta: KO minus WT. rep1, replicate 1. rep2, replicate 2.
Supplementary_files_format_and_content: CHART-seq: Uniquely mapped reads without PCR duplicates were used to generate fragment-per-million (fpm)-normalized CHART-seq coverage files (bigWig). WT, WT clone 1. KO, Smchd1-/- clone 1. cas, cas-specific reads. mus, mus-specific reads. comp, all reads. Uniquely mapped comp reads without PCR duplicates were then used to generate the input-subtracted Xist coverage profile by SPP as described in Simon et al., 2013 and scaled between WT and KO cells (files whose name starts with “SPP.normalized”). delta: KO minus WT. rep1, replicate 1. rep2, replicate 2.
Supplementary_files_format_and_content: In situ Hi-C: Allele-resolved Hi-C data were presented as Hi-C summary file (file names ending with “.summary.txt”), where the first 7 columns represent read names, chromosome for read 1, positions for read 1 (5’ end of read), strand of read 1 (+ or -), chromosome for read 2, positions for read 2 (5’ end of read), and strand of read 2 (+ or -), respectively. WT, WT clone 1. KO, Smchd1-/- clone 1. Scramble, scramble siRNA-treated. PRC1_KD, RING1A and RING1B siRNA-treated. HNRNPK_KD, HNRNPK siRNA-treated. cas, cas-specific reads. mus, mus-specific reads. comp, all reads. rep1, replicate 1. rep2, replicate 2. To match sequencing depths between samples, Hi-C summary files were randomly sampled to generate down-sampled Hi-summary files (file names starting with “Downsampled”). Principle component analysis was performed at 200-kb resolution using Homer. We also similarly re-analyzed published Hi-C data (GSE99991, GSE67516) of undifferentiated female ES cells (D0.ES, GSM3036556), day 4 embryoid bodies (D4.EB, GSM3036557), and day 7 embryoid bodies (D7.EB, GSM3036558) to derive the PC1 values of the X chromosome at 200-kb resolution using Homer. Principle component 1 or 2 were presented as bedGraph files (file names ending with “.PC1.200kb.bedGraph” or “.PC2.200kb.bedGraph”). Insulation scores were computed using iteratively corrected Hi-C contact matrices at 100-kb resolution and summarized in X_chromosome.insulation_score.txt. To investigate the relationships between TAD boundaries and borders of chromosome compartments, we additionally performed PCA at 100-kb resolution using Homer on the Hi-C data of WT and Smchd1-/- MEFs. Xa, comp (D0.ES) or cas (all others). Xi, mus.

treatment_protocol: To treat cells with 5-aza-2'-deoxycytidine (Aza, A3656, Sigma), MEFs were grown in MEF media containing either DMSO (control) or Aza (0.3μM), with media changed daily for 5 days. To deplete PRC1, MEFs were transfected with either scramble siRNAs (siGENOME Non-Targeting siRNA #1, D-001210-01, Dharmacon) or a mixture of siRNAs targeting RING1A (D-062335-03, Dharmacon) and RING1B (D-042180-01, Dharmacon) using Lipofectamine® RNAiMAX Transfection Reagent (13778075, Thermo Fisher Scientific) according to manufacturer's instructions. Transfection of siRNAs was performed once a day for 4 days.


title: RPL12 WT asynchronous cells rep1

description: 3'mRNAseq reads


title: RPL12 WT asynchronous cells rep2

description: 3'mRNAseq reads


title: RPL12 S38A asynchronous cells rep2

description: 3'mRNAseq reads


title: T47D-co EtOH(6hr)+IFN-alpha(18hr) rep2

city: San Antonio

first: Tianbao

last: Li

state: Texas

address: 7703 Floyd Curl

department: Molecular Medicine

institute: University of Texas Health Science Center at San Anotnio

data_processing:
RNA-seq reads per sample were mapped to the reference using Tophat v2.0.12
bam files sorted and indexed using Samtools1.2
Next, the mapped reads were processed using cufflinks v2.2.1 with the classic-fpkm library normalization method
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: FPKM normalized by Cufflinks

source_name: breast cancer cell line

growth_protocol: T47D cells were maintained in Minimum Essential Media (MEM; CellGro) supplemented with 5% FBS, 1% Penicillin/Streptomycin, 1% non-essential amino acids, and 6 ng/ml insulin (cMEM).

extract_protocol:
Trizol whole RNA extraction, as per manufacturer's protocol.
used as template to generate RNA-seq libraries for Illumina MiSeq sequencing

treatment_protocol: Cells were treated with interferon-alpha (20IU/ml IFNα for 18hrs) followed by 6hrs of EtOH or R5020 (10nM)

tag: agent

value: EtOH+IFN-alpha

value: T47D breast cancer cell line variants


title: T47D-co EtOH(6hr)+IFN-alpha(18hr) rep3


title: T47D-co EtOH(6hr)+IFN-alpha(18hr) rep1


title: T47D-co R5020(6hr)+water(18hr) rep2


title: T47D-co R5020(6hr)+water(18hr) rep1


title: T47D-co R5020(6hr)+IFN-alpha(18hr) rep3


title: T47D-co R5020(6hr)+IFN-alpha(18hr) rep2


title: T47D-co R5020(6hr)+water(18hr) rep3


title: T47D-co R5020(6hr)+IFN-alpha(18hr) rep1


title: HuKidney_WT_H3K27ac_rep1

city: Madison

first: Mark

middle: B

last: Meyer

state: WI

address: 1415 Linden Dr.

department: Nutritional Sciences

institute: University of Wisconsin-Madison

description: ChIP-DNA

data_processing:
ChIP-seq runs were all 100bp.  Barcoded samples were run over 4 lanes total and the fastq data were concatenated prior to Bowtie2 mapping.  12 barcoded samples were run in each lane, over 4 lanes total.  Barcodes were decoded by Illumina HiSeq2000 software automatically.  All samples were mapped from fastq files using Bowtie2 to hg19 [UCSC human genome build 19].  Triplicate lanes were analyzed separately for reproducibility and normalization of the peak calls.
Peaks were called by using MACS2. Peak finding for MACS2 was standard narrowPeak for TFs and broadPeak [--broad] for histones. Reported as bed files for narrowPeak and broadPeak files.
Peaks were called by using HOMER [http://biowhat.ucsd.edu/homer/]. HOMER also output the bedGraph files of read density for UCSC genome display. HOMER settings for peak finding were all standard settings.
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph files are suitable to display in the UCSC genome browser. *peaks.bed files were produced by HOMER. *narrowPeak files were produced by MACS2

source_name: adult human kidney cortex

extract_protocol:
Chromatin immunoprecipitation was performed as described previously (Meyer MB, JBC. 2017). Briefly, samples were subjected to immuno-precipitation using either a control IgG antibody or the indicated experimental antibody (VDR, pCREB, H3K4me1, or H3K27Ac).  The isolated DNA (or Input DNA acquired prior to precipitation) was then validated by quantitative real time PCR (qPCR) and further prepared for ChIP-seq analysis.
ChIP-seq libraries were prepared using the NEBNext DNA sample prep kit (NEB, #E6000L) with the Bioo NEXTflex ChIP-seq Barcodes (Bioo Scientific, Austin, TX, #514122) according to manufacturer’s protocols, with few exceptions.  During the NEBNext prep, the Illumina adapters were replaced with the Bioo Scientific Barcoded adapters according to Bioo protocols.  ChIP-DNA ligated libraries were cleaned up with Agencourt AMPureXP Magnetic Beads (Beckman-Coulter, #A63881).  A pre-size selection PCR was performed using Phusion polymerase, NEXTflex Primer Mix and purified ligation product for 4 cycles of PCR according to the Bioo Protocol.  Libraries were size selected using Invitrogen E-gels to a size of 400-500bp.  Samples were then PCR amplified for 14 cycles using Phusion polymerase, NEXTflex Primer mix and the size selected DNA as per Bioo protocol, followed by Agencourt bead clean up.  Libraries were validated for integrity using the Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA).  Clusters were formed and sequenced on the Illumina HiSeq2000 sequencers by the University of Wisconsin-Madison DNA Sequencing Facility in the University of Wisconsin-Madison Biotechnology Center.  DNA clusters were generated using a cBot Single Read Cluster Generation kit (ver.  3) on an Illumina cBot (Illumina, Carlsbad, CA) according to the manufacturer's instructions, to obtain an average of 1.5×108 clusters for each lane on a flowcell.  All sequencing runs for 100mers were performed on an Illumina HiSeq2000 using the Illumina Sequencing kit (ver.  3). Fluorescent images were analyzed using the CASAVA 1.8.2 (Illumina Carlsbad, CA) to obtain FASTQ formatted sequence data.  Twelve barcoded libraries were run per lane and this was repeated over 4 lanes.  After which, the raw FASTQ for each sample was concatenated from the 4 lanes prior to mapping to create a single sample.  The ChIP samples were repeated in biological triplicate. Sequences were mapped to the human genome (hg19) using BOWTIE (--best –m 1) to yield unique alignments.

tag: tissue

value: kidney cortex

tag: Sex

value: female

tag: antibody


title: HuKidney_WT_pCREB_rep2

description: ChIP-DNA

value: pCREB (EMD Millipore, 06-519, lot# 3108493)


title: HuKidney_WT_VDR_rep3

description: ChIP-DNA

value: VDR (Santa Cruz, C-20, sc-1008, lot# H1216)


title: HuKidney_WT_VDR_rep2

description: ChIP-DNA


title: HuKidney_WT_VDR_rep1

description: ChIP-DNA


title: HuKidney_WT_H3K4me1_rep2

description: ChIP-DNA


title: HuKidney_WT_H3K4me1_rep1

description: ChIP-DNA


title: HuKidney_WT_H3K27ac_rep3

description: ChIP-DNA


title: HuKidney_WT_pCREB_rep1

description: ChIP-DNA


title: HuKidney_WT_H3K4me1_rep3

description: ChIP-DNA


title: T47D-co EtOH(6hr)+water(18hr) rep2

value: EtOH+water


title: T47D-co EtOH(6hr)+water(18hr) rep3


title: T47D-co EtOH(6hr)+water(18hr) rep1


title: HuKidney_WT_Input

description: Input DNA


title: RPL12 S38A asynchronous cells rep1

description: 3'mRNAseq reads

tag: cell type


title: T47D-Y R5020(6hr)+IFN-alpha(18hr) rep3


title: T47D-Y R5020(6hr)+IFN-alpha(18hr) rep2


title: T47D-Y R5020(6hr)+IFN-alpha(18hr) rep1


title: T47D-Y EtOH(6hr)+IFN-alpha(18hr) rep3


title: T47D-Y EtOH(6hr)+IFN-alpha(18hr) rep1


title: T47D-Y R5020(6hr)+water(18hr) rep2


title: T47D-Y R5020(6hr)+water(18hr) rep1


title: HuKidney_WT_H3K27ac_rep2

description: ChIP-DNA


title: T47D-Y EtOH(6hr)+IFN-alpha(18hr) rep2


title: HuKidney_WT_pCREB_rep3

description: ChIP-DNA


title: T47D-Y EtOH(6hr)+water(18hr) rep3


title: T47D-Y EtOH(6hr)+water(18hr) rep2


title: T47D-Y R5020(6hr)+water(18hr) rep3


title: T47D-Y EtOH(6hr)+water(18hr) rep1


title: 80S_input_RPL12_WT1

data_processing:
Basecalls were converted to fastq files using Bcl2Fastq (v2.16.0.10). Next, the reads were demultiplexed and adapter sequences removed by Flexbar (v2.5) utilizing Illumina RPI index barcodes. Reads were then collapsed to remove PCR duplicates using collapse_reads.pl script (Jens, 2016; Lebedeva et al., 2011) and aligned to the human genome (version hg19) using the STAR aligner 2.4.2a with read counting mode enabled to obtain count tables. To account for the variability between input samples, we normalized the read counts by DESeq2-computed size factors (Love et al., 2014) obtained from ERCC spike-in read counts in the input samples. The same procedure was also applied to IP samples by using ERCC spike-in read counts from the IP samples. Next, pairwise comparisons of IP sample vs. input read counts were performed by DESeq2 using standard parameters. Log2-transformed fold changes provided in the DESeq2 output were used to quantify mRNA enrichment in IP vs. input.
Genome_build: hg19
Supplementary_files_format_and_content: txt files (read counts from STAR output)

source_name: HEK293 embryonic kidney cell line

growth_protocol: HEK293 cells (American Type Culture Collection) were cultured in Dulbecco’s modified Eagle’s medium (DMEM) (life technologies) complemented with glutamax (life technologies) and 10% fetal bovine serum (FBS) (PAN-Biotech).

extract_protocol:
Cycloheximide (50 µg/ml) was added to each pooled 80S fraction (1 ml) obtained by sucrose gradient fractionation. Aliquots of these input fractions were used for Western blot analysis (20 µl) and total RNA extraction with Trizol (50 µl). The rest of the sample was subjected to anti-FLAG immunoprecipitation. To prepare anti-FLAG conjugated magnetic beads, 15 µl of Dynabeads Protein G (Thermo Fisher Scientific) were used per sample, washed twice in 0.02 % of Tween 20/PBS (PBST) and resuspended in 30 µl of PBST containing 0.25 µg/µl anti-FLAG M2 monoclonal antibody (F3165, Sigma Aldrich). After a 1 hr incubation at room temperature with rotation, the beads were washed twice in PBST, resuspended into the fractionated sample, followed by incubation at 4 °C for 90 min. Next, the beads were concentrated and the supernatants removed, followed by 4 washing steps in 1 ml of washing buffer (0.05% (v/v) IGEPAL-CA630, 50 mM Tris pH 7.5, 150 mM KCl, 0.5 mM DTT, 50 µg/ml cycloheximide, 1x complete EDTA-free protease inhibitor cocktail (Roche)). Before concentrating the beads during the fourth washing step, 100 µl of suspension was removed for Western blot analysis, while the rest of the sample was used for RNA extraction.  After the concentration of beads and removal of the supernatant, the beads were either resuspended in 1 bead volume of 2x Laemmli sample buffer (Western analysis) or 1 ml of Trizol (RNA extraction). After standard Trizol extraction consisting of chloroform addition and centrifugation, the clean-up of the aqueous phase was carried out using miRNAeasy kit (Qiagen) according to manufacturer’s instruction.
Extracted RNA (either 1 µg of input samples or all of the immunoprecipitated material) was treated with 0.4 U Turbo DNase (Thermo Fisher) for 30 min at 37 ºC, phenol-chlorotorm extracted, ethanol-precipitated and resuspended in water. For input samples, equal amounts of total RNA (1 µg) and 2 µl of 1:100 dilution of ERCC Spike-in Control Mix 1 (Thermo Fisher) were mixed and adjusted to 50 µl final volume with water. All immunoprecipitated material per sample was mixed with 2 µl of 1:100 dilution of ERCC Spike-in Control Mix 1 and adjusted to 50 µl final volume with water. These 50-µl samples were then input into the Truseq stranded mRNA kit (Illumina) using 2 rounds of oligo-dT enrichment. Manufacturer's instructions were followed in all subsequent steps. cDNA libraries from different samples were multiplexed using Illumina RPI oligonucleotides and sequenced by multiplexing 6 samples per lane on a HiSeq 2000 instrument using 1x101+7 cycles.

treatment_protocol: RPL12 wild-type, S38A or S38D mutant coding sequences were recombined using LR Clonase II (Gateway, Thermo Fischer Scientific) into pFRT/TO/FLAG/HA-DEST (Addgene ID: 26360). The resulting vectors were used to generate stable HEK293 Flp-In T-Rex cells lines overexpressing FLAG/HA-tagged wild-type RPL12, or S38A and S38D RPL12 mutated proteins. Briefly, HEK293 Flp-In T-Rex cells were transfected in a 12-well format by mixing 100 µl of Opti-MEM with 1 µg of total plasmid DNA (9:1 ratio of pOG44 to destination vector) and 2 µl of Lipofectamine 2000 (Thermo Fischer Scientific). After a 5-minute incubation, the transfection mixture was added to the cells. Cells were re-seeded into 10-cm dishes after 48 hr and allowed to attach overnight. Hygromycin (100 µg/ml, InvivoGen) was added the next day and the cells were selected for 2-3 weeks by the addition of fresh hygromycin-containing cell culture media every 2-3 days resulting in expansion of monoclonal colonies.

value: embryonic kidney cell line; epithelial

tag: genotype/variation


title: 80S_input_RPL12_WT2


title: 80S_input_RPL12_S38D2


title: 80S_ip_RPL12_WT2

value: Mouse monoclonal anti-FLAG (M2) [Sigma-Aldrich, Cat# F3165 RRID:AB_259529]


title: 80S_ip_RPL12_S38D1


title: 80S_input_RPL12_S38D1


title: 80S_ip_RPL12_S38D2


title: 80S_ip_RPL12_S38A1


title: 80S_ip_RPL12_S38A2


title: 80S_ip_RPL12_WT1


title: 80S_input_RPL12_S38A1


title: Human glomeruli F14

city: Nanjing

first: Jingsong

last: Shi

state: China

address: No.305, Zhongshan East Road

department: National Clinical Research Center of Kidney Disease

country: China

institute: Jinling Hospital, Nanjing University School of Medicine

description: SST RMA expression value derived from Expression Console software

hyb_protocol: Array hybridization and washing was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US) in a Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and a Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Arrays were scanned by Affymetrix GeneChip® Scanner 3000 (Cat#00-00213, Affymetrix, Santa Clara, CA, US). Command Console Software (Affymetrix, Santa Clara, CA, US) was used to control the scanner and summarize probe cell intensity data (CEL file generation) with default settings.

data_processing: Raw data were processed with Expression Console software (Affymetrix) for background correction and normalization. Data analysis and statistical evaluations were performed with customized R codes (version 3.3.1, http://www.r-project.org/).

source_name: Focal Segmental glomerulosclerosis

label_protocol: Total RNA was amplified, labeled and purified by Ovation® Pico WTA System V2(Cat#3302, NuGEN, San Carlos, CA, US)and FL-Ovation™ cDNA Biotin Module V2(Cat#4200, NuGEN, San Carlos, CA, US) according to the manufacturer’s instructions to obtain biotin labeled cDNA.

growth_protocol: Kidney tissues were put into RNAlater (Ambion, Austin, TX) and stored at -80°C.

extract_protocol: Total RNA was extracted and purified using RNeasy micro kit(Cat#74004, QIAGEN, GmBH, Germany) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

treatment_protocol: Microdissection of glomeruli was performed manually under a stereomicroscope using two dissection needle holders in RNAlater at 4°C.

value: glomeruli


title: Human glomeruli F13

value: male


title: 80S_input_RPL12_S38A2

value: DMEM


title: Human glomeruli F15


title: Human glomeruli F11


title: Human glomeruli F10


title: Human glomeruli F20


title: M-MØ_siMAFB_donor3_rep1

city: Madrid

first: Ángel

middle: L

last: Corbí

state: Madrid

address: Ramiro de Maeztu, 9

department: Molecular Microbiology and Infection Biology

institute: Consejo Superior de Investigaciones Científicas

description: Gene expression in M-MØ after 24h of transfection with MAFB-specific siRNA

hyb_protocol: 1.65 ug of Cy3 labelled aRNA were hybridized for 17 hours at 65ºC in a hybridization oven (G2545A, Agilent) set to 10 rpm in a final concentration of 1X GEx Hybridization Buffer HI-RPM, according to manufacturer's instructions (One-Color Microarray-Based Gene Expression Analysis, Agilent Technologies).

scan_protocol: Arrays were scanned at 5um resolution on an Agilent DNA Microarray Scanner (G2565BA, Agilent Technologies) using the default settings for 4x44k format one-color arrays. Images provided by the scanner were analyzed using Feature Extraction software (Agilent Technologies).

data_processing: Data files from Feature Extraction were imported into GeneSpring® GX software version 9.0. (Agilent Technologies). Quantile normalization was performed and expression values (log2 transformed) were obtained for each probe.

source_name: siMAFB M-MØ Donor 3, replicate 1

label_protocol: For each sample, we have generated cyanine 3-labeled cRNA from one microgram of total RNA, using the Agilent Low RNA Input Linear Amplification Kit PLUS, One-Color. Briefly, total RNA is reverse-transcribed using T7-oligo (dT) primer; after first and second strand cDNA synthesis, cRNA is synthesized from the double-stranded cDNA using T7 RNA polymerase, which simultaneously incorporates cyanine 3.

growth_protocol: Human Peripheral Blood Mononuclear Cells (PBMC) were isolated from buffy coats from donors over a Lymphoprep gradient according to standard procedures. Monocytes were purified from PBMC by magnetic cell sorting using anti-CD14 microbeads (>95% CD14+ cells). Monocytes (0.5 x 106 cells/ml, >95% CD14+ cells) were cultured  in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) for 7 days in the presence of 10 ng/ml M-CSF to generate M-CSF-polarized macrophages (M-MØ).

extract_protocol: Total RNA was extracted using the NucleoSpin RNA/Protein kit (Macherey-Nagel, Düren, Germany). Qualitative analysis of total RNAs were performed in a bioanalizer Agilent 2100.

treatment_protocol: Macrophages were transfected with 50nM of either Control or MAFB-specific siRNA for 24h using HiPerFect (Qiagen)

tag: cells

value: Monocyte-derived M-CSF macrophages

tag: knockdown

value: MAFB-specific siRNA


title: M-MØ_siControl_donor1_rep1

description: Gene expression in M-MØ after 24h of transfection with Control siRNA

source_name: siControl M-MØ Donor 1, replicate 1

value: Control siRNA


title: M-MØ_siMAFB_donor2_rep1

source_name: siMAFB M-MØ Donor 2, replicate 1


title: Human glomeruli F12


title: Human glomeruli F03


title: M-MØ_siControl_donor3_rep1

source_name: siControl M-MØ Donor 3, replicate 1


title: Human glomeruli F18


title: Human glomeruli F16


title: Human glomeruli F04


title: Human glomeruli F17


title: Human glomeruli F19


title: Human glomeruli F09


title: M-MØ macrophage_healthy donor2_rep1

description: Gene expression in M-MØ derived from monocytes from a healthy donor

source_name: M-MØ Healthy Donor 2, replicate 1

extract_protocol: Total RNA was extracted using the NucleoSpin RNA/Protein kit (Macherey-Nagel, Düren, Germany).Qualitative analysis of total RNAs were performed in a bioanalyzer Agilent 2100

tag: disease

value: Healthy


title: M-MØ_siControl_donor2_rep1

source_name: siControl M-MØ Donor 2, replicate 1


title: Human glomeruli F08


title: M-MØ macrophage_MCTO donor1_rep2

description: Gene expression in M-MØ derived from monocytes from a donor with Multicentric Carpo Tarsal Osteolysis

source_name: M-MØ MCTO Donor 1, replicate 2

value: Multicentric Carpo Tarsal Osteolysis (MCTO)


title: Human glomeruli F06


title: M-MØ_siMAFB_donor1_rep1

source_name: siMAFB M-MØ Donor 1, replicate 1


title: Human glomeruli F07


title: P07_Day.Pre_PNK

first: Muneesh

last: Tewari

state: MI

address: 109 Zina Pitcher Pl

data_processing:
TruSeq sRNA adapter and STP oligo sequences were trimmed from reads using cutadapt (v1.91), filtering reads <15 nt.
Trimmed reads were aligned to several sequence databases provided with the sRNAnalyzer pipeline, including univec contaminates, small structural RNAs, microRNAs and bacterial sequences. Additional bowtie libraries were added to include RepeatMasker and SILVA rRNA libraries. sRNAnalyzer was thenrun using default parameters (allowing up to 2 mismatches), sequentially aligning to the sequence libraries using bowtie 1.
Reads not aligned during the previous stage were aligned to the human genome (GRCh38) using STAR. Parameters were altered to allow multi-mapping, disallow spliced alignments, and limit the extent of soft-clipped ends.
RepeatMasker coordinates (UCSC) and gencode small RNA coordinates (v27) were used to filter the genomic alignments. All alignments were removed for any read overlapping at least one RMSK or sRNA-annotated coordinate in either orientation.
Multi-mapping reads were weighted using a strategy similar to CSEM, and weighted reads aligning to mRNA or ncRNA exons were used to calcualte fragment abundances at the gene level.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delmited gene counts file contains multi-mapping-scaled read counts for Gencode (v27) mRNA and lncRNA genes, calculated from exon-aligning exRNA fragments after filtering repeat and structural small RNA reads.

source_name: platelet-poor blood plasma

extract_protocol:
Serial plasma sample from 2 patients undergoing allogeneic bone marrow transplantation were collected in 10-mL K2EDTA plasma tubes (Vacutainer 366643; Becton Dickinson) and processed within one hour of blood draw following a two centrifugation protocol to obtain platelet-poor plasma as previously described38: (i) 3,400 xg at room temperature for 10 minutes with high brake; and (ii) 1940 xg at room temperature for 10 minutes without brake. Plasma was stored at -80C until RNA isolation. RNA was isolated from 200 ul of plasma using the miRNeasy mini kit (Qiagen, Hilden, Germany)  according to the manufacturer’s protocol with the following modifications. Plasma samples were mixed with five sample volumes of QIAzol reagent and vortexed for 10 s. Samples in QIAzol were incubated at room temperature for 5 min to inactivate RNases. Next 0.2 volumes of chloroform were added to each sample. At that point, the manufacturer’s protocol was followed.
Untreated plasma sample libraries were prepared using 5 μl of  RNA.  RNA for Phospho-sRNA-seq plasma sample libraries were pretreated with T4 polynucleotide kinase (NEB, Ipswich, MA, US) using an RNA input of 7 ul in a final reaction volume reaction of 10 ul and following the manufacturer’s instructions. After the enzymatic treatment, biological RNA samples were purified by performing sequential washes in silica columns (Zymo, Irvine, CA, US): (i) 900 ul of buffer RWT (Qiagen, Hilden, Germany); (ii) 900 ul of buffer RPE (Qiagen, Hilden, Germany); (iii) 900 ul of ethanol 200 proof, molecular biology grade (Fisher Scientific, Waltham, MA, US) and; (iv) 900 ul of 80% ethanol. Standard ligation-based small RNA libraries were prepared from both untreated and PNK-treated RNA samples using the TruSeq small RNA kit (Illumina, San Diego, CA, US) according to the manufacturer’s instructions. Size selection was performed using pre-cast 6% acrylamide gels (Invitrogen, CarlsbadWaltham, CMA, US) including all products from 140-200 bp plus any additional visible bands of greater size

tag: treatment

value: PNK

tag: days from hsct


title: P07_Day.Pre_NoPNK

value: Untreated


title: P07_Day.7_PNK


title: Human glomeruli F05


title: M-MØ macrophage_healthy donor1_rep1

source_name: M-MØ Healthy Donor 1, replicate 1


title: Human glomeruli F02


title: M-MØ macrophage_MCTO donor1_rep1

source_name: M-MØ MCTO Donor 1, replicate 1


title: P07_Day.63_PNK


title: P07_Day.7_NoPNK


title: P07_Day.54_PNK


title: P07_Day.54_NoPNK


title: P07_Day.63_NoPNK


title: P07_Day.47_PNK


title: P07_Day.42_PNK


title: P07_Day.47_NoPNK


title: Human glomeruli N19

source_name: unaffected portion of tumor nephrectomies


title: Human glomeruli F01


title: P07_Day.35_PNK


title: P07_Day.42_NoPNK


title: Human glomeruli N15


title: Human glomeruli N17


title: Human glomeruli N08


title: Human glomeruli N12


title: Human glomeruli N10


title: Human glomeruli N18


title: P07_Day.35_NoPNK


title: P07_Day.22_PNK


title: P07_Day.29_PNK


title: P07_Day.29_NoPNK


title: Human glomeruli N13


title: Human glomeruli N07


title: P07_Day.22_NoPNK


title: Human glomeruli N16


title: Human glomeruli N20


title: P07_Day.14_PNK


title: P07_Day.0_PNK


title: P07_Day.14_NoPNK


title: Human glomeruli N14


title: MDA_MB_231_LM1_APC_2

city: Seoul

first: Chul Geun

last: Kim

address: wangsimni-ro 222

department: Life Science

country: South Korea

institute: Hanyang University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 whole genome using Bowtie2
Read count extraction and nomalization were performed using edgeR.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: MDA-MB-231 (LM1) cells

growth_protocol: MDA-MB-231 (LM1) cells were maintained in DMEM (HyClone, SH30243.01) supplemented with 10% fetal bovine serum (FBS; Cellsera. AU-FBS/PG) and 1% penicillin (Sigma Aldrich, P3032)/streptomycin (Sigma Aldrich, S9137).

extract_protocol:
RNA was harvested using QIAZOL reagent (QIAGEN). 400 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

treatment_protocol: Doxycycline was treated for 2 days as 1 μg·ml-1 in culture medium. Drug (ABA or APC) was treated for 2 days as 10 μM in culture medium

tag: cell types

value: Lung metastastic breast cancer cells

tag: cancer origin type

value: triple negative breast cancer

tag: doxycycline

tag: drug treat

value: APC 10 μM


title: MDA_MB_231_LM1_ABA_1

value: ABA 10 μM


title: Human glomeruli N11


title: MDA_MB_231_LM1_p66⍺_KD_2


title: Human glomeruli N05

value: female


title: P07_Day.0_NoPNK


title: Human glomeruli N04


title: MDA_MB_231_LM1_ABA_2


title: MDA_MB_231_LM1_p66⍺_KD_1


title: P04_Day.Pre_PNK


title: Human glomeruli N09


title: Human glomeruli N06


title: Human glomeruli N01


title: MDA_MB_231_LM1_WT2


title: Human glomeruli N03


title: MDA_MB_231_LM1_APC_1


title: MDA_MB_231_LM1_MBD2_KD_1


title: Human glomeruli N02


title: P04_Day.62_NoPNK


title: P04_Day.Pre_NoPNK


title: MDA_MB_231_LM1_WT1


title: P04_Day.62_PNK


title: P04_Day.6_NoPNK


title: 92

city: Toronto

first: Shraddha

last: Pai

state: ON

address: 160 College Street, Room 602

country: Canada

institute: University of Toronto

description: Ribo-depleted RNA

data_processing:
Base calling was done by Illumina NextSeq Control Software (NCS) v2.0 and output of NCS was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v1.9.0.
Trimgalore (v0.11.5) was used for adapter removal prior to genome alignment. STAR33 (v2.3.5a) index was generated using Ensemble GRCh38 p10 primary assembly genome and the Gencode v26 primary assembly annotation. Read alignment was performed using a STAR two-pass mode.
Gene counts matrix was imported into R (3.4.1) and low expressed genes (counts per million (CPM) < 1 in all samples) were removed prior to differential expression in EdgeR. Gene counts were normalized using the trimmed mean of M-values, fitted in a generalized linear model and differentially tested using a likelihood ratio test. The generalized linear model contained covariates age, sex, post mortem interval and neuronal cell composition.
Genome_build: hg38
Supplementary_files_format_and_content: SCZ_RNAseq_STAR_counts.csv - raw gene-level transcript counts per sample. CSV format

source_name: frontal cortex of the human brain

extract_protocol: none provided by the submitter

value: HCTYZ

tag: age

value: Male

tag: race

value: White

value: Control

tag: tissuebank

value: UM Brain Endowment Bank

tag: pmi


title: 94

description: Ribo-depleted RNA

value: HBDB

tag: Sex

value: Bipolar


title: P04_Day.6_PNK


title: P04_Day.55_PNK


title: P04_Day.48_PNK


title: 86

description: Ribo-depleted RNA

value: HCtWL


title: P04_Day.55_NoPNK


title: 87

description: Ribo-depleted RNA

value: HBDL

value: Female


title: 82

description: Ribo-depleted RNA

value: HCcPL


title: P04_Day.41_PNK

value: PNK


title: P04_Day.41_NoPNK

value: Untreated


title: P04_Day.34_NoPNK


title: 77

description: Ribo-depleted RNA

value: HSQ

value: Schizophrenia


title: P04_Day.27_PNK


title: P04_Day.27_NoPNK


title: 74

description: Ribo-depleted RNA

value: HCtWI


title: 80

description: Ribo-depleted RNA

value: HCtRP


title: P04_Day.20_PNK


title: MDA_MB_231_LM1_MBD2_KD_2

value: Lung metastastic breast cancer cells

value: triple negative breast cancer


title: P04_Day.13_PNK


title: P04_Day.20_NoPNK


title: 69

description: Ribo-depleted RNA

value: HCtDM

value: Male

value: White


title: 70

description: Ribo-depleted RNA

value: HQQ

value: UM Brain Endowment Bank


title: 88

description: Ribo-depleted RNA

value: HCtKN

value: Control


title: P04_Day.0_PNK


title: 73

description: Ribo-depleted RNA

value: HCtCR

value: Female


title: 66

description: Ribo-depleted RNA

value: HCtVB


title: P04_Day.13_NoPNK

value: Untreated


title: P04_Day.48_NoPNK


title: 58

description: Ribo-depleted RNA

value: HXN


title: 57

description: Ribo-depleted RNA

value: HTA

value: Black

value: Schizophrenia


title: 56

description: Ribo-depleted RNA

value: HCtTA


title: 81

description: Ribo-depleted RNA

value: HCtLI


title: PNK_Control_ULMC157_2

extract_protocol:
Plasma samples from 5 healthy donors and serial plasma sample from 2 patients undergoing allogeneic bone marrow transplantation were collected in 10-mL K2EDTA plasma tubes (Vacutainer 366643; Becton Dickinson) and processed within one hour of blood draw following a two centrifugation protocol to obtain platelet-poor plasma as previously described38: (i) 3,400 xg at room temperature for 10 minutes with high brake; and (ii) 1940 xg at room temperature for 10 minutes without brake. Plasma was stored at -80C until RNA isolation. RNA was isolated from 200 ul of plasma using the miRNeasy mini kit (Qiagen, Hilden, Germany)  according to the manufacturer’s protocol with the following modifications. Plasma samples were mixed with five sample volumes of QIAzol reagent and vortexed for 10 s. Samples in QIAzol were incubated at room temperature for 5 min to inactivate RNases. Next 0.2 volumes of chloroform were added to each sample. At that point, the manufacturer’s protocol was followed.
Untreated plasma sample libraries were prepared using 5 μl of  RNA.  RNA for Phospho-sRNA-seq plasma sample libraries were pretreated with T4 polynucleotide kinase (NEB, Ipswich, MA, US) using an RNA input of 7 ul in a final reaction volume reaction of 10 ul and following the manufacturer’s instructions. After the enzymatic treatment, biological RNA samples were purified by performing sequential washes in silica columns (Zymo, Irvine, CA, US): (i) 900 ul of buffer RWT (Qiagen, Hilden, Germany); (ii) 900 ul of buffer RPE (Qiagen, Hilden, Germany); (iii) 900 ul of ethanol 200 proof, molecular biology grade (Fisher Scientific, Waltham, MA, US) and; (iv) 900 ul of 80% ethanol. Standard ligation-based small RNA libraries were prepared from both untreated and PNK-treated RNA samples using the TruSeq small RNA kit (Illumina, San Diego, CA, US) according to the manufacturer’s instructions. Size selection was performed using pre-cast 6% acrylamide gels (Invitrogen, CarlsbadWaltham, CMA, US) including all products from 140-200 bp plus any additional visible bands of greater size


title: P04_Day.0_NoPNK


title: P04_Day.34_PNK

value: PNK


title: 75

description: Ribo-depleted RNA

value: HCcFH

value: Male


title: PNK_Control_ULMC157_3


title: PNK_Control_ULMC157_1


title: 39

description: Ribo-depleted RNA

value: White

value: Bipolar

value: Harvard HBTRC


title: PNK_Control_ULMC148_3


title: 38

description: Ribo-depleted RNA


title: 72

description: Ribo-depleted RNA

value: HCcKT

value: UM Brain Endowment Bank


title: PNK_Control_ULMC148_1

value: Female


title: 41

description: Ribo-depleted RNA


title: PNK_Control_ULMC148_2


title: 31

description: Ribo-depleted RNA

value: Control


title: 79

description: Ribo-depleted RNA

value: HCtQX


title: 25

description: Ribo-depleted RNA


title: PNK_Control_ULMC135_2


title: 33

description: Ribo-depleted RNA


title: 21

description: Ribo-depleted RNA

value: Sepulveda


title: PNK_Control_ULMC134_3


title: PNK_Control_ULMC134_2


title: PNK_Control_ULMC134_1


title: 20

description: Ribo-depleted RNA


title: 9

description: Ribo-depleted RNA


title: PNK_Control_ULMC123_2


title: 2

description: Ribo-depleted RNA


title: 4

description: Ribo-depleted RNA


title: Untreated_Control_ULMC157_3

description: ULMCControls_Control157plasmaUntreatedRep3


title: Untreated_Control_ULMC157_2

description: ULMCControls_Control157plasmaUntreatedRep2


title: PNK_Control_ULMC123_1


title: Untreated_Control_ULMC157_1

description: ULMCControls_Control157plasmaUntreatedRep1


title: PNK_Control_ULMC135_1


title: Untreated_Control_ULMC148_3

description: ULMCControls_Control148plasmaUntreatedRep3


title: 15

description: Ribo-depleted RNA


title: Untreated_Control_ULMC148_2

description: ULMCControls_Control148plasmaUntreatedRep2


title: 27

description: Ribo-depleted RNA

value: unknown


title: PNK_Control_ULMC135_3


title: TG_FUS_9wk, 4

city: Moscow

first: Alexander

middle: Pertovich

last: Rezvykh

state: Moscow

address: Vavilova, 32

department: Russian Academy of Sciences

country: Russia

institute: Engelhardt Molecular Biology Institute

data_processing:
Read trimming were performed by Trimmomatic
Reads obtained were aligned to rererence genome (GRCm38) using STAR genome aligner (v 2.5.0a)
Read counting were preformed by featureCounts (v1.5.0-p1)
Genome_build: GRCm38
Supplementary_files_format_and_content: text files generated by featureCounts: GeneID; count number per gene

source_name: Spinal cord

extract_protocol:
Total RNA was extracted from thoracic spinal cord of 9 weeks old male mice using RNeasy Plus Mini Kit with genomic DNA eliminator columns (Qiagen).
cDNA libraries for the dual indexed single-end sequence analysis were prepared from equal amounts (270 ng) of each total RNA sample using Illumina TruSeq Stranded Total RNA LT Sample Prep Kit. Following libraries’ quality checks and normalisation, cDNA libraries were sequenced on Illumina NextSeq 500 to generate single end 75 bp reads.

tag: strain

value: 9 weeks

value: transgenic FUS

value: male


title: WT_9wk,4

value: wild-type


title: TG_FUS_9wk, 2


title: TG_FUS_9wk, 1


title: Untreated_Control_ULMC135_2

description: ULMCControls_Control135plasmaUntreatedRep2


title: Untreated_Control_ULMC135_3

description: ULMCControls_Control135plasmaUntreatedRep3


title: PNK_Control_ULMC123_3


title: 10

description: Ribo-depleted RNA


title: WT_9wk,2


title: Untreated_Control_ULMC148_1

description: ULMCControls_Control148plasmaUntreatedRep1


title: Untreated_Control_ULMC135_1

description: ULMCControls_Control135plasmaUntreatedRep1


title: WT_9wk,3


title: Untreated_Control_ULMC134_3

description: ULMCControls_Control134plasmaUntreatedRep3


title: Untreated_Control_ULMC134_2

description: ULMCControls_Control134plasmaUntreatedRep2