title: RatEO_H3K4me3

city: Bethesda

first: Hong-wei

last: Sun

state: MD

address: 9000 Rockville Pile

department: Office of Science & Technology

institute: NIAMS

data_processing:
Sequence reads were obtained and mapped to the mouse rn5 genomes using Bowtie 1.1.2. All reads mapping with two or fewer mismatches were retained.
Peak detection was performed with MACS 1.4.2 using Input as control and p-value threshold as 1e-5.
Bedgraph files where genrated using Homer
Genome_build: rn5
Supplementary_files_format_and_content: bedgraph files contain the signal for each sequence experiment, the bed files contain the regions of the called peaks

source_name: Rat enamel organ

extract_protocol:
Dissected enamel organs were chemically cross linked by 1% formaldehyde. Cell lysates were made by appropriate sonication and protein-DNA complexes were isolated with antibodies.
Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired and the blunt, phosphorylated ends were treated with Taq polymerase and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation, DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on HiSeq 2000 or 2500 following the manufacturer's protocols.

value: enamal organ

tag: genotype/variation

value: wildtype

tag: developmental stage

value: adult

tag: chip antibody


title: PS16.14.03

status: Public on Feb 11 2020

type: SRA

city: New York

first: Jennifer

last: Chan

state: New York

address: 1470 Madison Ave, Hess 9-201

department: Neuroscience

country: USA

institute: Icahn School of Medicine at Mount Sinai

description: NormalizedHumanSpermMirs.csv

library_source: transcriptomic

data_processing:
Reads were trimmed at the 3’ end to remove any trailing adaptor sequence using the Trimmomatic tool.
After read trimming, reads shorter than 15 bp were discarded before downstream analyses.
Trimmed reads were then aligned to the human reference genome build GRCh38 using the Bowtie short read aligner, allowing for 2 mismatches and a seed length of 15. The expression of each known miRNA from miRbase v22 were computed using HTSeq python.
Genome_build: GRCh38
Supplementary_files_format_and_content: Comma separated values file containing log2 normalized abundance measures
Genome_build: GRCm38.p6
Genome_build: GRCh38

molecule: total RNA

organism: Homo sapiens

source_name: Sperm

extract_protocol:
Cryopreserved sperm samples were thawed, suspended in PureSperm Buffer (Nidacon), then mature sperm were enriched by centrifugation (300 g, 15 min) through a 50% PureSperm density gradient (Nidacon). Sperm were then lysed in TRIzol-LS (Thermo Fisher) reagent, supplemented with 0.2 M β-mercaptoethanol and 100 mg of nuclease-free stainless-steel beads, by homogenization on a Disruptor Genie (Scientific Industries) at 3000 rpm for 5 min. RNA, enriched for small RNA, was isolated using Qiagen’s miRNeasy Mini kit according to manufacturer’s instructions.
Libraries were constructed using the TruSeq small RNA Library Prep Kit (Illumina) with 10 ng of small RNA according to the manufacturer’s protocol. Post-PCR cleanup and size selection for products > 100 bp was performed using AMPure XP bead purification. Library size distribution and quantification was performed using on a TapeStation 4200 (Agilent) using their High Sensitivity D1000 screentape. Individually barcoded libraries were pooled to achieve ~10 million reads per sample and sequenced on an Illumina NextSeq 550 (36-bp single-end).

tag: subject

tag: collection

tag: stress category

value: Stable-stress


title: ATAC-seq_DP_BL6_Rep1B_3T

city: Philadelphia

first: Naomi

last: Goldman

state: PA

address: 324 BRB II/III, 421 Curie Blvd

institute: University of Pennsylvania

library_source: genomic

data_processing:
ATAC-seq libraries were pair-end sequenced by Illumina NextSeq 500. Bowtie2 was used for alignment. In NOD mice, aligned reads were shifted to BL6 coordinates with MMARGE (PMID: 29893919) utilizing the NOD VCF files (version 5) from the Mouse Genomes Project (PMID: 21921910). Reads aligned to the mitochondrial genome or chrY as well as reads mapping to multiple genomic loci were discarded from downstream analyses. Additionally, Picard was used to mark and remove duplicates. Furthermore, for each ATAC-seq library the insert size was calculated by Picard.
Genome_build: GRCm38
Supplementary_files_format_and_content: Bigwig files were generated by bedtools genomecov and wigToBigWig normalizing tracks to tags-per-million

molecule: genomic DNA

organism: Mus musculus

source_name: CD4+ CD8+ thymocytes

extract_protocol:
ATAC-seq was performed as previously described with minor modifications (Buenrostro et al., 2013). Fifty thousand cells were pelleted at 550 x g and washed with 1 mL 1x PBS, followed by treatment with 50 μL lysis buffer (10 mM Tris-HCl [pH 7.4], 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). After pelleting nuclei, the pellets were resuspended in 50 μL transposition reaction with 2.5 μL Tn5 transposase (FC-121-1030; Illumina). The reaction was incubated in a 37°C water bath for 45 minutes. Tagmented DNA was purified using a MinElute Reaction Cleanup Kit (Qiagen) and amplified with varying cycles, depending on the side reaction results. Libraries were purified using a QIAQuick PCR Purification Kit (Qiagen).
Libraries were paired-end sequenced (38bp+38bp) on a NextSeq 550 (Illumina). Libraries were validated for quality and size distribution using a TapeStation 2200 (Agilent).

treatment_protocol: Thymi of mice were dissociated through a 70µM mesh filter (Falcon) in RPMI 1640 (Corning) with 1% FBS (Sigma-Aldrich), and single cell suspensions were stained with 7AAD (Biolegend) for live cell distinction, as well as PE CD4 (RM404) and APC CD8a (53-6.7) for double-positive CD4+ CD8+ T cell isolation. Sorting was performed on FACS Aria II (BD Biosciences), with forward scatter–height by forward scatter–width and side scatter–height by side scatter–width parameters being used to exclude doublets. Purity was verified after sorting.

tag: tissue

value: Thymus

tag: strain


title: ATAC-seq_DP_NOD_Rep1B_3T

value: NOD/ShiLtJ


title: PS16.14.02

description: NormalizedHumanSpermMirs.csv


title: PS16.14.04

description: NormalizedHumanSpermMirs.csv


title: RatEO_DLX3

organism: Rattus norvegicus


title: PS16.12.05

description: NormalizedHumanSpermMirs.csv

value: Recovering-stress


title: PS16.18.05

description: NormalizedHumanSpermMirs.csv


title: PS16.12.06

description: NormalizedHumanSpermMirs.csv


title: PS16.12.01

description: NormalizedHumanSpermMirs.csv


title: PS16.12.03

description: NormalizedHumanSpermMirs.csv


title: PS16.12.04

description: NormalizedHumanSpermMirs.csv


title: PS16.18.01

description: NormalizedHumanSpermMirs.csv


title: HC 1a

city: Beijing

first: Yu

last: Peng

address: No. 1, Shuaifu yuan

country: China

institute: Peking Union Medical College Hospital

data_processing:
Firstly, ribosomal RNA was removed by Epicentre Ribo-zero rRNA Removal Kit (Epicentre, USA), and rRNA free residues was cleaned up by ethanol precipitation. Subsequently, sequencing libraries were generated using the rRNA-depleted RNA by NEBNext Directional RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations.
Then, we used the Qubit RNA Assay Kit and Qubit 2.0 Flurometer (Life Technologies, CA, USA) to quantify RNAs.
RNA integrity was assessed using the RNA Mano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
The libraries were sequenced on an Illumina Hiseq 2500 platform and 125 bp paired-end reads were generated.
Genome_build: HISAT2
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: Peripheral blood mononuclear cells

extract_protocol:
Peripheral blood (10 mL) was obtained from each subject and all the samples were collected in the ethylene diamine tetraacetic acid (EDTA) tubes. Peripheral blood mononuclear cells (PBMCs) were isolated using the Ficoll density gradient centrifugation and were counted using Cellometer Auto T4 (Nexcelom Bioscience, USA).Total RNA was extracted using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) and the concentration of total RNA was measured by NanoDrop2000c spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: condition

value: healthy control


title: HC 2


title: SS 4a

value: Sjogren's syndrome


title: SS 2


title: SS 3


title: HC 5a


title: PS16.11.04

description: NormalizedHumanSpermMirs.csv


title: SS 5


title: PS16.11.05

description: NormalizedHumanSpermMirs.csv


title: HC 3


title: SS 1


title: PS16.11.03

description: NormalizedHumanSpermMirs.csv


title: PS16.12.02

description: NormalizedHumanSpermMirs.csv


title: RatEO_INPUT


title: PS16.14.01

description: NormalizedHumanSpermMirs.csv


title: HC 4


title: PS16.11.01

description: NormalizedHumanSpermMirs.csv


title: PS16.07.06

description: NormalizedHumanSpermMirs.csv


title: HD-mesenchymal stem cell- conditioned monocytes, rep2

city: Minneapolis

first: Jeffrey S

last: Miller

state: MN

address: 420 Delaware St. SE

institute: University of Minnesota

description:
DGE CD33-MSC HD vs CD33-MDS MSC GEO
443CD33T131440

data_processing:
Raw sequence that passed CASAV 1.8P/F filter were assessed by fastqc (http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Read mapping was performed via Bowtie2 (2.2.4.0) using the human genome (hg19) as a reference.
Cuffdiff 2.2.1 was used to quantify the expression level of each known gene in units of FPKM (fragment mapped per kilobase of exons per million mapped reads)
Differentially expressed genes were identified using the edgeR (negative binomial) feature in CLCGWB (Qiagen, Redwood city, CA) using raw read counts.
Genome_build: hg19
Supplementary_files_format_and_content: raw read counts, FPKMs, diffex

growth_protocol: MSCs were cultured in α-MEM for 4 passages before RNA isolation.

extract_protocol:
RNA was extracted using the RNAeasy Kit from Qiagen
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Monocytes were co-cultured with HD or MDS-MSCs prior to bead re-isolation and later RNA isolation.

tag: disease state

value: healthy donor

tag: cell type

value: Monocytes

tag: growth protocol

value: co-cultured with MSCs

tag: isolation

value: Bead-sorted

tag: marker


title: HD-mesenchymal stem cell- conditioned monocytes, rep1

description:
DGE CD33-MSC HD vs CD33-MDS MSC GEO
438CD33T131580


title: PS16.07.05

description: NormalizedHumanSpermMirs.csv


title: MDS-mesenchymal stem cell- conditioned monocytes, rep4

description:
DGE CD33-MSC HD vs CD33-MDS MSC GEO
438CD33MSC1250038

value: MDS


title: HD-mesenchymal stem cell- conditioned monocytes, rep3

description:
DGE CD33-MSC HD vs CD33-MDS MSC GEO
443CD33T131580


title: PS16.07.04

description: NormalizedHumanSpermMirs.csv


title: PS16.07.03

description: NormalizedHumanSpermMirs.csv


title: PS16.07.01

description: NormalizedHumanSpermMirs.csv


title: HD-mesenchymal stem cell- conditioned monocytes, rep4

description:
DGE CD33-MSC HD vs CD33-MDS MSC GEO
443CD33T1313281


title: PS16.07.02

description: NormalizedHumanSpermMirs.csv


title: PS16.05.06

description: NormalizedHumanSpermMirs.csv


title: PS16.05.05

description: NormalizedHumanSpermMirs.csv


title: Bone marrow mesenchymal cells from hip bone replacement patients, rep5

description:
DGE MDS-MSC vs HD-MSC GEO
T131580

value: Mesenchymal stem cells

value: cultured MSCs (adherent cells)


title: MDS-mesenchymal stem cell- conditioned monocytes, rep1

description:
DGE CD33-MSC HD vs CD33-MDS MSC GEO
443CD33MSC9150071


title: Bone marrow mesenchymal cells from hip bone replacement patients, rep2

description:
DGE MDS-MSC vs HD-MSC GEO
T131565


title: PS16.05.02

description: NormalizedHumanSpermMirs.csv


title: Bone marrow mesenchymal cells from hip bone replacement patients, rep1

description:
DGE MDS-MSC vs HD-MSC GEO
T132023


title: PS16.05.01

description: NormalizedHumanSpermMirs.csv


title: PS16.11.02

description: NormalizedHumanSpermMirs.csv


title: Bone marrow mesenchymal cells from MDS patients, rep5

description:
DGE MDS-MSC vs HD-MSC GEO
9150320


title: PS16.02.06

description: NormalizedHumanSpermMirs.csv


title: Bone marrow mesenchymal cells from MDS patients, rep4

description:
DGE MDS-MSC vs HD-MSC GEO
1250038


title: MDS-mesenchymal stem cell- conditioned monocytes, rep3

description:
DGE CD33-MSC HD vs CD33-MDS MSC GEO
443CD33MSC1250056


title: PS16.02.02

description: NormalizedHumanSpermMirs.csv


title: PS16.02.03

description: NormalizedHumanSpermMirs.csv


title: Bone marrow mesenchymal cells from MDS patients, rep1

description:
DGE MDS-MSC vs HD-MSC GEO
9150318


title: Bone marrow mesenchymal cells from hip bone replacement patients, rep4

description:
DGE MDS-MSC vs HD-MSC GEO
T1313281


title: Bone marrow mesenchymal cells from MDS patients, rep2

description:
DGE MDS-MSC vs HD-MSC GEO
9150071


title: PS16.05.03

description: NormalizedHumanSpermMirs.csv


title: Bone marrow mesenchymal cells from hip bone replacement patients, rep3

description:
DGE MDS-MSC vs HD-MSC GEO
T131440


title: PS16.02.01

description: NormalizedHumanSpermMirs.csv


title: PS16.01.06

description: NormalizedHumanSpermMirs.csv


title: PS16.01.05

description: NormalizedHumanSpermMirs.csv


title: PS16.02.04

description: NormalizedHumanSpermMirs.csv


title: PS16.01.04

description: NormalizedHumanSpermMirs.csv


title: all_Jurkat_rep1_nostim_gDNA

city: Cambridge

first: Carl

middle: G

last: de Boer

state: MA

address: 415 Main St

institute: The Broad Institute

data_processing:
A bowtie index of the ordered probe sequences and 16Ns for the barcode was created and the long reads for mapping barcodes to enhancers aligned to this index using Bowtie2. Associated barcodes were extracted and classified into those that map uniquely to a specific error-free probe, and those that do not (probe_barcode_association_3.4E6_2.map.gz).
MPRA RNA output and DNA input sequencing reads were mapped to the known tag sequences using a custom python script (quantifyRNATags.py), allowing for up to four mismatches within the constant region (the common sequence before the tag sequence) and no mismatches within the tag sequence.
The barcode counts were input, and tags having fewer than 30 reads in the input (DNA) or 4 reads in the output (RNA) were excluded from subsequent analysis.
The log(DNA/RNA) ratio (“expression”) was calculated using raw counts, scaled so that the median expression is 0, and the expression levels G+C-content normalized such that the mean expression for every %G+C was 0.
Finally, to eliminate instances where the tag sequence modifies the apparent expression level, any tags containing any one of eight blackballed 5-mer DNA sequences were excluded. Blackballed 5-mers were defined as those for which the absolute value of the average expression level of all tags containing that 5-mer was greater than 0.15.
SNPs were tested for allele-specific reporter activity by a two-sided Student’s t-test, comparing the normalized log(RNA/DNA) expression values for the tags for allele A compared to the tags for allele B. Only SNPs for which we had at least 80 good tags between the two alleles were tested. P-values were corrected for multiple hypothesis testing by Benjamini-Hochberg FDR correction. Only SNPs that had an FDR<0.1 for at least two of the replicates and where the direction of allele- specific reporter activity was consistent between all replicates were considered to be significant.
Genome_build: hg19
Supplementary_files_format_and_content: gzipped tab delimited or fasta; barcodes for each element, enhancer sequences

source_name: T lymphocyte from acute T cell leukemia

growth_protocol: BJAB, Jurkat, U937, and GM12878 cell lines were cultured using RPMI 1640 (ThermoFisher, 21870092) containing 10% fetal bovine serum (FBS, VWR, 97068-091; 20% for GM12878) with 1% Penn/strep (VWR, 45000-652), 1% L-Glutamine (ThermoFisher, 25030081), and 1% HEPES (Sigma, H0887-100ML). Cells were maintained at a culture density between 100K-1M cells/mL.

extract_protocol:
Total RNA was extracted from cells using Qiagen Maxi RNeasy (Qiagen, 75162) following the manufacturer’s protocol including the on-column DNase digestion. A second DNase treatment was performed on the purified RNA using 5 μL of Turbo DNase (Life Technologies, AM2238) with buffer, in 750 μL of total volume for 1 hour at 37°C. The digestion was stopped with the addition of 7.5 μL 10% SDS and 75 μL of 0.5M EDTA followed by a 5 minute incubation at 70°C. The total reaction was then used for pulldown of GFP mRNA. Water was added to the DNase digested RNA to bring the total volume to 898 μL to which 900 μL of 20X SSC (Life Technologies, 15557-044), 1800 μL of Formamide (Life Technologies, AM9342) and 2 μL of 100 uM biotin-labeled GFP probe (GFP_BiotinCapture_1-3, IDT, Ext. Data Table 10) were added and incubated for 2.5 hours at 65°C. Biotin probes were captured using 400 μL of pre- washed Streptavidin beads (Life Technologies, 65001) eluted in 500 μL of 20X SSC. The hybridized RNA/probe bead mixture was agitated on a nutator at room temperature for 15 minutes. Beads were captured by magnet and washed once with 1x SSC and twice with 0.1x SSC. Elution of RNA was performed by the addition of 25 μL water and heating of the water/bead mixture for 2 minutes at 70°C followed by immediate collection of eluent on a magnet. A second elution was performed by incubating the beads with an additional 25 μL of water at 80°C. A final DNase treatment was performed in 50 μL total volume using 1 μL of Turbo DNase with addition of the buffer incubated for 60 minutes at 37°C followed by inactivation with 1 μL of 10% SDS and purification using RNA clean SPRI beads (Beckman Coulter, A63987).
First-strand cDNA was synthesized from half of the DNase-treated GFP mRNA with SuperScript III and a primer specific to the 3’ UTR (MPRA_v3_Amp2Sc_R) using the manufacturer’s recommended protocol, modifying the total reaction volume to 40 μL and performing the elongation step at 47°C for 80 minutes. Single-stranded cDNA was purified by SPRI and eluted in 30 μL EB.  To minimize amplification bias during the creation of cDNA tag sequencing libraries, samples were amplified by qPCR to estimate relative concentrations of GFP cDNA using 1 μL of sample in a 10 μL PCR reaction containing 5 μL Q5 NEBNext master mix, 1.7 μL Sybr green I diluted 1:10,000 (Life Technologies, S-7567) and 0.5 uM of TruSeq_Universal_Adapter and MPRA_Illumina_GFP_F primers (Ext. Data Table 10). Samples were amplified with the following qPCR conditions: 95°C for 20 seconds, 40 cycles (95°C for 20 sec, 65°C for 20 sec, 72°C for 30 sec), 72°C for 2 min. The number of cycles for sample amplification was 1-n (the number of cycles it took for each sample to pass the threshold) from the qPCR. To add Illumina sequencing adapters, 10  uL of cDNA samples and mpra:pTNFAIP3:gfp plasmid control (diluted to the qPCR cycle range of the samples) were amplified using the reaction conditions from the qPCR scaled to 50 uL, excluding Sybrgreen I. Amplified cDNA was SPRI purified and eluted in 40 μL of EB. Individual sequencing barcodes were added to each sample by amplifying the entire 40 μL elution in a 100 μL Q5 NEBNext reaction with 0.5 uM of TruSeq_Universal_Adapter primer and a reverse primer containing a unique 8 bp index (Illumina_Multiplex, Ext. Data Table 10) for sample demultiplexing post-sequencing. Samples were amplified at 95°C for 20 seconds, 6 cycles (95°C for 20 sec, 64°C for 30 sec, 72°C for 30 sec), 72°C for 2 minutes. Indexed libraries were SPRI purified and pooled according to molar estimates from Agilent TapeStation quantifications. Samples were sequenced using 1x30 bp chemistry on an Illumina HiSeq 2500 or NextSeq.   To determine oligo/barcode combinations within the MPRA pool, Illumina libraries were prepared from the mpra∆orf plasmid library by performing 4 separate amplifications with 200 ng of plasmid in a 100 μL Q5 NEBNext PCR reaction containing 0.5 uM of TruSeq_Universal_Adapter and MPRA_v3_TruSeq_Amp2Sa_F primers with the following conditions: 95°C for 20 sec, 6 cycles (95°C for 20 sec, 62°C for 15 sec, 72°C for 30 sec), 72°C for 2 minutes. Amplified material was SPRI purified using a 0.6x bead/sample ratio and eluted with 30 μL of EB. Sequencing indexes were then attached using 20 μL of the eluted product and the same reaction conditions as for the tag-seq protocol, except the number of enrichment cycles was lowered to 5. Samples were molar pooled and sequenced using 2x150 bp chemistry on Illumina HiSeq 2500 and NextSeq.
MPRA library preparation

treatment_protocol: Jurkat T cells were stimulated with 2.5 ug/mL of anti-CD3 (Biolegend, 317304) and 10 ng/mL of PMA (Sigma, P1585-1MG) for 1 hour prior to harvesting. BJAB and GM12878 B cells were stimulated with 2.5 ug/ml of anti-IgM and 2 ug/ml anti-CD40 for 2 hours. U937 monocytes were stimulated with 100 ng/mL LPS for 2 hours.

tag: stim condition

tag: cell line

value: Jurkat

tag: vector delivery

value: lentiviral transduction

tag: replicate


title: MPRAv2_U937_unstim_rep2

source_name: monocyte from histiocytic lymphoma


title: MPRAv2_U937_stim_rep1

value: 100ng/mL LPS


title: PS16.01.03

description: NormalizedHumanSpermMirs.csv


title: PS16.01.02

description: NormalizedHumanSpermMirs.csv


title: PS16.01.01

description: NormalizedHumanSpermMirs.csv


title: Bone marrow mesenchymal cells from MDS patients, rep3

description:
DGE MDS-MSC vs HD-MSC GEO
9150180


title: U937_4

data_processing:
align reads using bowtie2 to hg19 (bowtie2 --maxins 2000 -x hg19)
remove duplicates and collect insert sizes using picard (java -Xmx2g -jar picard.jar MarkDuplicates REMOVE_DUPLICATES=true; java -jar picard.jar CollectInsertSizeMetrics)
create bed files from bam files (bedtools bamtobed)
convert to cut sites marking start of F read and end of R read
remove mitochondrial reads
create bedgraph (bedtools genomecov -bg -5)
create bigwig (bedGraphToBigWig)
call peaks using homer (makeTagDirectory/findPeaks -style dnase)
Genome_build: hg19
Supplementary_files_format_and_content: bed files containing peak calls and bigwig (bw) files

growth_protocol: BJAB, Jurkat, U937, and THP-1 cell lines were cultured using RPMI 1640 (ThermoFisher, 21870092) containing 10% fetal bovine serum (FBS, VWR, 97068-091; 20% for GM12878) with 1% Penn/strep (VWR, 45000-652), 1% L-Glutamine (ThermoFisher, 25030081), and 1% HEPES (Sigma, H0887-100ML). Cells were maintained at a culture density between 100K-1M cells/mL.

extract_protocol:
We used the previously described FAST-ATAC protocol49. 10,000-20,000 cells were sorted into RPMI 1640 containing 10% fetal bovine serum. The cells were centrifuged at 500g for 5 minutes at 4C. All of the supernatant was aspirated, ensuring that the pellet was not disturbed. The pellet was then resuspended in the tagmentation reaction mix (25 uL 2X TD Buffer (Illumina, 15027866), 2.5 uL TD Enzyme (Illumina, 15038061), 0.5 uL 1% Digitonin (Promega, G9441), 22 uL H2O) and shaken at 300 RPMs at 37C for 30 minutes on an Eppendorf Thermomixer. Immediately after the incubation, samples were purified using a minElute kit (Qiagen, 28006), eluting in 10 uL. The entire sample was PCRed (a 50 uL reaction with 25 uL NEBNext, 2.5 uL F+R custom nextera primers (10 uM each; Ext. Data Table 10), 10 uL of tagmented DNA, and 12.5 uL H2O) for 5 cycles with the following program (72C, 5 minutes; 98C, 30 seconds; 5 cycles of 98C, 15 seconds, 63C, 15 seconds, 72C, 1 minute). 5 uL of the sample was qPCRed to determine the number of additional cycles required, while the rest remained on ice.
The 5ul of sample was added to a qPCR mix (5 uL of PCR, 5ul of NEBNext, 0.5 uL F+R custom nextera primers, 0.09 uL of 100X SYBR (Invitrogen, S7563), 4.41 uL H2O) and qPCRed (98C, 30 seconds; 20 cycles of 98C, 15 seconds, 63C, 15 seconds, 72C, 1 minute). The number of cycles that it took to reach ⅓ the maximum fluorescence threshold in the qPCR was then applied via PCR to the original PCR sample. Libraries were cleaned using 1.5X Agencourt XP beads and ethanol washes per manufacturer's protocol. The DNA concentration of the sample was measured using Qubit and the average fragment size was determined using a TapeStation. Samples were then multiplexed and sequenced using 50 bp paired end chemistry at an average read-count of 30M reads per sample.

treatment_protocol: Cells were maintained at a culture density between 100K-1M cells/mL. Jurkat T cells were stimulated with 2.5 ug/mL of anti-CD3 (Biolegend, 317304) and 10 ng/mL of PMA (Sigma, P1585-1MG) for 0, 1, or 4 hours prior to harvesting. BJAB B cells were stimulated with 2.5 ug/ml of anti-IgM and 2 ug/ml anti-CD40 for 0, 1, and 4 hours. THP-1 and U937 monocytes were stimulated with 100 ng/mL LPS for 0, 1, and 4 hours.

tag: stimulation time (h)

tag: stimulation condition

value: 100 ng/ml LPS


title: MPRAv2_Jurkat_stim_rep1

value: 2.5ug/ml anti-CD3 + 50 ng/ml PMA 1 hour


title: U937_1


title: MPRAv2_U937_stim_rep2


title: MPRAv2_Jurkat_stim_rep2


title: MPRAv2_U937_unstim_rep1


title: MPRAv2_BJAB_unstim_rep1

source_name: Human Burkitt lymphoma B cell line.

value: BJAB


title: MPRAv2_BJAB_stim_rep1

value: 2.5ug/ml anti-IgM + 2.0 ug/ml anti-CD40 2 hours


title: MPRAv2_BJAB_stim_rep2


title: U937_0


title: MPRAv2_Jurkat_unstim_rep2


title: Jurkat_4

value: 2.5ug/ml anti-CD3 + 50 ng/ml PMA


title: Jurkat_1


title: MPRAv2_Jurkat_unstim_rep1


title: BJAB_1

value: 2.5ug/ml anti-IgM + 2.0 ug/ml anti-CD40


title: BJAB_4


title: CRISPRi_U937_FF2_E

data_processing:
Library strategy: CRISPR guide-seq
For CRISPRi/a analysis, reads covering the guide sequences from each bin were aligned to the designed guide sequences using Bowtie2 (2.2.1; default settings), and the total number of each guide observed in each bin counted.
Guide-level and element-level effects were estimated using MAUDE (https://github.com/Carldeboer/MAUDE/), where elements corresponded to either targeted SNPs (CRIPSRa), or targeted open chromatin regions (CRISPRi).
For an element to be considered significantly regulating TNFAIP3, we required that both replicates’ Benjamini-Hochberg FDRs were less than sqrt(0.1) (i.e. combined FDR<0.1, and both replicates close to significant independently) and for which the direction of expression change was identical.  In cases where there were more than two replicates, we included only the two replicates for which the TNFAIP3 promoter positive control guides showed the strongest effect.
Supplementary_files_format_and_content: Tab-delimited text containing guide IDs/sequences, and count matrices for each sample.

growth_protocol: BJAB, Jurkat, U937, THP-1, and GM12878 cell lines were cultured using RPMI 1640 (ThermoFisher, 21870092) containing 10% fetal bovine serum (FBS, VWR, 97068-091; 20% for GM12878) with 1% Penn/strep (VWR, 45000-652), 1% L-Glutamine (ThermoFisher, 25030081), and 1% HEPES (Sigma, H0887-100ML). Cells were maintained at a culture density between 100K-1M cells/mL.

extract_protocol:
Cells expressing CRISPRi or CRISPRa constructs along with sgRNA libraries were sorted into six 10% bins, sorting on the extremes of expression (30% on either the low or high portion of the expression distribution, each divided into three contiguous bins each comprised of approximately 10% of the overall distribution). For each experiment and cell type, between 300K and 1M cells were sorted per bin. Genomic DNA for each sample was then reverse-crosslinked using ChIP Lysis Buffer (1% SDS, 0.01M EDTA, 0.05M Tris HCl pH 7.5). Briefly, sorted cells were spun at 800g for 10 min at 4C, the supernatant was aspirated, and the cells were resuspended in 50 μL of ChIP Lysis Buffer, and incubated at 65C for 10 min. The samples were then cooled to 37C and 2 μL of RNase Cocktail (ThermoFisher, AM2286) was added to each sample and the sample was mixed well by pipetting, followed by incubation at 37C for 30 min. 10μL of Proteinase K (NEB, P8107S) was added to each sample and the sample was mixed well by pipetting, followed by incubation at 37C for 2 hours and then 95C for 20 min. gDNA was extracted using Agencourt XP beads at 0.7X following the manufacturers protocol, and the sample was eluted at 100 μL.
Libraries were prepared by PCR of each sample, splitting each in to 4 50 μL reactions (25 μL NEB Next Master Mix, 2.5 μL barcoded sequencing forward and reverse primers (Ext. Data Table 10), 11.5 μL gDNA, and 11.5 μL ddH2O; program: 98C for 30s, 25 cycles of 98C for 15s, 62C for 15s, 72C for 16s, then 72C for 2 min. The libraries were then gel purified using a 2% gel (expected band size of 206 bp). Samples were sequenced aiming to get >1,000,000 reads per bin, on either an Illumina HiSeq 2500 or MiSeq using a custom sequencing and index primers for CRISPRi and CRISPRa (Ext. Data Table 10).

treatment_protocol: Jurkat T cells were stimulated with 2.5 ug/mL of anti-CD3 (Biolegend, 317304) and 10 ng/mL of PMA (Sigma, P1585-1MG) for 1 hour prior to harvesting for CRISPRi. BJAB and GM12878 B cells were stimulated with 2.5 ug/ml of anti-IgM and 2 ug/ml anti-CD40 for 2 hours for CRISPRi. THP-1 and U937 monocytes were stimulated with 100 ng/mL LPS for 2 hours for CRISPRi. CRISPRa samples were unstimulated.

tag: screen type

value: CRISPRi

tag: replicate id

tag: sorting bin

value: E

value: 100 ng/mL LPS for 2 hours


title: CRISPRi_U937_FF2_F

value: F


title: CRISPRi_U937_FF2_D

value: D


title: CRISPRi_U937_FF2_NS

value: NS


title: CRISPRi_U937_FF2_C

value: C


title: CRISPRi_U937_FF2_B

value: B


title: BJAB_0


title: MPRAv2_BJAB_unstim_rep2


title: CRISPRi_U937_FF2_A

value: A


title: CRISPRi_U937_FF_NS

value: FF


title: Jurkat_0

value: Jurkat


title: CRISPRi_U937_FF_F


title: CRISPRi_U937_FF_E


title: CRISPRi_U937_FF_D


title: CRISPRi_U937_FF_C


title: CRISPRi_U937_FF_A


title: CRISPRi_U937_FF_B


title: CRISPRa_U937_CRISPRa2_NS

value: CRISPRa


title: CRISPRa_U937_CRISPRa2_C


title: CRISPRa_U937_CRISPRa2_F


title: CRISPRa_U937_CRISPRa2_B


title: CRISPRa_U937_CRISPRa2_A


title: CRISPRa_U937_CRISPRa1_NS


title: CRISPRa_U937_CRISPRa1_B


title: CRISPRa_U937_CRISPRa1_F


title: CRISPRa_U937_CRISPRa1_A


title: CRISPRi_THP1_FF2_NS


title: CRISPRi_THP1_FF2_F


title: CRISPRa_U937_CRISPRa1_D


title: MDS-mesenchymal stem cell- conditioned monocytes, rep2

description:
DGE CD33-MSC HD vs CD33-MDS MSC GEO
443CD33MSC9150318

value: MDS

value: Monocytes

value: co-cultured with MSCs

value: Bead-sorted


title: CRISPRi_THP1_FF2_D


title: CRISPRa_U937_CRISPRa1_E


title: CRISPRa_U937_CRISPRa2_E


title: CRISPRi_THP1_FF_NS


title: CRISPRi_THP1_FF2_A


title: CRISPRi_THP1_FF2_C


title: CRISPRi_THP1_FF2_B


title: CRISPRi_THP1_FF_F


title: CRISPRi_THP1_FF_E


title: CRISPRi_THP1_FF_D


title: CRISPRi_THP1_FF_C


title: CRISPRi_THP1_FF_B


title: CRISPRi_THP1_FF_A


title: CRISPRa_U937_CRISPRa1_C


title: CRISPRi_Jurkat_FF2_D

source_name: Jurkat

value: 2.5 ug/mL of anti-CD3 (Biolegend, 317304) and 10 ng/mL of PMA (Sigma, P1585-1MG) for 1 hour


title: CRISPRi_Jurkat_FF2_E

value: CRISPRi


title: CRISPRi_Jurkat_FF2_C


title: CRISPRi_Jurkat_FF2_F


title: CRISPRi_Jurkat_FF2_NS


title: CRISPRi_Jurkat_FF2_B


title: CRISPRi_Jurkat_FF_NS


title: CRISPRi_THP1_FF2_E

value: E


title: H29-PKA4

city: Vienna

first: Julia

last: Arand

address: Schwarzspanierstr. 16

country: Austria

institute: Medical University of Vienna

data_processing:
Reads were mapped to human reference genome hg19 with STAR2.5.1b using default settings. Genes that have at least ten reads in at least half of the samples from one condition were used for further analysis. Differentially expressed genes were obtained using DEseq2.
Genome_build: hg19
Supplementary_files_format_and_content: excel file with FPM values and Deseq2 output

source_name: H29, cells infected with lentivirus expressing active form of PRKACA (aPKA)

growth_protocol: H29 and 82 cells were infected with a lentivirus to express either a dox inducible GFP (control) of active form of PRKACA (aPKA). Puromycin resistant cells were injected into NSG mice and animals were given doxycycline (2mg/ml) in the drinking water.

extract_protocol:
Tumors were collected and snap frozen before RNA was extracted for library preparation. Frozen tumor samples were ground with a motor and pestle and total RNA was extracted using the RNeasy Mini Kit (Qiagen).
2 μg of total RNA was used to prepare cDNA libraries with the TruSeq Stranded Total RNA LT Kit (Illumina)

value: Small cell lung cancer (SCLC)

tag: genotype/variation

tag: batch


title: CRISPRi_Jurkat_FF_E


title: CRISPRi_Jurkat_FF_C


title: CRISPRi_Jurkat_FF_D


title: H29-PKA2

value: cells infected with lentivirus expressing active form of PRKACA (aPKA)


title: H29-GFP4

source_name: H29, cells infected with lentivirus expressing dox inducible GFP (control)


title: ATAC-seq_DP_F1_34_Rep1B_Rep2T

tag: tissue

value: Thymus

tag: strain

value: (NOD/ShiLtJ X C57BL/6) F1 mice


title: CRISPRi_Jurkat_FF_A

tag: cell type


title: H29-GFP3

value: cells infected with lentivirus expressing dox inducible GFP (control)


title: CRISPRa_Jurkat_CRISPRa2_NS

value: NS


title: CRISPRa_Jurkat_CRISPRa2_F

value: F


title: H29-GFP2


title: CRISPRi_Jurkat_FF_B

value: FF

value: B


title: CRISPRa_Jurkat_CRISPRa2_E

value: CRISPRa

value: Jurkat


title: CRISPRi_Jurkat_FF2_A

value: A


title: CRISPRa_Jurkat_CRISPRa2_B


title: CRISPRa_Jurkat_CRISPRa2_C

value: C


title: CRISPRa_Jurkat_CRISPRa2_D

value: D


title: CRISPRi_Jurkat_FF_F

value: 2.5 ug/mL of anti-CD3 (Biolegend, 317304) and 10 ng/mL of PMA (Sigma, P1585-1MG) for 1 hour


title: H82-PKA6

source_name: H82, cells infected with lentivirus expressing active form of PRKACA (aPKA)


title: H82-PKA5


title: H82-PKA3


title: CRISPRa_U937_CRISPRa2_D


title: H29-PKA3


title: H82-PKA2


title: CRISPRa_Jurkat_CRISPRa1_NS


title: CRISPRa_Jurkat_CRISPRa2_A


title: CRISPRa_Jurkat_CRISPRa1_F


title: H29-PKA1


title: CRISPRa_Jurkat_CRISPRa1_E


title: CRISPRa_Jurkat_CRISPRa1_D


title: H82-GFP6

source_name: H82, cells infected with lentivirus expressing dox inducible GFP (control)


title: CRISPRa_Jurkat_CRISPRa1_C


title: PS16.02.05

description: NormalizedHumanSpermMirs.csv

tag: subject

tag: collection

tag: stress category

value: Stable-stress


title: H82-PKA1


title: H82-GFP5


title: CRISPRa_Jurkat_CRISPRa1_B


title: H82-GFP4


title: H29-GFP1


title: CRISPRa_Jurkat_CRISPRa1_A


title: H82-GFP2


title: H82-PKA4


title: CRISPRi_GM_CRISPRi2_NS

source_name: GM

value: CRISPRi

value: GM

value: 2.5 ug/ml of anti-IgM and 2 ug/ml anti-CD40 for 2 hours


title: H82-GFP1

value: Small cell lung cancer (SCLC)


title: CRISPRi_GM_CRISPRi2_F


title: CRISPRi_GM_CRISPRi2_E

value: E


title: H82-GFP3

value: cells infected with lentivirus expressing dox inducible GFP (control)


title: CRISPRi_GM_CRISPRi2_D


title: CRISPRi_GM_CRISPRi2_B


title: CRISPRi_GM_CRISPRi2_C


title: 40412-08

city: Bar Harbor

first: Abigail

last: Tadenev

state: ME

address: 600 Main St

institute: The Jackson Laboratory

description:
19-Burgess-002-Sample-19
40412-08_GT19-08550_CTGCTTCC-GATCTATC_S2

data_processing:
Filtering of reads was perfomed using NGSQCToolkit/2.3 and custom perls scripts
Read alignment was done using bowtie2/2.2.0
Read count estimations were performed using rsem/1.2.12
Genome_build: We used the Mus musculus GRCm38v74 genome for this work
Supplementary_files_format_and_content: Read counts matrix from rsem

source_name: E196K/E196K_spinal cord

extract_protocol:
Total RNA was extracted from spinal cord. Tissues were lysed and homogenized in TRIzol Reagent (Ambion), then RNA was isolated using the miRNeasy Mini kit (Qiagen), according to manufacturers’ protocols, including the optional DNase digest step. Sample concentration and quality were assessed using the Nanodrop 2000 spectrophotometer (Thermo Scientific) and the RNA 6000 Nano LabChip assay (Agilent Technologies).
Libraries were prepared by the Genome Technologies core facility at The Jackson Laboratory using the KAPA Stranded mRNA-Seq Kit (KAPA Biosystems) and the KAPA mRNA HyperPrep Kit (KAPA Biosystems), according to the manufacturer’s instructions. Briefly, the protocol entails isolation of polyA containing mRNA using oligo-dT magnetic beads, RNA fragmentation, first and second strand cDNA synthesis, ligation of Illumina-specific adapters containing a unique barcode sequence for each library, and PCR amplification.  Libraries were checked for quality and concentration using the D5000 assay on the TapeStation (Agilent Technologies) and quantitative PCR (KAPA Biosystems), according to the manufacturers’ instructions.  Libraries were pooled and sequenced 75 bp paired-end on the NextSeq 500 (Illumina) using NextSeq High Output Kit v2 and v2.5 reagents (Illumina).

tag: strain background

tag: genotype

tag: age

value: 7 months

value: spinal cord


title: 40412-11

description:
19-Burgess-002-Sample-22
40412-11_GT19-08553_GAACCGCG-TAAGGTCA_S1

source_name: WT_spinal cord

value: WT


title: 40412-04

description:
19-Burgess-002-Sample-16
40412-04_GT19-08547_ACAGGCGC-AGGCAGAG_S18


title: 40412-10

description:
19-Burgess-002-Sample-21
40412-10_GT19-08552_AGGTTATA-CGGAACTG_S9

source_name: E196K/+_spinal cord


title: 40412-07

description:
19-Burgess-002-Sample-18
40412-07_GT19-08549_GGTCACGA-CATAATAC_S8


title: CRISPRi_GM_CRISPRi1_NS

value: NS


title: 40412-09

description:
19-Burgess-002-Sample-20
40412-09_GT19-08551_TCATCCTT-AGCTCGCT_S20


title: 40412-03

description:
19-Burgess-002-Sample-15
40412-03_GT19-08546_CATAGAGT-TGGTGGCA_S17


title: CRISPRi_GM_CRISPRi1_E


title: CRISPRi_GM_CRISPRi1_C


title: CRISPRi_GM_CRISPRi1_F

value: F


title: 40411-07

description:
19-Burgess-002-Sample-12
40411-07_GT19-08543_AGTACTCC-AACAGGTT_S15


title: 40412-01

description:
19-Burgess-002-Sample-13
40412-01_GT19-08544_GACGTCTT-GGTGAACC_S12


title: 40412-02

description:
19-Burgess-002-Sample-14
40412-02_GT19-08545_TGCGAGAC-CAACAATG_S7


title: CRISPRi_GM_CRISPRi2_A


title: CRISPRi_GM_CRISPRi1_A


title: 40411-05

description:
19-Burgess-002-Sample-10
40411-05_GT19-08541_CAATTAAC-ATATCTCG_S6


title: 40411-06

description:
19-Burgess-002-Sample-11
40411-06_GT19-08542_TGGCCGGT-GCGCTCTA_S14


title: CRISPRi_BJAB_FF2_NS

source_name: BJAB

value: BJAB


title: CRISPRi_BJAB_FF2_F


title: CRISPRi_BJAB_FF2_E


title: 40411-02

description:
19-Burgess-002-Sample-7
40411-02_GT19-08538_ATTGTGAA-GCAATGCA_S3


title: 40411-03

description:
19-Burgess-002-Sample-8
40411-03_GT19-08539_ACTCGTGT-GTTCCAAT_S19


title: CRISPRi_GM_CRISPRi1_D


title: 40412-05

description:
19-Burgess-002-Sample-17
40412-05_GT19-08548_GTGAATAT-GAATGAGA_S10


title: 40411-04

description:
19-Burgess-002-Sample-9
40411-04_GT19-08540_GTCTACAC-ACCTTGGC_S22


title: 39992-09

description:
19-Burgess-002-Sample-6
39992-09_GT19-08537_GCCACAGG-ATGGCATG_S21


title: 39992-05

description:
19-Burgess-002-Sample-3
39992-05_GT19-08534_GTGTCGGA-GCGCAAGC_S5


title: 39992-02

description:
19-Burgess-002-Sample-2
39992-02_GT19-08533_ACACTAAG-ATATGGAT_S4


title: CRISPRi_BJAB_FF2_A

value: A


title: CRISPRi_BJAB_FF2_B

value: B


title: CRISPRi_GM_CRISPRi1_B


title: 39992-08

description:
19-Burgess-002-Sample-5
39992-08_GT19-08536_CCTTCACC-GGAGCGTC_S11


title: 39992-06

description:
19-Burgess-002-Sample-4
39992-06_GT19-08535_TTCCTGTT-AAGATACT_S16


title: CRISPRi_BJAB_FF_D

value: FF

value: D


title: CRISPRi_BJAB_FF_C

value: C


title: 25004-2-HetWT-Male

description:
18-Burgess-011-Sample-23
25004-2-HetWT-Male_GT19-00401_ATTGTGAA-GCAATGCA_S11

source_name: HetWT-male_spinal cord

value: 8 weeks


title: 25103-5-HetWT-Male

description:
18-Burgess-011-Sample-22
25103-5-HetWT-Male_GT19-00400_GCCACAGG-ATGGCATG_S3


title: 25103-3-HetWT-Male

description:
18-Burgess-011-Sample-21
25103-3-HetWT-Male_GT19-00399_CCTTCACC-GGAGCGTC_S10


title: 24906-4-HetWT-Female

description:
18-Burgess-011-Sample-24
24906-4-HetWT-Female_GT19-00402_ACTCGTGT-GTTCCAAT_S5

source_name: HetWT-Female_spinal cord


title: CRISPRi_BJAB_FF_B

value: CRISPRi


title: CRISPRi_BJAB_FF_F

value: 2.5 ug/ml of anti-IgM and 2 ug/ml anti-CD40 for 2 hours


title: 25005-1-HetHet-Female

description:
18-Burgess-011-Sample-20
25005-1-HetHet-Female_GT19-00398_TTCCTGTT-AAGATACT_S19

source_name: HetHet-Female_spinal cord


title: CRISPRa_BJAB_CRISPRa2_NS

value: CRISPRa


title: CRISPRa_BJAB_CRISPRa2_F


title: CRISPRi_BJAB_FF2_D


title: 24905-3-HetHet-Male

description:
18-Burgess-011-Sample-18
24905-3-HetHet-Male_GT19-00396_ACACTAAG-ATATGGAT_S12

source_name: HetHet-male_spinal cord


title: 25102-5-HetHet-Female

description:
18-Burgess-011-Sample-19
25102-5-HetHet-Female_GT19-00397_GTGTCGGA-GCGCAAGC_S20


title: 25102-8-HetHet-Male

description:
18-Burgess-011-Sample-17
25102-8-HetHet-Male_GT19-00395_CCATTCGA-CGGACAAC_S21


title: CRISPRi_BJAB_FF2_C


title: CRISPRa_BJAB_CRISPRa2_D


title: CRISPRa_BJAB_CRISPRa2_E

value: E


title: 39992-01

description:
19-Burgess-002-Sample-1
39992-01_GT19-08532_CCATTCGA-CGGACAAC_S13


title: 24906-2-HomoHet-Female

description:
18-Burgess-011-Sample-16
24906-2-HomoHet-Female_GT19-00394_TTGCCTAG-TAAGTGGT_S4

source_name: HomoHet-Female_spinal cord


title: CRISPRi_BJAB_FF_E


title: CRISPRi_BJAB_FF_NS


title: CRISPRa_BJAB_CRISPRa2_B


title: CRISPRa_BJAB_CRISPRa1_NS


title: 24906-1-HomoHet-Male

description:
18-Burgess-011-Sample-14
24906-1-HomoHet-Male_GT19-00392_CGGAACTG-TCGTAGTG_S24

source_name: HomoHet-male_spinal cord


title: CRISPRi_BJAB_FF_A


title: 25102-4-HomoHet-Female

description:
18-Burgess-011-Sample-15
25102-4-HomoHet-Female_GT19-00393_TAAGGTCA-CTACGACA_S15


title: 25103-2-HomoHet-Male

description:
18-Burgess-011-Sample-13
25103-2-HomoHet-Male_GT19-00391_AGCTCGCT-GATTCTGC_S14


title: 25102-6-HomoHet-Male

description:
18-Burgess-011-Sample-12
25102-6-HomoHet-Male_GT19-00390_GATCTATC-AGCCTCAT_S16


title: CRISPRa_BJAB_CRISPRa1_F


title: CRISPRa_BJAB_CRISPRa2_A


title: 25006-5-HomoWT-Female

description:
18-Burgess-011-Sample-11
25006-5-HomoWT-Female_GT19-00389_CATAATAC-CGTTAGAA_S8

source_name: HomoWT-Female_spinal cord


title: CRISPRa_BJAB_CRISPRa1_E


title: CRISPRa_BJAB_CRISPRa1_D


title: 24905-2-HomoWT-Female

description:
18-Burgess-011-Sample-10
24905-2-HomoWT-Female_GT19-00388_TGCGGCGT-TACCGAGG_S1


title: 24906-7-HomoWT-Male

description:
18-Burgess-011-Sample-9
24906-7-HomoWT-Male_GT19-00387_GAATGAGA-AATGCCTC_S13

source_name: HomoWT-male_spinal cord


title: CRISPRa_BJAB_CRISPRa1_C


title: 24905-1-WTHet-Female

description:
18-Burgess-011-Sample-7
24905-1-WTHet-Female_GT19-00385_TGGTGGCA-TTACAGGA_S22

source_name: WTHet-Female_spinal cord


title: 25103-8-WTHet-Female

description:
18-Burgess-011-Sample-8
25103-8-WTHet-Female_GT19-00386_AGGCAGAG-GGCATTCT_S9


title: CRISPRa_BJAB_CRISPRa1_B


title: CRISPRa_BJAB_CRISPRa1_A


title: 25801-2-WTHet-Female

description:
18-Burgess-011-Sample-6
25801-2-WTHet-Female_GT19-00384_CAACAATG-CCGTGAAG_S18


title: 24905-4-WTHET-Male

description:
18-Burgess-011-Sample-5
24905-4-WTHET-Male_GT19-00383_GGTGAACC-TCCAACGC_S17

source_name: WTHET-male_spinal cord


title: C

city: Geneva

first: Sylvain

last: LEMEILLE

address: 1 rue Michel-Servet

department: Department of Pathology and Immunology

country: Switzerland

institute: University of Geneva Medical School

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads were mapped to the reference genome using bowtie version 0.12.7 with -m 1
Raw count measurements were obtained with bedtools (v2.14.2)
Genome_build: GRCh38.76

source_name: V MABs

extract_protocol:
Total RNA was extracted using Qiagen RNEasy Mini Kit columns and reagents; Cat #74142
Libraries were prepared according to Illumina's instructions using the Truseq RNA-seq protocol.

value: Fetus 2

value: Ventricle

value: 13 weeks


title: D

source_name: Sk MABs

value: Skeletal muscle


title: 25801-3-WTWT-Female

description:
18-Burgess-011-Sample-4
25801-3-WTWT-Female_GT19-00382_AACAGGTT-CTTGGTAT_S2

source_name: WTWT-Female_spinal cord

value: spinal cord


title: A

source_name: Ao MABs

value: Aorta


title: B

source_name: At MABs

value: Atrium


title: CRISPRa_BJAB_CRISPRa2_C

value: BJAB


title: 04

value: Fetus 1

value: 12 weeks


title: 25102-1-WTWT-Male

description:
18-Burgess-011-Sample-1
25102-1-WTWT-Male_GT19-00379_ACCTTGGC-ATGAGGCC_S6

source_name: WTWT-male_spinal cord


title: 24906-3-WTWT-Male

description:
18-Burgess-011-Sample-3
24906-3-WTWT-Male_GT19-00381_GCGCTCTA-GTCGGAGC_S23


title: 02


title: 25102-7-WTWT-Male

description:
18-Burgess-011-Sample-2
25102-7-WTWT-Male_GT19-00380_ATATCTCG-ACTAAGAT_S7


title: 03


title: Mouse11-ETAQ-M

description:
Mouse11-ETAQ-M_GT18-08896_GGCTAC_S2
18-Burgess-006-Sample-11

source_name: ETAQ+/-_spinal cord

value: ETAQ+/-


title: 01


title: Mouse12-WT-F

description:
Mouse12-WT-F_GT18-08897_CTTGTA_S7
18-Burgess-006-Sample-12

source_name: ETAQ+/+_spinal cord

value: ETAQ+/+


title: Mouse8-ETAQ-F

description:
Mouse8-ETAQ-F_GT18-08893_ACTTGA_S10
18-Burgess-006-Sample-8

value: 8 weeks


title: Mouse10-WT-F

description:
Mouse10-WT-F_GT18-08895_TAGCTT_S3
18-Burgess-006-Sample-10


title: Mouse7-WT-F

description:
Mouse7-WT-F_GT18-08892_CAGATC_S4
18-Burgess-006-Sample-7


title: Mouse9-ETAQ-F

description:
Mouse9-ETAQ-F_GT18-08894_GATCAG_S9
18-Burgess-006-Sample-9


title: RNA-seq_DP_NOD_Rep1B_Rep1T

data_processing:
RNA-seq libraries were pair-end sequenced by Illumina NextSeq 550. RNA-seq samples were aligned by STAR_2.5.0a_alpha with parameters ‘--readFilesCommand zcat --outFilterMultimapNmax 1--outSAMtype SAM--alignEndsTypeLocal--outReadsUnmapped Fastx--outFilterMismatchNmax 1--alignMatesGapMax 400000--sjdbGTFfile’, with the GTF file being either the mus musculus GRCm38.91 gtf file for C57BL/6 strain or the mus musculus GRCm38.91 gtf shifted to NOD coordinates for the NOD strain.
HTSeq v0.6.1 facilitated counting RNA-seq reads on Gencode vM11 gene models with parameters ‘-s yes-t exon-m intersection-nonempty’.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files with read count

source_name: CD4+ CD8+ thymocytes

extract_protocol:
washed with 1 x PBS (Corning, cat# 21031CV) and lysed with 350 μl RLT Plus buffer (Qiagen) supplemented with 10% 2-mercaptoethanol (Sigma, cat# M6250), vortexed briefly, snap-frozen on dry ice, and stored at -80°C. Subsequently, total RNA was isolated using the RNeasy Plus Micro Kit (Qiagen, cat# 74034).
Libraries were prepared with SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Takara). Indexed libraries were validated for quality and size distribution using a TapeStation 2200 (Agilent). Paired end sequencing (38 bp+37 bp) was performed on a NextSeq 550 following the manufacturer's protocol.

tag: tag

value: Thymus

value: NOD/ShiLtJ


title: Mouse6-ETAQ-M

description:
Mouse6-ETAQ-M_GT18-08891_GCCAAT_S11
18-Burgess-006-Sample-6


title: RNA-seq_DP_NOD_Rep2B_Rep2T


title: RNA-seq_DP_NOD_Rep1B_Rep2T


title: Mouse5-ETAQ-M

description:
Mouse5-ETAQ-M_GT18-08890_ACAGTG_S12
18-Burgess-006-Sample-5


title: RNA-seq_DP_BL6_Rep2B_Rep2T


title: Mouse4-WT-M

description:
Mouse4-WT-M_GT18-08889_TGACCA_S5
18-Burgess-006-Sample-4


title: Mouse3-WT-M

description:
Mouse3-WT-M_GT18-08888_TTAGGC_S6
18-Burgess-006-Sample-3


title: Mouse2-WT-M

description:
Mouse2-WT-M_GT18-08887_CGATGT_S8
18-Burgess-006-Sample-2


title: Mouse1-ETAQ-F

description:
Mouse1-ETAQ-F_GT18-08886_ATCACG_S1
18-Burgess-006-Sample-1


title: HiChIP_Smc1_DP_NOD_Rep1B

data_processing:
Library strategy: HiChIP
Raw reads for each HiChIP sample were processed with HiC-Pro (version v2.5.0) (Servant et al., 2015) to obtain putative interactions with default parameters except LIGATION_SITE = GATCGATC and GENOME_FRAGMENT generated for MboI restriction enzyme.
The valid pairs (allValidPairs file) from HiC-Pro were used to generate .hic file using Juicer tools (version 1.7.6) ‘pre’ command.
Valid pairs (VI), self-circle (SC) and dangling-end (DE) interactions in cis were used as input for significant interaction calling in ‘.bedpe’ format. Mango (version 1.2.0) step 4 identified putative significant interaction anchors by MACS peak calling (Zhang et al., 2008) with MACS_qvalue = 0.05 and MACS_shiftsize = 75. Mango step 5 identified significant interactions with default parameters except maxinteractingdist = 2000000 and MHT = found. In NOD mice, the BEDPE was shifted to BL6 coordinates with MMARGE (PMID: 29893919) utilizing the NOD VCF files (version 5) from the Mouse Genomes Project (PMID: 21921910).
Genome_build: GRCm38
Supplementary_files_format_and_content: Mango BEDPE file of signficant interactions

extract_protocol:
HiChIP was performed as described (Mumbach et al., 2016) using antibody against Smc1 (Bethyl, cat# A300-055A). Briefly, 2 x 107 cells were crosslinked with 1% formaldehyde (Thermo Scientific, cat# 28908) for 10 min and subsequently quenched with 0.125M glycine (Invitrogen, cat# 15527-013). Chromatin was digested using MboI restriction enzyme (NEB, Cat#R0147), followed by biotin incorporation with Biotin-14-dATP (Invitrogen, 19524-016) in end-repair step, ligation, and sonication. Sheared chromatin was 4-fold diluted with ChIP dilution buffer (16.7mM Tris pH 7.5, 167mM NaCl, 1.2mM EDTA, 0.01% SDS, 1.1% Triton X-100) and cleared and then incubated with anti-Smc1 antibody at 4°C for overnight. Chromatin-antibody complexes were captured by Protein-A magnetic beads (Pierce, cat# 88846) and subsequently washed with Low Salt Wash Buffer, High Salt Wash Buffer, LiCl Wash Buffer and eluted.
DNA was purified with MinElute PCR Purification Kit (Qiagen, cat# 28004) and quantified using Qubit dsDNA HS Assay Kit (Invitrogen, cat# Q32851). 50-150ng was used for capture with Dynabeads MyOne Streptavidin C-1 (Invitrogen, cat# 65001) and an appropriate amount of Tn5 enzyme was added to captured DNA to generate sequencing library. Paired-end sequencing (38 bp+38 bp) was performed on a NextSeq 550.

tag: chip antibody

value: H3K27Ac (Abcam ab4729)


title: RNA-seq_DP_BL6_Rep1B_Rep2T


title: HiChIP_Smc1_DP_NOD_Rep2B


title: RNA-seq_DP_BL6_Rep2B_Rep1T


title: RNA-seq_DP_BL6_Rep1B_Rep1T


title: RNA-seq_DP_NOD_Rep2B_Rep1T


title: HiChIP_Smc1_DP_BL6_Rep2B


title: HiChIP_Smc1_DP_F1_Rep1B_Rep1T

value: (NOD/ShiLtJ X C57BL/6) F1 mice

value: Smc1 (Bethyl A300-055A)


title: HiChIP_Smc1_DP_NOD_Rep1B_2T


title: HiChIP_Smc1_DP_BL6_Rep1B


title: HiChIP_Smc1_DP_NOD_Rep1B_1T


title: 20401-6-NegCtrlWT_GT18-02951

description:
18-Burgess-002-Sample-22
20401-6-NegCtrlWT_GT18-02951_ATTCCT_S2

source_name: NegCtrlWT_spinal cord

extract_protocol:
Our protocol was adapted from the University of Washington McKnight Lab Protocol (http://depts.washington.edu/mcklab/RiboTag.html).  All buffer recipes can be found here and were made fresh on the day of use.  All equipment used was made RNAse-free by spraying with RNase-Zap RNase decontamination solution (Thermo Fisher) and rinsing with diethyl pyrocarbonate (DEPC) (Sigma)-treated water.  All reagents were made RNAse-free by treating with 1:1000 DEPC overnight and autoclaving.  Mice were euthanized and spinal cords were removed within 1-2 minutes and snap frozen in liquid nitrogen.  Samples were stored at -80oC until use.  Spinal cords were homogenized on dry ice using the Cryogrinder (POS Diagnostics) until a fine powder.  Powder was then transferred to a 2ml dounce homogenizer on ice and homogenized further in 1ml supplemented homogenization buffer.  Sample was transferred to a 1.5ml tube, sonicated for 20 seconds at 18 Watts, and centrifuged at 4oC at 10,000 g for 10 minutes. Supernatant was transferred to a new 1.5ml tube and 50ul of washed Protein G Sepharose 4 Fast Flow beads (GE Life Sciences) were added and incubated for 1 hour at 4oC with continuous mixing.  Samples were centrifuged at 5,000 g for 30 seconds at room temperature to pellet beads.  Supernatant was removed and added to 50ul of supplemented homogenization buffer containing 2µl Rabbit anti-HA antibody (4µl if first diluted in glycerol) (Sigma H6908).  Samples were continuously mixed at 4oC for 4 hours.  Magnetic Protein G Dynabeads (Thermo Fisher) were washed in supplemented homogenization buffer for 15 minutes at 4oC with continuous mixing.  Wash was removed and antibody-tissue homogenates were added to the Dynabeads and allowed to incubate at 4oC overnight with continuous mixing.  The following day, beads were washed with 800µl of high salt buffer 3 times for 10 minutes each at 4oC with continuous mixing.  350µl lysis buffer was added to the samples immediately after the final high salt wash and vortexed for 30 seconds. Samples were placed on a magnetic rack and supernatant transferred to a new tube.  Directions in the RNeasy Micro kit (Qiagen) were then followed exactly, starting with adding 350µl 70% ethanol to each sample. RNA was eluted in 14µl RNase-free water and stored at -80oC until sequencing.
RNA concentration and quality were assessed using the Nanodrop 2000 spectrophotometer (Thermo Scientific) and the RNA 6000 Pico LabChip assay (Agilent Technologies).  Libraries were prepared by the Genome Technologies core facility at The Jackson Laboratory using the Ovation RNA-seq System V2 (Nugen) and Hyper Prep Kit (Kapa Biosystems). Briefly, the protocol entails first and second strand cDNA synthesis and cDNA amplification utilizing Nugen’s Ribo-SPIA technology, cDNA fragmentation, ligation of Illumina-specific adapters containing a unique barcode sequence for each library, and PCR amplification. Library quality and concentration were evaluated using the D5000 ScreenTape assay (Agilent Technologies) and quantitative PCR (Kapa Biosystems), according to the manufacturers’ instructions.  Libraries were pooled and sequenced 75 bp paired-end on the NextSeq 500 (Illumina) using NextSeq High Output Kit v2 and v2.5 reagents (Illumina).

value: 2 weeks

tag: molecule subtype

value: Ribosome-associated mRNA


title: 20303-1-NegCtrlC201R_GT18-02948

description:
18-Burgess-002-Sample-19
20303-1-NegCtrlC201R_GT18-02948_GTGGCC_S4

source_name: NegCtrlC201R_spinal cord


title: 20301-3-NegCtrlC201R_GT18-02949

description:
18-Burgess-002-Sample-20
20301-3-NegCtrlC201R_GT18-02949_GTTTCG_S3


title: 20302-3-RplChAT_GT18-02952

description:
18-Burgess-002-Sample-23
20302-3-RplChAT_GT18-02952_ACTGAT_S8

source_name: RplChAT_spinal cord


title: 20401-5-RplC201RChAT_GT18-02945

description:
18-Burgess-002-Sample-16
20401-5-RplC201RChAT_GT18-02945_CCGTCC_S1

source_name: RplC201RChAT_spinal cord


title: ChIP_seq_smc1_NOD_DP_rep2B

data_processing:
ChIP-seq libraries were pair-end sequenced by Illumina NextSeq 550. bowtie2 was used for alignment of ChIP-seq data. In NOD mice, aligned reads were shifted to BL6 coordinates with MMARGE (PMID: 29893919) utilizing the NOD VCF files (version 5) from the Mouse Genomes Project (PMID: 21921910). Reads aligned to the mitochondrial genome or chrY as well as reads mapping to multiple genomic loci were discarded from downstream analyses.
Genome_build: GRCm38
Supplementary_files_format_and_content: Bigwig files were generated by bedtools genomecov and wigToBigWig normalizing tracks to tags-per-million

extract_protocol:
Cells were chemically cross-linked by 1% formaldehyde. Samples were sonicated and protein-DNA complexes were isolated with antibody.
Libraries were prepared according to instructions accompanying the NEBNext Ultra II Library Prep Kit for Illuina (Part# E7645S). Indexed libraries were validated for quality and size distribution using a TapeStation 2200 (Agilent). Paired end sequencing (38 bp+37 bp) was performed on a NextSeq 550 following the manufacturer's protocol.


title: ChIP_seq_smc1_F1_DP_rep2B


title: ChIP_seq_smc1_F1_DP_rep1B


title: HiChIP_Smc1_DP_BL6_Rep1B_1T


title: 18405-3-RplC201RChAT_GT18-02950

description:
18-Burgess-002-Sample-21
18405-3-RplC201RChAT_GT18-02950_CGTACG_S22


title: 20401-3-NegCtrlWT_GT18-02947

description:
18-Burgess-002-Sample-18
20401-3-NegCtrlWT_GT18-02947_GTGAAA_S16


title: 20301-8-NegCtrlC201R_GT18-02942

description:
18-Burgess-002-Sample-13
20301-8-NegCtrlC201R_GT18-02942_AGTCAA_S21


title: 20304-6-RplChAT_GT18-02943

description:
18-Burgess-002-Sample-14
20304-6-RplChAT_GT18-02943_AGTTCC_S6


title: ChIP_seq_smc1_NOD_DP_rep1B


title: ChIP_seq_smc1_BL6_DP_rep2B


title: 20301-4-NegCtrlC201R_GT18-02941

description:
18-Burgess-002-Sample-12
20301-4-NegCtrlC201R_GT18-02941_CTTGTA_S11


title: ChIP_seq_smc1_BL6_DP_rep1B


title: ChIP-seq_CTCF_DP_NOD_Rep2B

value: CTCF (Millipore 07-729)


title: 18405-2-RplC201RChAT_GT18-02940

description:
18-Burgess-002-Sample-11
18405-2-RplC201RChAT_GT18-02940_GGCTAC_S17

value: spinal cord


title: ChIP-seq_CTCF_DP_NOD_Rep1B


title: ChIP-seq_CTCF_DP_BL6_Rep1


title: ChIP-seq_CTCF_DP_BL6_Rep2B


title: HiChIP_Smc1_DP_BL6_Rep1B_2T


title: 20401-4-NegCtrlWT_GT18-02946

description:
18-Burgess-002-Sample-17
20401-4-NegCtrlWT_GT18-02946_GTCCGC_S7


title: 20302-5-RplC201RChAT_GT18-02937

description:
18-Burgess-002-Sample-8
20302-5-RplC201RChAT_GT18-02937_ACTTGA_S13


title: 20302-6-RplC201RChAT_GT18-02935

description:
18-Burgess-002-Sample-7
20302-6-RplC201RChAT_GT18-02935_CAGATC_S12


title: 20301-7-NegCtrlWT_GT18-02944

description:
18-Burgess-002-Sample-15
20301-7-NegCtrlWT_GT18-02944_ATGTCA_S23


title: 20401-7-RplC201RChAT_GT18-02938

description:
18-Burgess-002-Sample-9
20401-7-RplC201RChAT_GT18-02938_GATCAG_S5


title: ChIP-seq_input_DP_NOD_Rep1B


title: 20401-1-RplChAT_GT18-02934

description:
18-Burgess-002-Sample-6
20401-1-RplChAT_GT18-02934_GCCAAT_S19


title: ChIP-seq_input_DP_BL6_Rep1B


title: ChIP-seq_K27ac_DP_NOD_Rep2B


title: ChIP-seq_K27ac_DP_BL6_Rep2B


title: 18405-1-NegCtrlC201R_GT18-02931

description:
18-Burgess-002-Sample-3
18405-1-NegCtrlC201R_GT18-02931_TTAGGC_S9


title: 20301-5-NegCtrlWT_GT18-02932

description:
18-Burgess-002-Sample-4
20301-5-NegCtrlWT_GT18-02932_TGACCA_S18


title: 20301-1-NegCtrlC201R_GT18-02930

description:
18-Burgess-002-Sample-2
20301-1-NegCtrlC201R_GT18-02930_CGATGT_S10


title: 20302-1-NegCtrlWT_GT18-02929

description:
18-Burgess-002-Sample-1
20302-1-NegCtrlWT_GT18-02929_ATCACG_S14


title: 20302-4-RplChAT_GT18-02939

description:
18-Burgess-002-Sample-10
20302-4-RplChAT_GT18-02939_TAGCTT_S20


title: ChIP-seq_K27ac_DP_NOD_Rep1B


title: ChIP-seq_K27ac_DP_BL6_Rep1B


title: male-249-mouse3

description:
18-Burgess-001-Sample-3
male-249-mouse3_GT18-00728_TAGCTT_S10

source_name: male-249-spinal cord

value: 1 week


title: male-249-mouse5

description:
18-Burgess-001-Sample-5
male-249-mouse5_GT18-00729_GGCTAC_S2


title: male-249-mouse13

description:
18-Burgess-001-Sample-13
male-249-mouse13_GT18-00730_CTTGTA_S12


title: Input-8hrs-A

city: San Francisco

first: Xuan

last: Luong

state: CA

address: 505 Parnassus Ave

institute: UCSF

description:
ribsome-bound mRNA
cpm_input-cpm10.csv
X9.a2.lnoutBhrA_S9_R1_001.txt

data_processing:
The quality of the raw sequence data was checked via FASTQC. The sequence files were then trimmed using tools in Trimmomatic-0.36. The following were removed: Illumina TruSeq3 single-ended adapter sequences, bases with a quality score lower than 3 at the start and end of a read, bases that had an average quality per base of below 15 calculated using a sliding window to average four bases, and any reads that were shorter than 36 bases. Input reads were single-ended and input qualities were ASCII characters equal to the Phred quality plus 33.
HiSat2 was used to build indexes from the Reference Consortium Mouse Build 38 (mm10) and to align sequence reads to the genome
The resulting .bam files were sorted and indexed with SAMtools.
Count files for each group were created with HTSeq using the Mouse GENCODE Gene set release M11. The input data were .bam files, the data were not from a strand-specific assay, and the feature type used was ‘gene.’
The Bioconductor packages edgeR and limma were used for statistical analyses. Only reads with greater or equal to 10 counts per million (CPM) in at least 2 samples were kept. TMM-normalization was then performed on HA reads and input reads, separately. Using the raw counts, dispersion, and design matrix, the negative binomial generalized linear model was fitted for each gene. Finally, pairwise likelihood ratio tests for 2, 4, 6, and 8 hrs versus 0 hrs were conducted.
Genome_build: mm10
Supplementary_files_format_and_content: Two separate .csv files containing filtered and TMM-normalized counts for HA and input samples

source_name: Oocyte RiboTag-IP

growth_protocol: Three-week old, Zp3-Cre+ RiboTag female mice were injected with 5 I.U. PMSG to induce superovulation. Forty-four hrs after injection, the mice were euthanized and the ovaries dissected into media containing HEPES and 1 µM cilostamide. The antral follicles were punctured, allowing release of cumulus-oocyte complexes (COCs). Repeated aspiration through a glass pipette allowed for removal of the surrounding cumulus cells. Denuded oocytes were maintained at prophase I arrest in MEM Alpha supplemented with sodium pyruvate and penicillin-streptomycin in addition to 1 µM cilostamide at 37°C under 5% CO2. Oocytes were then transferred to cilostamide-free MEM Alpha, allowed to mature, and collected at various time points.

extract_protocol:
Oocytes were collected in 5 µl 0.1% polyvinylpyrrolidone in 1x PBS, flash frozen in liquid nitrogen, and stored at -80°C. Oocytes were then lysed and RiboTag-IP was performed according to the protocol described under Materials and Methods. Ribosome-bound mRNA was extracted and purified via the RNeasy Plus Micro Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Isolated COC oocytes

tag: time post-meiotic resumption

value: 8 hrs


title: Input-6hrs-A

description:
ribsome-bound mRNA
cpm_input-cpm10.csv
X7.g1.lnout6hr_A_S7_R1_001.txt

value: 6 hrs


title: Input-8hrs-B

description:
ribsome-bound mRNA
cpm_input-cpm10.csv
X10.b2.Input_8hr_B_S10_R1_001.txt


title: male-wt-mouse19

description:
18-Burgess-001-Sample-19
male-wt-mouse19_GT18-00727_GATCAG_S7

source_name: male-wt-spinal cord

value: wt


title: male-wt-mouse9

description:
18-Burgess-001-Sample-9
male-wt-mouse9_GT18-00726_ACTTGA_S6


title: Input-4hrs-A

description:
ribsome-bound mRNA
cpm_input-cpm10.csv
X5.e1.lnout4hrA_S5_R1_001.txt

value: 4 hrs


title: male-wt-mouse6

description:
18-Burgess-001-Sample-6
male-wt-mouse6_GT18-00725_CAGATC_S11


title: Input-4hrs-B

description:
ribsome-bound mRNA
cpm_input-cpm10.csv
X6.f1.lnout4hr_B_S6_R1_001.txt


title: Input-2hrs-B

description:
ribsome-bound mRNA
cpm_input-cpm10.csv
X4.d1.lnout2hr_B_S4_R1_001.txt

value: 2 hrs


title: Input-2hrs-A

description:
ribsome-bound mRNA
cpm_input-cpm10.csv
X3.c1.lnput2hr_A_S3_R1_001.txt


title: female-249-mouse10

description:
18-Burgess-001-Sample-10
female-249-mouse10_GT18-00724_GCCAAT_S3

source_name: female-249-spinal cord


title: female-249-mouse7

description:
18-Burgess-001-Sample-7
female-249-mouse7_GT18-00723_ACAGTG_S5


title: female-249-mouse4

description:
18-Burgess-001-Sample-4
female-249-mouse4_GT18-00722_TGACCA_S4


title: 20401-2-RplChAT_GT18-02933

description:
18-Burgess-002-Sample-5
20401-2-RplChAT_GT18-02933_ACAGTG_S15


title: Input-0hrs-B

description:
ribsome-bound mRNA
cpm_input-cpm10.csv
X2.b1.Input_Ohr_B_S2_R1_001.txt

value: 0 hrs


title: Input-0hrs-A

description:
ribsome-bound mRNA
cpm_input-cpm10.csv
X1.a1.Input_Ohr_A_S1_R1_001.txt


title: HA-8hrs-A

description:
ribsome-bound mRNA
cpm_HA-cpm10.csv
X19.c3.HA8hrA_S19_R1_001.txt


title: NegCtrl-249-17408-2

description:
17-burgess-004_NegCtrl-249-17408-2_GT17-02395_GAGTGG_S5
17-Burgess-004-Sample-18

source_name: NegCtrl_spinal cord

value: 8 weeks


title: HA-8hrs-B

description:
ribsome-bound mRNA
cpm_HA-cpm10.csv
X20.d3.HA8hr_B_S20_R1_001.txt


title: HA-6hrs-B

description:
ribsome-bound mRNA
cpm_HA-cpm10.csv
X18.b3.HA_6hrB_S18_R1_001.txt


title: Input-6hrs-B

description:
ribsome-bound mRNA
cpm_input-cpm10.csv
X8.h1.lnout6hr_B_S8_R1_001.txt


title: NegCtrl-249-17405-2

description:
17-burgess-004_NegCtrl-249-17405-2_GT17-02394_CGTACG_S9
17-Burgess-004-Sample-17


title: HA-4hrs-B

description:
ribsome-bound mRNA
cpm_HA-cpm10.csv
X16.h2.HA4hrB_S16_R1_001.txt


title: NegCtrl-249-17405-1

description:
17-burgess-004_NegCtrl-249-17405-1_GT17-02393_GTTTCG_S4
17-Burgess-004-Sample-16


title: NegCtrl-WT-18402-9

description:
17-burgess-004_NegCtrl-WT-18402-9_GT17-02392_GTGGCC_S3
17-Burgess-004-Sample-15

source_name: NegCtrl-WT_spinal cord


title: HA-2hrs-B

description:
ribsome-bound mRNA
cpm_HA-cpm10.csv
X14.f2.HA2hr_B_S14_R1_001.txt


title: HA-4hrs-A

description:
ribsome-bound mRNA
cpm_HA-cpm10.csv
X15.g2.HA4hrA_S15_R1_001.txt


title: NegCtrl-WT-18402-3

description:
17-burgess-004_NegCtrl-WT-18402-3_GT17-02391_GTGAAA_S6
17-Burgess-004-Sample-14


title: NegCtrl-WT-17402-2

description:
17-burgess-004_NegCtrl-WT-17402-2_GT17-02390_GTCCGC_S7
17-Burgess-004-Sample-13


title: HA-2hrs-A

description:
ribsome-bound mRNA
cpm_HA-cpm10.csv
X13.e2.HA2hrA_S13_R1_001.txt


title: Rpl-ChAT-Cre-17409-8

description:
17-burgess-004_Rpl-ChAT-Cre-17409-8_GT17-02388_CCGTCC_S2
17-Burgess-004-Sample-12

source_name: Rpl-ChAT-Cre_spinal cord


title: HA-0hrs-B

description:
ribsome-bound mRNA
cpm_HA-cpm10.csv
X12.d2.HAOhrB_S12_R1_001.txt


title: Rpl-249-ChAT-Cre-17409-6

description:
17-burgess-004_Rpl-249-ChAT-Cre-17409-6_GT17-02386_ATTCCT_S7
17-Burgess-004-Sample-10

source_name: Rpl-249-ChAT-Cre_spinal cord


title: HA-0hrs-A

description:
ribsome-bound mRNA
cpm_HA-cpm10.csv
X11.c2.HA_Ohr_A_S11_R1_001.txt


title: Rpl-ChAT-Cre-17409-4

description:
17-burgess-004_Rpl-ChAT-Cre-17409-4_GT17-02387_ATGTCA_S1
17-Burgess-004-Sample-11


title: female-wt-mouse2

description:
18-Burgess-001-Sample-2
female-wt-mouse2_GT18-00720_CGATGT_S8

source_name: female-wt-spinal cord


title: female-wt-mouse14

description:
18-Burgess-001-Sample-14
female-wt-mouse14_GT18-00721_TTAGGC_S9


title: female-wt-mouse1

description:
18-Burgess-001-Sample-1
female-wt-mouse1_GT18-00719_ATCACG_S1


title: NegCtrl-249-17402-3

description:
17-burgess-004_NegCtrl-249-17402-3_GT17-02383_GAGTGG_S8
17-Burgess-004-Sample-8


title: NegCtrl-249-17401-1

description:
17-burgess-004_NegCtrl-249-17401-1_GT17-02381_GTTTCG_S2
17-Burgess-004-Sample-6


title: Rpl-249-ChAT-Cre-17405-3

description:
17-burgess-004_Rpl-249-ChAT-Cre-17405-3_GT17-02385_ACTGAT_S3
17-Burgess-004-Sample-9


title: NegCtrl-WT-17408-4

description:
17-burgess-004_NegCtrl-WT-17408-4_GT17-02380_GTGGCC_S4
17-Burgess-004-Sample-5


title: NegCtrl-WT-17410-3

description:
17-burgess-004_NegCtrl-WT-17410-3_GT17-02379_GTGAAA_S10
17-Burgess-004-Sample-4


title: Rpl-249-ChAT-Cre-17409-7

description:
17-burgess-004_Rpl-249-ChAT-Cre-17409-7_GT17-02374_ATGTCA_S6
17-Burgess-004-Sample-1


title: HA-6hrs-A

description:
ribsome-bound mRNA
cpm_HA-cpm10.csv
X17.a3.HA6hr_A_S17_R1_001.txt


title: 12-C201R-female

description:
17-Burgess-001-Sample-12
12-WT_GT17-02081_S3


title: Rpl-ChAT-Cre-18402-5

description:
17-burgess-004_Rpl-ChAT-Cre-18402-5_GT17-02377_GTCCGC_S1
17-Burgess-004-Sample-3


title: Rpl-ChAT-Cre-17410-2

description:
17-burgess-004_Rpl-ChAT-Cre-17410-2_GT17-02376_CCGTCC_S5
17-Burgess-004-Sample-2


title: 11-C201R-female

description:
17-Burgess-001-Sample-11
11-WT_GT17-02080_S9


title: 9-WT-male

description:
17-Burgess-001-Sample-9
9-C201R_GT17-02078_S12

source_name: WT-male


title: 10-C201R-male

description:
17-Burgess-001-Sample-10
10-C201R_GT17-02079_S2


title: 8-WT-male

description:
17-Burgess-001-Sample-8
8-WT_GT17-02077_S5


title: 7-WT-male

description:
17-Burgess-001-Sample-7
7-WT_GT17-02076_S11


title: 6-WT-female

description:
17-Burgess-001-Sample-6
6-WT_GT17-02075_S8

source_name: WT-female


title: 5-WT-female

description:
17-Burgess-001-Sample-5
5-WT_GT17-02074_S1


title: 1-C201R-female

description:
17-Burgess-001-Sample-1
1-C201R_GT17-02070_S7


title: 4-WT-female

description:
17-Burgess-001-Sample-4
4-C201R_GT17-02073_S6


title: WT_male_mouse12

description:
16NGS-003-Burgess-Sample-12
WT-male-mouse12-GT16-03574_S9

value: wild type


title: 3-C201R-male

description:
17-Burgess-001-Sample-3
3-C201R_GT17-02072_S10


title: NegCtrl-249-17402-1

description:
17-burgess-004_NegCtrl-249-17402-1_GT17-02382_CGTACG_S9
17-Burgess-004-Sample-7


title: WT_male_mouse11

description:
16NGS-003-Burgess-Sample-11
WT-male-mouse11-GT16-03573_S7


title: P278KY_female_mouse9

description:
16NGS-003-Burgess-Sample-9
249-female-mouse9-GT16-03571_S5

value: heterozygous


title: WT_female_mouse10

description:
16NGS-003-Burgess-Sample-10
WT-female-mouse10-GT16-03572_S8


title: WT_male_mouse5

description:
16NGS-003-Burgess-Sample-5
WT-male-mouse5-GT16-03567_S1


title: P278KY_male_mouse6

description:
16NGS-003-Burgess-Sample-6
249-male-mouse6-GT16-03568_S4


title: WT_female_mouse1

description:
16NGS-003-Burgess-Sample-1
WT-female-mouse1-GT16-03563_S10


title: WT_female_mouse2

description:
16NGS-003-Burgess-Sample-2
WT-female-mouse2-GT16-03564_S11


title: P278KY_female_mouse3

description:
16NGS-003-Burgess-Sample-3
249-female-mouse3-GT16-03565_S12


title: P278KY_male_mouse8

description:
16NGS-003-Burgess-Sample-8
249-male-mouse8-GT16-03570_S6


title: P278KY_female_mouse4

description:
16NGS-003-Burgess-Sample-4
249-female-mouse4-GT16-03566_S2


title: WT_14701-9

description:
16NGS-002-Burgess-Sample-24
Rpl-ChAT-sc-14701-9-GES16-01926_S3

source_name: WT


title: P278KY_male_mouse7

description:
16NGS-003-Burgess-Sample-7
249-male-mouse7-GT16-03569_S3


title: WT Negative Ctrl_14702-6

description:
16NGS-002-Burgess-Sample-22
WT-Negative-Ctrl-sc-14702-6-GES16-02259_S15

source_name: WT Negative Ctrl


title: WT Negative Ctrl_14702-4

description:
16NGS-002-Burgess-Sample-20
14702-4-WT-Negative-Ctrl-sc-GES16-02262_S22


title: WT Negative Ctrl_14702-5

description:
16NGS-002-Burgess-Sample-21
WT-Negative-Ctrl-sc-14702-5-GES16-02256_S16


title: WT Negative Ctrl_14702-1

description:
16NGS-002-Burgess-Sample-19
WT-Negative-Ctrl-sc-14702-1-GES16-02258_S14


title: WT Negative Ctrl_14701-1

description:
16NGS-002-Burgess-Sample-18
Negative-Ctrl-sc-14701-1-GES16-01927_S1


title: WT Negative Ctrl_14004-4

description:
16NGS-002-Burgess-Sample-17
WT-Negative-Ctrl-sc-14004-4-GES16-02251_S12


title: WT 14703-5

description:
16NGS-002-Burgess-Sample-16
14703-5-Rpl-ChAT-sc-GES16-02261_S24


title: 2-C201R-male

description:
17-Burgess-001-Sample-2
2-C201R_GT17-02071_S4


title: WT 14002-6

description:
16NGS-002-Burgess-Sample-13
Rpl-ChAT-sc-14002-6-GES16-01931_S5


title: WT 14004-6

description:
16NGS-002-Burgess-Sample-14
Rpl-ChAT-sc-14004-6-GES16-02257_S17


title: C201R_14703-4

description:
16NGS-002-Burgess-Sample-12
14703-4-C201R-Rpl-Chat-sc-GES16-02264_S20


title: C201R_14004-5

description:
16NGS-002-Burgess-Sample-11
Rpl-C201R-ChAT-sc-14004-5-GES16-02249_S8


title: KDM3A shRNA RD cells, replicate 3

city: Aurora

first: Andrew

last: Goodspeed

state: CO

address: 12801 E 17th Ave, Mail Stop 8303

institute: University of Colorado Anschutz Medical Campus

data_processing:
Quality trim to a minimum of Q15
Map to the GRCh38 genome using GSNAP version 2014-12-17 using the commandline /vol2/home/analysiscore/bin/gsnap_20141217_250/gsnap -d GRCh38_nonRedundant -v GRCh38_nonRedundant.snp142 --use-splicing=GRCh38_nonRedundant.ensembl.splicesites --max-mismatches=0.06 -i2 -n2 -Q --gunzip --force-xs-dir --nofails -B5 -t12 --read-group-id=$j --read-group-name=$j --read-group-library=$j --read-group-platform=illumina -A sam ./Illumina_data/${j}_filtered.fastq.gz > ./Illumina_data/$j.sam
sort and index using SAMTOOLS
split forward and reverse reads using SAMTOOLS
call FPKM using CUFFLINKS, applying anti-sense reads to sense genes, and sense reads to anti-sense genes
Genome_build: GRCh38
Supplementary_files_format_and_content: text file containing FPKM values

molecule: polyA RNA

source_name: RD (ATCC® CCL-136™)

growth_protocol: RD cells were grown in DMEM with 10% Fetal bovine serum, 1% Pen/Strep, 10mM Hepes, 1X MEM non-essential amino acids, and 1mM Sodium Pyruvate. Rh30 cells were grown in RPMI with 10% Fetal bovine serum, 1% Pen/Strep, 10mM Hepes, 1X MEM non-essential amino acids, and 1mM Sodium Pyruvate.

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen), and further purified using the Qiagen MinElute column kit.
Illumina directional mRNA prep
HiSeq4000 using 1x151bp format

treatment_protocol: Cells were transduced with control (Scrambled) or KDM3A-targeting shRNA lentivirus and selected with 1 ug/ml Puromycin.

value: Rhabdomyosarcoma Cell

tag: shRNA

value: KDM3A shRNA

tag: cell line

value: RD


title: KDM3A shRNA RD cells, replicate 1


title: KDM3A shRNA RD cells, replicate 2


title: C201R_14003-4

description:
16NGS-002-Burgess-Sample-10
Rpl-C201R-ChAT-sc-14003-4-GES16-01929_S7

value: Ribosome-associated mRNA


title: C201R Negative Ctrl_14702-9

description:
16NGS-002-Burgess-Sample-9
14702-9-C201R-Negative-Ctrl-sc-GES16-02263_S23

source_name: C201R Negative Ctrl


title: control shRNA RD cells, replicate 3

value: control shRNA


title: C201R Negative Ctrl_14702-8

description:
16NGS-002-Burgess-Sample-8
14702-8-C201R-Negative-Ctrl-sc-GES16-02265_S21

value: spinal cord


title: control shRNA RD cells, replicate 2


title: WT_14004-3

description:
16NGS-002-Burgess-Sample-23
Rpl-ChAT-sc-14004-3-GES16-02250_S11


title: C201R Negative Ctrl_14004-7

description:
16NGS-002-Burgess-Sample-7
C201R-Negative-Ctrl-sc-14004-7-GES16-02252_S9


title: C201R Negative Ctrl_14003-2

description:
16NGS-002-Burgess-Sample-4
C201R-Negative-Ctrl-sc-14003-2-GES16-01930_S4


title: C201R Negative Ctrl_14003-3

description:
16NGS-002-Burgess-Sample-5
C201R-Negative-Ctrl-sc-14003-3-GES16-02255_S19


title: C201R Negative Ctrl_14004-8

description:
16NGS-002-Burgess-Sample-6
C201R-Negative-Ctrl-sc-14004-8-GES16-02260_S13


title: control shRNA RD cells, replicate 1


title: KDM3A shRNA Rh30 cells, replicate 3

source_name: Rh30 (SJRH30; ATCC® CRL-2061™)


title: C201R 14701-5

description:
16NGS-002-Burgess-Sample-3
Rpl-C201R-ChAT-sc-14701-5-GES16-01925_S2


title: KDM3A shRNA Rh30 cells, replicate 2


title: KDM3A shRNA Rh30 cells, replicate 1


title: WT 14702-3

description:
16NGS-002-Burgess-Sample-15
Rpl-ChAT-sc-14702-3-GES16-02254_S18


title: control shRNA Rh30 cells, replicate 3


title: control shRNA Rh30 cells, replicate 2


title: C201R 14003-1

description:
16NGS-002-Burgess-Sample-1
Rpl-C201R-ChAT-sc-14003-1-GES16-01928_S6


title: C201R 14004-2

description:
16NGS-002-Burgess-Sample-2
Rpl-C201R-ChAT-sc-14004-2-GES16-02253_S10


title: control shRNA Rh30 cells, replicate 1


title: Rpl22 Chat Ctrl uncrushed spinal cord 11302 6

source_name: Rpl22 Chat Ctrl uncrushed spinal cord

treatment_protocol: For the unilateral sciatic nerve crush surgery mice were anesthetized with isofluorane and placed on a heating pad to maintain body temperature.  Ophthalmic ointment was placed over the eyes and .5mg/ml carprofen was administered through subcutaneous injection at a dose of .1µl/10g body weight.  Hair was removed from the leg and the mouse was moved to a sterile surgical area.  The area of skin to be cut was cleaned with 70% ethanol and chlorhexidine diluted 1:256 in water.  A 1-2mm incision was made in the skin directly below the femur.  Connective tissue is gently cleared away with forceps and the sciatic nerve is identified.  The nerve was crushed with forceps for 10 seconds, released, and crushed once more for 10 seconds.  The incision site is sutured and 1-2 drops of 2.5 mg/ml bupivacaine is administered to the wound site. Mouse is placed in a warmed cage and monitored until it returns to consciousness.


title: 96h PF-9927 activated CD3+ rep 3

city: San Diego

first: Patrick

middle: J

last: Metz

address: 10777 Science Center Dr.

institute: Pfizer, Oncology Research, Development, & Medical

description:
tagmented DNA
CD3.T.cells_9927_3
processed data file:

data_processing:
ATAC samples were aligned to hg38 reference genome using bowtie2 v2.1.0
Peak calling was performed using MACS2 v2.1.0
Genome_build: hg38
Supplementary_files_format_and_content: .bigwig and .narrowPeak files for chromatin accessibility

source_name: 96h PF-9927 activated CD3+

growth_protocol: Naïve T cells were isolated from peripheral blood and activated with platebound anti-CD3/anti-CD28 + IL-2 for 72 or 96 hours

extract_protocol:
Cells were slow frozen in Cell freezing media
Tagmented DNA was prepared by the UCSD Center for Epigenomic

treatment_protocol: Cells were treated with DMSO or 300 nM PF-9927

value: peripheral blood

value: Naive T lymphocytes

tag: treatment


title: Rpl22 Chat Ctrl uncrushed spinal cord 11302 4


title: Rpl22 Chat uncrushed spinal cord 11302 3

source_name: Rpl22 Chat uncrushed spinal cord


title: Rpl22 Chat crushed spinal cord 52

source_name: Rpl22 Chat crushed spinal cord

value: 9 weeks


title: Rpl22 Chat Ctrl crushed spinal cord 58

source_name: Rpl22 Chat Ctrl crushed spinal cord


title: 96h DMSO activated CD3+ rep 1

description:
tagmented DNA
CD3.T.cells_DMSO_1
processed data file:

source_name: 96h DMSO activated CD3+

value: 96h DMSO


title: 96h DMSO activated CD3+ rep 3

description:
tagmented DNA
CD3.T.cells_DMSO_3
processed data file:


title: 72h PF-9927 activated CD8+ rep 3

description:
9927_CD8+_3_L6.D712
processed data file:
TPM_all.txt
A3SS.MATS.ReadsOnTargetAndJunctionCounts_DMSO.9927.CD8.txt
A5SS.MATS.ReadsOnTargetAndJunctionCounts_DMSO.9927.CD8.txt
MXE.MATS.ReadsOnTargetAndJunctionCounts_DMSO.9927.CD8.txt
RI.MATS.ReadsOnTargetAndJunctionCounts_DMSO.9927.CD8.txt
SE.MATS.ReadsOnTargetAndJunctionCounts_DMSO.9927.CD8.txt

data_processing:
Gene expression and splicing data were aligned to the hg19 reference genome using STAR 2.5.2
Gene expression was determined using edgeR 3.16.5
Splicing analysis was performed using rMATS 3.2.5
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimted text files for TPM counts for gene expression and for on-target and junction read counts for splicing

source_name: 72h PF-9927 activated CD8+

extract_protocol:
Cells were stored in RNAprotect cell reagent (Qiagen Cat# 76526) and isolated by Q2 solutions using Rneasy mini kits (Qiagen 72014)
RNA libraries were prepared for sequencing using standard Illumina protocols


title: Rpl22 Chat crushed spinal cord 35

value: 18 weeks


title: 72h PF-9927 activated CD8+ rep 1

description:
9927_CD8+_1_L6.D710
processed data file:
TPM_all.txt
A3SS.MATS.ReadsOnTargetAndJunctionCounts_DMSO.9927.CD8.txt
A5SS.MATS.ReadsOnTargetAndJunctionCounts_DMSO.9927.CD8.txt
MXE.MATS.ReadsOnTargetAndJunctionCounts_DMSO.9927.CD8.txt
RI.MATS.ReadsOnTargetAndJunctionCounts_DMSO.9927.CD8.txt
SE.MATS.ReadsOnTargetAndJunctionCounts_DMSO.9927.CD8.txt


title: Rpl22 Chat Ctrl crushed spinal cord 51


title: 72h PF-9927 activated CD8+ rep 2

description:
9927_CD8+_2_L6.D711
processed data file:
TPM_all.txt
A3SS.MATS.ReadsOnTargetAndJunctionCounts_DMSO.9927.CD8.txt
A5SS.MATS.ReadsOnTargetAndJunctionCounts_DMSO.9927.CD8.txt
MXE.MATS.ReadsOnTargetAndJunctionCounts_DMSO.9927.CD8.txt
RI.MATS.ReadsOnTargetAndJunctionCounts_DMSO.9927.CD8.txt
SE.MATS.ReadsOnTargetAndJunctionCounts_DMSO.9927.CD8.txt


title: 5327 WT, Nicotine (M)

data_processing:
Basecalls performed using CASAVA version 1.8.2
Raw reads were all trimmed to 50bp and mapped to the reference genome using STAR 2.4 with --outFilterMultimapNmax 1
Raw count measurements were obtained with featureCounts 1.4.6 keeping only unambiguous reads
Genome_build: GRCm38.80
Supplementary_files_format_and_content: Raw counts

source_name: Lung

growth_protocol: C57BL/6J mice, obtained from the mice facility of University of Geneva were kept under specific-pathogen-free conditions. Housing conditions were 12 hours day and 12 hours night. Mice had access to food and drinking water ad libitum.

extract_protocol:
Offspring lungs were collected at PND2, snap frozen in liquid nitrogen and stored at -80˚C. RNA was isolated and purified using Macherey-Nagel purification kit (Germany). Six offspring lung were used for the saccharin group and five offspring lung were used for nicotine group. cDNA libraries were constructed by the Genomic platform of the University of Geneva using the Illumina TruSeq RNA Sample Preparation Kit (CA, USA) according to the manufacturer's protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Nicotine (200 mg/L) was started immediately after mating and administered to the females in drinking water supplemented with 2% saccharin for the whole period of gestation and lactation (nicotine group). As a control, we used drinking water with 2% saccharin (saccharin group).

value: Lung

value: post natal day 2

tag: gender

value: M

tag: agent

value: Nicotine


title: 72h DMSO activated CD8+ rep 3

description:
DMSO_CD8+_3_L6.D709
processed data file:
TPM_all.txt
A3SS.MATS.ReadsOnTargetAndJunctionCounts_DMSO.naive.CD8.txt
A5SS.MATS.ReadsOnTargetAndJunctionCounts_DMSO.naive.CD8.txt
MXE.MATS.ReadsOnTargetAndJunctionCounts_DMSO.naive.CD8.txt
RI.MATS.ReadsOnTargetAndJunctionCounts_DMSO.naive.CD8.txt
SE.MATS.ReadsOnTargetAndJunctionCounts_DMSO.naive.CD8.txt
A3SS.MATS.ReadsOnTargetAndJunctionCounts_DMSO.9927.CD8.txt
A5SS.MATS.ReadsOnTargetAndJunctionCounts_DMSO.9927.CD8.txt
MXE.MATS.ReadsOnTargetAndJunctionCounts_DMSO.9927.CD8.txt
RI.MATS.ReadsOnTargetAndJunctionCounts_DMSO.9927.CD8.txt
SE.MATS.ReadsOnTargetAndJunctionCounts_DMSO.9927.CD8.txt

source_name: 72h DMSO activated CD8+

tag: tissue

value: 72h DMSO


title: 5328 WT, Nicotine (M)

tag: strain

value: wild type


title: 72h DMSO activated CD8+ rep 1

description:
DMSO_CD8+_1_L6.D707
processed data file:
TPM_all.txt
A3SS.MATS.ReadsOnTargetAndJunctionCounts_DMSO.naive.CD8.txt
A5SS.MATS.ReadsOnTargetAndJunctionCounts_DMSO.naive.CD8.txt
MXE.MATS.ReadsOnTargetAndJunctionCounts_DMSO.naive.CD8.txt
RI.MATS.ReadsOnTargetAndJunctionCounts_DMSO.naive.CD8.txt
SE.MATS.ReadsOnTargetAndJunctionCounts_DMSO.naive.CD8.txt
A3SS.MATS.ReadsOnTargetAndJunctionCounts_DMSO.9927.CD8.txt
A5SS.MATS.ReadsOnTargetAndJunctionCounts_DMSO.9927.CD8.txt
MXE.MATS.ReadsOnTargetAndJunctionCounts_DMSO.9927.CD8.txt
RI.MATS.ReadsOnTargetAndJunctionCounts_DMSO.9927.CD8.txt
SE.MATS.ReadsOnTargetAndJunctionCounts_DMSO.9927.CD8.txt

tag: cell type


title: 5324 WT, saccharin (F)

value: F

value: saccharin


title: 96h PF-9927 activated CD3+ rep 1

description:
tagmented DNA
CD3.T.cells_9927_1
processed data file:


title: 5323 WT, saccharin (F)


title: 72h DMSO activated CD8+ rep 2

description:
DMSO_CD8+_2_L6.D708
processed data file:
TPM_all.txt
A3SS.MATS.ReadsOnTargetAndJunctionCounts_DMSO.naive.CD8.txt
A5SS.MATS.ReadsOnTargetAndJunctionCounts_DMSO.naive.CD8.txt
MXE.MATS.ReadsOnTargetAndJunctionCounts_DMSO.naive.CD8.txt
RI.MATS.ReadsOnTargetAndJunctionCounts_DMSO.naive.CD8.txt
SE.MATS.ReadsOnTargetAndJunctionCounts_DMSO.naive.CD8.txt
A3SS.MATS.ReadsOnTargetAndJunctionCounts_DMSO.9927.CD8.txt
A5SS.MATS.ReadsOnTargetAndJunctionCounts_DMSO.9927.CD8.txt
MXE.MATS.ReadsOnTargetAndJunctionCounts_DMSO.9927.CD8.txt
RI.MATS.ReadsOnTargetAndJunctionCounts_DMSO.9927.CD8.txt
SE.MATS.ReadsOnTargetAndJunctionCounts_DMSO.9927.CD8.txt


title: 96h PF-9927 activated CD3+ rep 2

description:
tagmented DNA
CD3.T.cells_9927_2
processed data file:


title: 5322 WT, saccharin (F)


title: FLAG_Foxf2_ChIP

city: Cincinnati

first: Jingyue

last: Xu

state: Ohio

address: 3333 burnet avenue

department: Developmental Biology

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Raw FASTQ files were aligned to mouse mm9 reference genome using Bowtie 1.0.0
Sam files were converted to bam using samtools (0.1.19)
Peak calling was performed using the HOMER (Hypergeometric Optimization of Motif EnRichment, version 4.8) software.
The input samples were used as the control for calling peaks from the Foxf2-FLAG ChIP-seq data set.
Genome_build: mm9
Supplementary_files_format_and_content: bed file was generated by Homer including the peak information

source_name: palate cells

growth_protocol: We generated mice carrying 3xFLAG epitope-tagged endogenous Foxf2 protein using the CRISPR/Cas9-mediated genome editing technology. 50 pairs of palatal shelves were dissected from Foxf2FLAG/FLAG embryos at E13.5.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with anti-FLAG antibody.
Sequencing libraries were generated using Rubicon ThruPLEX DNA sequencing kit (Rubicon Genomics, Ann Arbor MI).

value: palate cells

tag: developmental stage

value: anti-FLAG


title: Naïve CD8+ rep 2

description:
Naïve_CD8+_2_L5.D705
processed data file:
TPM_all.txt
A3SS.MATS.ReadsOnTargetAndJunctionCounts_DMSO.naive.CD8.txt
A5SS.MATS.ReadsOnTargetAndJunctionCounts_DMSO.naive.CD8.txt
MXE.MATS.ReadsOnTargetAndJunctionCounts_DMSO.naive.CD8.txt
RI.MATS.ReadsOnTargetAndJunctionCounts_DMSO.naive.CD8.txt
SE.MATS.ReadsOnTargetAndJunctionCounts_DMSO.naive.CD8.txt

source_name: Naïve CD8+


title: Naïve CD8+ rep 1

description:
Naïve_CD8+_1_L5.D704
processed data file:
TPM_all.txt
A3SS.MATS.ReadsOnTargetAndJunctionCounts_DMSO.naive.CD8.txt
A5SS.MATS.ReadsOnTargetAndJunctionCounts_DMSO.naive.CD8.txt
MXE.MATS.ReadsOnTargetAndJunctionCounts_DMSO.naive.CD8.txt
RI.MATS.ReadsOnTargetAndJunctionCounts_DMSO.naive.CD8.txt
SE.MATS.ReadsOnTargetAndJunctionCounts_DMSO.naive.CD8.txt


title: 72h PF-9927 activated CD4+ rep 3

description:
9927_CD4+_3_L5.D703
processed data file:
TPM_all.txt
A3SS.MATS.ReadsOnTargetAndJunctionCounts_DMSO.9927.CD4.txt
A5SS.MATS.ReadsOnTargetAndJunctionCounts_DMSO.9927.CD4.txt
MXE.MATS.ReadsOnTargetAndJunctionCounts_DMSO.9927.CD4.txt
RI.MATS.ReadsOnTargetAndJunctionCounts_DMSO.9927.CD4.txt
SE.MATS.ReadsOnTargetAndJunctionCounts_DMSO.9927.CD4.txt

source_name: 72h PF-9927 activated CD4+


title: 5197 WT, saccharin (F)


title: 5196 WT, saccharin (M)


title: 96h DMSO activated CD3+ rep 2

description:
tagmented DNA
CD3.T.cells_DMSO_2
processed data file:


title: 5195 WT, saccharin (M)


title: 72h PF-9927 activated CD4+ rep 1

description:
9927_CD4+_1_L5.D701
processed data file:
TPM_all.txt
A3SS.MATS.ReadsOnTargetAndJunctionCounts_DMSO.9927.CD4.txt
A5SS.MATS.ReadsOnTargetAndJunctionCounts_DMSO.9927.CD4.txt
MXE.MATS.ReadsOnTargetAndJunctionCounts_DMSO.9927.CD4.txt
RI.MATS.ReadsOnTargetAndJunctionCounts_DMSO.9927.CD4.txt
SE.MATS.ReadsOnTargetAndJunctionCounts_DMSO.9927.CD4.txt


title: 5124 WT, Nicotine (F)

value: post natal day 16


title: 5120 WT, saccharin (M)


title: 5171 WT, Nicotine (F)


title: Naïve CD4+ rep 2

description:
Naïve_CD4+_2_L4.D708
processed data file:
TPM_all.txt
A3SS.MATS.ReadsOnTargetAndJunctionCounts_DMSO.naive.CD4.txt
A5SS.MATS.ReadsOnTargetAndJunctionCounts_DMSO.naive.CD4.txt
MXE.MATS.ReadsOnTargetAndJunctionCounts_DMSO.naive.CD4.txt
RI.MATS.ReadsOnTargetAndJunctionCounts_DMSO.naïve.CD4.txt
SE.MATS.ReadsOnTargetAndJunctionCounts_DMSO.naïve.CD4.txt

source_name: Naïve CD4+


title: TNF_rep1

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads were mapped to the reference genome using STAR 2.4 with --outFilterMultimapNmax 1
Raw count measurements were obtained with featureCounts 1.4.6 keeping only unambiguous reads
Genome_build: GRCm38.89
Supplementary_files_format_and_content: Raw counts measurements

extract_protocol:
RNA was isolated from 3 independent skin donors with mirVana miRNA Isolation Kit from Invitrogen (Oslo, Norway).
cDNA libraries were constructed by the Genomic platform of the University of Geneva using the Illumina TruSeq RNA stranded Kit according to the manufacturer's protocol.

value: Skin

value: TNF


title: Naïve CD4+ rep 3

description:
Naïve_CD4+_3_L1
processed data file:
TPM_all.txt
A3SS.MATS.ReadsOnTargetAndJunctionCounts_DMSO.naive.CD4.txt
A5SS.MATS.ReadsOnTargetAndJunctionCounts_DMSO.naive.CD4.txt
MXE.MATS.ReadsOnTargetAndJunctionCounts_DMSO.naive.CD4.txt
RI.MATS.ReadsOnTargetAndJunctionCounts_DMSO.naïve.CD4.txt
SE.MATS.ReadsOnTargetAndJunctionCounts_DMSO.naïve.CD4.txt

value: peripheral blood

value: Naive T lymphocytes


title: TNF_rep2


title: 5170 WT, Nicotine (F)


title: 72h DMSO activated CD4+ rep 2

description:
DMSO_CD4+_2_L2
processed data file:
TPM_all.txt
A3SS.MATS.ReadsOnTargetAndJunctionCounts_DMSO.naive.CD4.txt
A5SS.MATS.ReadsOnTargetAndJunctionCounts_DMSO.naive.CD4.txt
MXE.MATS.ReadsOnTargetAndJunctionCounts_DMSO.naive.CD4.txt
RI.MATS.ReadsOnTargetAndJunctionCounts_DMSO.naïve.CD4.txt
SE.MATS.ReadsOnTargetAndJunctionCounts_DMSO.naïve.CD4.txt
A3SS.MATS.ReadsOnTargetAndJunctionCounts_DMSO.9927.CD4.txt
A5SS.MATS.ReadsOnTargetAndJunctionCounts_DMSO.9927.CD4.txt
MXE.MATS.ReadsOnTargetAndJunctionCounts_DMSO.9927.CD4.txt
RI.MATS.ReadsOnTargetAndJunctionCounts_DMSO.9927.CD4.txt
SE.MATS.ReadsOnTargetAndJunctionCounts_DMSO.9927.CD4.txt

source_name: 72h DMSO activated CD4+


title: TGFB_rep3

value: TGFB


title: FLAG_Foxf2_Input

value: none input


title: 5114 WT, saccharin (M)

value: Lung


title: 5119 WT, saccharin (F)


title: Naïve CD8+ rep 3

description:
Naïve_CD8+_3_L5.D706
processed data file:
TPM_all.txt
A3SS.MATS.ReadsOnTargetAndJunctionCounts_DMSO.naive.CD8.txt
A5SS.MATS.ReadsOnTargetAndJunctionCounts_DMSO.naive.CD8.txt
MXE.MATS.ReadsOnTargetAndJunctionCounts_DMSO.naive.CD8.txt
RI.MATS.ReadsOnTargetAndJunctionCounts_DMSO.naive.CD8.txt
SE.MATS.ReadsOnTargetAndJunctionCounts_DMSO.naive.CD8.txt


title: 72h DMSO activated CD4+ rep 1

description:
DMSO_CD4+_1_L4.D710
processed data file:
TPM_all.txt
A3SS.MATS.ReadsOnTargetAndJunctionCounts_DMSO.naive.CD4.txt
A5SS.MATS.ReadsOnTargetAndJunctionCounts_DMSO.naive.CD4.txt
MXE.MATS.ReadsOnTargetAndJunctionCounts_DMSO.naive.CD4.txt
RI.MATS.ReadsOnTargetAndJunctionCounts_DMSO.naïve.CD4.txt
SE.MATS.ReadsOnTargetAndJunctionCounts_DMSO.naïve.CD4.txt
A3SS.MATS.ReadsOnTargetAndJunctionCounts_DMSO.9927.CD4.txt
A5SS.MATS.ReadsOnTargetAndJunctionCounts_DMSO.9927.CD4.txt
MXE.MATS.ReadsOnTargetAndJunctionCounts_DMSO.9927.CD4.txt
RI.MATS.ReadsOnTargetAndJunctionCounts_DMSO.9927.CD4.txt
SE.MATS.ReadsOnTargetAndJunctionCounts_DMSO.9927.CD4.txt


title: TGFB_rep1


title: 72h DMSO activated CD4+ rep 3

description:
DMSO_CD4+_3_L4.D712
processed data file:
TPM_all.txt
A3SS.MATS.ReadsOnTargetAndJunctionCounts_DMSO.naive.CD4.txt
A5SS.MATS.ReadsOnTargetAndJunctionCounts_DMSO.naive.CD4.txt
MXE.MATS.ReadsOnTargetAndJunctionCounts_DMSO.naive.CD4.txt
RI.MATS.ReadsOnTargetAndJunctionCounts_DMSO.naïve.CD4.txt
SE.MATS.ReadsOnTargetAndJunctionCounts_DMSO.naïve.CD4.txt
A3SS.MATS.ReadsOnTargetAndJunctionCounts_DMSO.9927.CD4.txt
A5SS.MATS.ReadsOnTargetAndJunctionCounts_DMSO.9927.CD4.txt
MXE.MATS.ReadsOnTargetAndJunctionCounts_DMSO.9927.CD4.txt
RI.MATS.ReadsOnTargetAndJunctionCounts_DMSO.9927.CD4.txt
SE.MATS.ReadsOnTargetAndJunctionCounts_DMSO.9927.CD4.txt


title: TNF_rep3


title: 5126 WT, Nicotine (M)


title: 5172 WT, Nicotine (F)

value: post natal day 2


title: 5115 WT, saccharin (M)

value: M


title: 5125 WT, Nicotine (F)

value: Nicotine


title: Naïve CD4+ rep 1

description:
Naïve_CD4+_1_L4.D707
processed data file:
TPM_all.txt
A3SS.MATS.ReadsOnTargetAndJunctionCounts_DMSO.naive.CD4.txt
A5SS.MATS.ReadsOnTargetAndJunctionCounts_DMSO.naive.CD4.txt
MXE.MATS.ReadsOnTargetAndJunctionCounts_DMSO.naive.CD4.txt
RI.MATS.ReadsOnTargetAndJunctionCounts_DMSO.naïve.CD4.txt
SE.MATS.ReadsOnTargetAndJunctionCounts_DMSO.naïve.CD4.txt


title: 5116 WT, saccharin (F)


title: 72h PF-9927 activated CD4+ rep 2

description:
9927_CD4+_2_L5.D702
processed data file:
TPM_all.txt
A3SS.MATS.ReadsOnTargetAndJunctionCounts_DMSO.9927.CD4.txt
A5SS.MATS.ReadsOnTargetAndJunctionCounts_DMSO.9927.CD4.txt
MXE.MATS.ReadsOnTargetAndJunctionCounts_DMSO.9927.CD4.txt
RI.MATS.ReadsOnTargetAndJunctionCounts_DMSO.9927.CD4.txt
SE.MATS.ReadsOnTargetAndJunctionCounts_DMSO.9927.CD4.txt


title: TGFB_rep2


title: Rpl22 Chat uncrushed spinal cord 11302 10

value: 8 weeks

value: spinal cord

value: Ribosome-associated mRNA


title: IL17ATNF_rep3


title: IL17ATNF_rep2


title: IL17ATGFB_rep3


title: IL-17A_rep2


title: IL17ATNF_rep1


title: CTRL_rep3


title: CTRL_rep1


title: IL-17A_rep1


title: RSC96 cells, replicate 2

type: RNA

city: Neuherberg

first: Dietrich

last: Trümbach

address: Ingolstädter Landstraße 1

department: Institute for Developmental Genetics

country: Germany

institute: Helmholtz Zentrum München German Research Center for Environmental Health

description: Gene expression of rat Schwann control cells, i.e. RSC96 cells

hyb_protocol: After fragmentation, 600 ng of labeled cRNA from each sample was hybridized in in situ hybridization oven (Agilent) for 17 h at 65ºC and washed during 1 min at rt in Gene Expression Wash Buffer 1 (Agilent) and 1 min at 37 ºC with Gene Expression Wahs buffer 2 (Agilent).

scan_protocol: Scanned on an Agilent G2539A scanner at 3um resolution and 100%PMT. The intensity data of each individual hybridization were extracted and the quality was assessed with the Feature Extraction software 10.7 (Agilent).

data_processing: Raw data was corrected for background noise using the normexp method. Quantile normalization was applied to assure comparability across samples.

source_name: RSC96 control cells, replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100ng of total RNA using the LowInputQuick Amp Labeling kit – Agilent 5190-2305 according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA purification was done using the RNeasy mini kit (Qiagen) according to the manufacturer protocol.

tag: cell line name

value: Spontaneously immortalized Schwann cell


title: H3_correction_RGC_D10_p22_S19

city: INDIANAPOLIS

first: Xiaoyu

last: Lu

state: IN

address: 410W 10TH ST

department: school of medicine

institute: INDIANA UNIVERSITY

data_processing:
Data is mapping to human genome GRCh38 using STAR software
counts data are extract using featureCounts
Genome_build: GRCh38
Supplementary_files_format_and_content: counts data

source_name: OPTN correction iPSC-dervied RGC

growth_protocol: hPSCS were differentiated into retinal organoids. Retinal organoids were then dissoicated and RGCs were purified, and then plated on coverslips for 10 days. RNA was collected directly from the coverslips.

extract_protocol:
The RGCs were lysed and total RNA was extracted  with the PicoPure RNA isolation kit.
RNA libraries were prepared for sequencing using standard protocols

value: human pluripotent stem cell-derived retinal ganglion cells

tag: passage

tag: genotype/variation

value: WT Optineurin (OPTN) gene

tag: time point

value: 45 days of differentiation with additional 10 days after RGCs purification


title: H3_correction_RGC_D10_p24_S20


title: H3_E50K_RGC_D10_p35_S17

source_name: OPTN (E50K) iPSC-dervied RGC

value: E50K mutation in the Optineurin (OPTN) gene


title: H3_correction_RGC_D10_p21_S18


title: IL17ATGFB_rep1

value: Skin


title: IL-17A_rep3


title: IL17ATGFB_rep2


title: CTRL_rep2


title: H3_correction_RGC_D10_p25_S21


title: H3_E50K_RGC_D10_p34_S16


title: H3_E50K_RGC_D10_p32_S15


title: RSC96 cells, replicate 3

source_name: RSC96 control cells, replicate 3


title: SW480R Clone2

city: Shenyang

first: Yong

last: Zhou

state: Liaoning

address: 4 Chongshan Road

institute: the Fourth Affiliated Hospital of China Medical University

description:
Test
long non-coding RNAs
SAMPLE 5

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: https://geneglobe.qiagen.com/cn/analyze/
For the normalization it uses the average of five housekeeping genes: ACTB, B2M, GAPDH, HPRT1, RPLP0.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
Fold Change data file reports test/control (SW480R/SW480) ratios.

label: SYBR Green

source_name: SW480R Clone2

label_protocol: RT2 lncRNA qPCR Assay were performed using the Custom RT2 PCR Arrays (QIAGEN, Hilden, Germany) following the Manufacturer’s instructions. 1 mg RNA was reverse transcribed to cDNA in 20μl system by First Strand cDNA Synthesis Kit for RT-PCR (Merck & Co., Inc., Kenilworth, NJ, USA). Real-time PCR was performed using the Mx3000P real-time PCR system (Thermo Fisher Scientific, Waltham, MA, USA). PCR was carried out as follows: 40 cycles of 94 °C for 15s, 60 °C for 10s and 72 °C for 20s.

growth_protocol: SW480 obtained from American Type Culture Collection (Manassas, VA, USA) and was exposed to stepwise increasing Regorafenib for over 12 months. The survival cells were subsequently passaged and grew under the same conditions for more than 20 passages with 0.02μM Regorafenib. The regorafenib-adapted cells were termed SW480R. Cells were grown in RPMI-1640, supplemented with 10% FBS. All cell lines were maintained in a humidified incubator with 5% of CO2 and 95% air at 37°C.

extract_protocol: Total RNA was extracted by 1 mL TRIzol (Merck & Co., Inc., Kenilworth, NJ, USA)according to the manufacturer’s protocol.

value: regorafenib-resistant derived SW480

tag: phenotype

value: regorafenib-resistant cell line (passage 10)

value: colon cancer cell


title: SW480R Clone1

description:
Test
long non-coding RNAs
SAMPLE 4

source_name: SW480R Clone1


title: RSC96_Sox2+ cells, clone 2, replicate 2

description: Gene expression of rat Schwann cells after overexpression of Sox2, i.e. RSC96_Sox2+ cells

source_name: Sox2 overexpressing RSC96 cells of clone 2, replicate 2


title: RSC96_Sox2+ cells, clone 1, replicate 3

source_name: Sox2 overexpressing RSC96 cells of clone 1, replicate 3


title: RSC96 cells, replicate 1

source_name: RSC96 control cells, replicate 1


title: RSC96_Sox2+ cells, clone 1, replicate 2

source_name: Sox2 overexpressing RSC96 cells of clone 1, replicate 2


title: SW480R Clone3

description:
Test
long non-coding RNAs
SAMPLE 6

source_name: SW480R Clone3


title: RSC96_Sox2+ cells, clone 2, replicate 3

source_name: Sox2 overexpressing RSC96 cells of clone 2, replicate 3


title: SW480 Clone3

description:
Control
long non-coding RNAs
SAMPLE 3

source_name: SW480 Clone3

value: parental cell line (passage 0)


title: RSC96_Sox2+ cells, clone 1, replicate 1

source_name: Sox2 overexpressing RSC96 cells of clone 1, replicate 1


title: RSC96_Sox2+ cells, clone 2, replicate 1

source_name: Sox2 overexpressing RSC96 cells of clone 2, replicate 1