title: Urea TKS403C Skin 60s CTCF

extract_protocol:
Primary epidermal keratinocyotes  isolated from skin of Satb1+/+  mice (P5)  were cross-linked with 1% formaldehyde for 10 min at room temperature, followed by addition of glycine at 0.125 M for 5 min to quench cross-linking reaction. These cells were washed with 1X PBS, suspended in 1% BSA-PBS and cells were precipitated in a tube.  These cells were re-suspended in lysis buffer (4% SDS, 50 mM Tris-HCl [pH 8.0], 10 mM EDTA, 100 mM NaCl) with Protease inhibitor (Roche) and RNase inhibitor.  The resulting cell lysate was incubated for 30 min at room temperature and loaded on top of 8 M urea followed by ultracentrifugation in a Beckman TL-100 Ultracentrifuge for 4-5 hrs at 45K rpm (181,000g, g=relative centrifugation force or RCF; TLS55 rotor).  Recovered chromatin pellet was sonicated to generate fragment size ranging 300–1,000bp using Branson sonifier (20% power, 10 sec on and 30 sec off for 4-6 cycles) in 300ml of sonication buffer [0.5% Na-laurylsarcosine, 0.1% deoxycholate (DOC), 1mM EDTA, 0.5mM EGTA, 10mM TrisHCl, 100mM NaCl] with Protease inhibitor and RNase inhibitor. Note: urea-purified crosslinked chromatin is highly vulnerable to sonication, therefore, it needs to adjust the sonication condition depending on cell type and/or the size of the precipitate DNA.  The sonicated chromatin with 1% Triton X-100 were dialyzed against dialysis buffer (10 mM Tris-HCl [pH 8.0], 100 mM NaCl, 1 mM EDTA, 5% glycerol), and dialyzed for 16 hrs at 4°C (this dialysis is optional).  The chromatin sample was centrifuged at 15,000g for 5 min at 4°C to remove a trace amount of residual insoluble components.  The test-reverse cross-linking of chromatin aliquot (5-10ml of the final volume) was done at 65°C for 2-3 hrs in buffer containing 1% SDS, 100 mM NaCl, 1 mM EDTA, 10mMTris.  Samples were further treated by 100 µg/ml RNase A at 37°C for 1 hr, 200 µg/ml proteinase K at 60°C for more than 3 hrs, followed by DNA purification using QIAquick PCR purification kit (Qiagen), and shearing efficiency was examined by Bioanalyzer 2100 (Agilent Technologies Inc.). For chromatin-immunoprecipitation, 1 µg of an antibody of choice were added to 10 ~ 20 µg of sonicated solubilized chromatin in 350 ml in dilution buffer (1% Triton X-100, 0.01% SDS, 1 mM EDTA, 15 mM Tris-HCl, 100 mM NaCl) and incubated overnight with rotation at 4°C.  At least three chromatin samples were prepared for ChIP-seq from independent experiments to confirm the results. The chromatin fragments bound to antibodies (after incubation overnight) were captured using 20 µl of protein-A, protein-G or protein AG Dynabeads (Invitrogen; pre-washed with 0.1% BSA [Fraction V, Sigma), by 4 hrs incubation time at 4°C.  Dynabeads bound to chromatin fragments were washed twice with Binding buffer (10 mM Tris, pH8.0, 1 mM EDTA, 1 mM EGTA, 0.5% Triton X-100, 0.1% DOC, 100 mM NaCl), twice with LiCl buffer (100 mM Tris [pH 8.0], 1 mM EDTA, 250 mM LiCl, 0.5% NP-40, and 0.5% DOC).  The tubes were changed and washed twice with 0.1M NaCl-TE buffer. The immunoprecipitated samples were eluted from Dynabeads by elution buffer (10 mM Tris-HCl [pH 8.0], 1 mM EDTA, 100 mM NaCl and 1% SDS) at 65oC for 20 min.  After elution, ChIP DNAs was reverse-crosslinked at 65oC for 6 hrs, followed by RNase-A treatment at 37°C for 1 hr and proteinase K treatments for 3 hrs at 60°C. The recovered DNA was further purified with a QIAquick PCR purification kit (Qiagen), with elution in 15µl of Qiagen Elution Buffer (alternatively, Phenol-chloroform extraction and ethanol precipitation).
Briefly for library construction, ChIP DNA fragments were end-repaired and ligated to indexed sequencing adapters (NEB or Rubicon library kit) and amplified with 8-11 rounds of PCR, depending on the DNA amount.  Using SPRI beads (Beckmancoulter), small fragments (<200bp) were removed from the amplified library. The size-selected library was sequenced to 50bp single-end read lengths on an Illumina HiSeq4000 (Vincent J. Coates Genomic Sequencing Laboratory, UC Berkeley).

value: Skin

value: CTCF

value: Active MOTIF


title: D3 ES Jpx-AS CHART-seq, rep1

status: Public on Dec 01 2021

type: SRA

city: Boston

first: Hyun Jung

last: Oh

state: MA

address: 185 Cambridge St.

country: USA

institute: MGH

library_source: genomic

data_processing:
Library strategy: CHART-seq
CHART-Seq: CHART-seq reads were subjected to the trimming of adapter sequence and removal of duplicates using Trim Galore! (v0.4.1) and cutadapt (v1.2.1) and then mapped to CAST/EiJ (Mus m. castaneus; cas) and 129S1/SvImJ (Mus m. musculus; mus) genomes using Novoalign (v3.00.02) with the parameters (-i300 100 -t180 -F STDFQ -rRandom -h180 180 -v180). From the independent mapping to cas and mus reads, we generated composite (sum of neutral, cas-specific and mus-specific) reads mapped back to the mm9 genome using a previously published pipeline (Pinter et al. Spreading of X chromosome inactivation via a hierarchy of defined Polycomb stations. 2012). Composite bam files having only uniquely aligned reads were used. The input-subtracted coverage (bigWig) files for each CHART experiment were generated using SPP software with a window of 500 bp and step size 100 bp (get.smoothed.tag.density). Coverage (bigWig) of input was normalized by FPM (Fragments Per Million mapped reads) scaling factor.
Genome_build: mm9
Supplementary_files_format_and_content: Input-subtracted coverage (bigWig) files generated by SPP. FPM-normalized coverage (bigWig) files are provided for input.

molecule: genomic DNA

organism: Mus musculus

source_name: Day 3 ES cells

growth_protocol: Undifferentiated female mouse embryonic stem cells were grown on the irradiated MEF feeders in regular DMEM medium (high-glucose) with 15% FBS and LIF. For differentiation, cells were trypsinizied and incubated in the medium at 37 °C for at least 40 min. After separation of ES cells from attached feeders, ES cells were re-plated on non-gelatinized petri dishes in the complete DMEM medium without LIF. Embryonic bodies (EB) formed from ES cells were transferred to the gelatinized cell culture plates on day 4 of differentiation. Cells were harvested on indicated days.

extract_protocol: CHART-seq: Cells were crosslinked with 1% formaldehyde and nuclei were further crosslinked with 3% formaldehyde. Nuclei chromatin was sheared by sonication to yield the majority of fragments with approximately 3kb. The resulting extracts were hybridized with either Jpx CHART probes (biotinylated DNA oligonucleotides that were complementary to Jpx) or Jpx AS CHART probes (the reverse complement of Jpx CHART probes) and then captured by streptavidin beads. After washes, DNA was eluted in the elution buffer with RNase H. No-RNaseH CHART was generated from Jpx CHART eluant in the absence of RNase H. CHART enriched DNA was further sonicated and subjected to library construction steps including end-repair, dA-tailing, adaptor ligation, double-size selection and PCR amplification using NEBNext® ChIP-Seq Library Prep Master Mix Set for Illumina.

tag: strain

value: CAST/EiJ x 129S1

tag: cell type

value: Differentiating mESC (day 3)

tag: molecule subtype

value: Jpx AS CHART-enriched DNA


title: D7 ES no-RNase H CHART-seq, rep1

source_name: Day 7 ES cells

value: Differentiating mESC (day 7)

value: DNA enriched by no-RNase H elution for Jpx CHART


title: D3 ES Jpx CHART-seq, rep1

value: Jpx CHART-enriched DNA


title: D0 ES no-RNase H CHART-seq, rep1

source_name: Day 0 ES cells

value: Undifferentiated mESC (day 0)


title: D0 ES CHART-seq input, rep1

value: Input DNA


title: D3 ES no-RNase H CHART-seq, rep1


title: Urea TKS345 Brain 10 cycles Satb1 1583D (replica 1)

status: Public on Dec 28 2021

city: San Francisco

first: Terumi

last: Kohwi-Shigematsu

state: CA

address: 513 Parnassus Ave (HSW810)

department: Department of Orofacial Sciences

institute: UCSF

data_processing:
Sequenced reads were quality-checked using FastQC prior to downstream analysis. Unaligned reads were mapped to the mouse reference genome (NCBI37/mm9) using Bowtie2 (version 2.3.1).  Candidate binding sites were called using MACS2 (v2.2.7) using a q-value threshold of 0.01. Coverage tracks are presented in RPM (read pileups per million reads) and utilities from UCSC were used for creating browser tracks.
assembly: mmp9

source_name: SATB1 Wild-type

extract_protocol:
Single cell suspension was prepared from cortex of Satb1+/+ mice (P13).  Isolated cells (note: only neurons express SATB1) were cross-linked with 1% formaldehyde for 10 min at room temperature, followed by addition of glycine at 0.125 M for 5 min to quench cross-linking reaction. These cells were washed with 1X PBS, suspended in 1% BSA-PBS and cells were precipitated in a tube.  These cells were re-suspended in lysis buffer (4% SDS, 50 mM Tris-HCl [pH 8.0], 10 mM EDTA, 100 mM NaCl) with Protease inhibitor (Roche) and RNase inhibitor.  The resulting cell lysate was incubated for 30 min at room temperature and loaded on top of 8 M urea followed by ultracentrifugation in a Beckman TL-100 Ultracentrifuge for 4-5 hrs at 45K rpm (181,000g, g=relative centrifugation force or RCF; TLS55 rotor).  Recovered chromatin pellet was sonicated to generate fragment size ranging 300–1,000bp using Branson sonifier (20% power, 10 sec on and 30 sec off for 4-6 cycles) in 300ml of sonication buffer [0.5% Na-laurylsarcosine, 0.1% deoxycholate (DOC), 1mM EDTA, 0.5mM EGTA, 10mM TrisHCl, 100mM NaCl] with Protease inhibitor and RNase inhibitor. Note: urea-purified crosslinked chromatin is highly vulnerable to sonication, therefore, it needs to adjust the sonication condition depending on cell type and/or the size of the precipitate DNA.  The sonicated chromatin with 1% Triton X-100 were dialyzed against dialysis buffer (10 mM Tris-HCl [pH 8.0], 100 mM NaCl, 1 mM EDTA, 5% glycerol), and dialyzed for 16 hrs at 4°C (this dialysis is optional).  The chromatin sample was centrifuged at 15,000g for 5 min at 4°C to remove a trace amount of residual insoluble components.  The test-reverse cross-linking of chromatin aliquot (5-10ml of the final volume) was done at 65°C for 2-3 hrs in buffer containing 1% SDS, 100 mM NaCl, 1 mM EDTA, 10mMTris.  Samples were further treated by 100 µg/ml RNase A at 37°C for 1 hr, 200 µg/ml proteinase K at 60°C for more than 3 hrs, followed by DNA purification using QIAquick PCR purification kit (Qiagen), and shearing efficiency was examined by Bioanalyzer 2100 (Agilent Technologies Inc.). For chromatin-immunoprecipitation, 1 µg of an antibody of choice were added to 10 ~ 20 µg of sonicated solubilized chromatin in 350 ml in dilution buffer (1% Triton X-100, 0.01% SDS, 1 mM EDTA, 15 mM Tris-HCl, 100 mM NaCl) and incubated overnight with rotation at 4°C.  At least three chromatin samples were prepared for ChIP-seq from independent experiments to confirm the results. The chromatin fragments bound to antibodies (after incubation overnight) were captured using 20 µl of protein-A, protein-G or protein AG Dynabeads (Invitrogen; pre-washed with 0.1% BSA [Fraction V, Sigma), by 4 hrs incubation time at 4°C.  Dynabeads bound to chromatin fragments were washed twice with Binding buffer (10 mM Tris, pH8.0, 1 mM EDTA, 1 mM EGTA, 0.5% Triton X-100, 0.1% DOC, 100 mM NaCl), twice with LiCl buffer (100 mM Tris [pH 8.0], 1 mM EDTA, 250 mM LiCl, 0.5% NP-40, and 0.5% DOC).  The tubes were changed and washed twice with 0.1M NaCl-TE buffer. The immunoprecipitated samples were eluted from Dynabeads by elution buffer (10 mM Tris-HCl [pH 8.0], 1 mM EDTA, 100 mM NaCl and 1% SDS) at 65oC for 20 min.  After elution, ChIP DNAs was reverse-crosslinked at 65oC for 6 hrs, followed by RNase-A treatment at 37°C for 1 hr and proteinase K treatments for 3 hrs at 60°C. The recovered DNA was further purified with a QIAquick PCR purification kit (Qiagen), with elution in 15µl of Qiagen Elution Buffer (alternatively, Phenol-chloroform extraction and ethanol precipitation).
Briefly for library construction, ChIP DNA fragments were end-repaired and ligated to indexed sequencing adapters (NEB or Rubicon library kit) and amplified with 8-11 rounds of PCR, depending on the DNA amount.  Using SPRI beads (Beckmancoulter), small fragments (<200bp) were removed from the amplified library. The size-selected library was sequenced to 50bp single-end read lengths on an Illumina HiSeq4000 (Vincent J. Coates Genomic Sequencing Laboratory, UC Berkeley).

value: Brain

tag: age

value: 5 weeks

tag: antibody

value: Satb1 1583D

tag: chip antibody vendor

value: home made

tag: genotype

value: SATB1 Wild-type

tag: chromatin

value: urea purified chromatin


title: D0 ES Jpx-AS CHART-seq, rep1


title: D0 ES Jpx CHART-seq, rep1

data_processing:
Library strategy: CHART-seq
CHART-Seq:  CHART-seq reads were subjected to the trimming of adapter sequence and removal of duplicates using Trim Galore! (v0.4.1) and cutadapt (v1.2.1) and then mapped to CAST/EiJ (Mus m. castaneus; cas) and 129S1/SvImJ (Mus m. musculus; mus) genomes using Novoalign (v3.00.02) with the parameters (-i300 100 -t180 -F STDFQ -rRandom -h180 180 -v180). From the independent mapping to cas and mus reads, we generated composite (sum of neutral, cas-specific and mus-specific) reads mapped back to the mm9 genome using a previously published pipeline (Pinter et al. Spreading of X chromosome inactivation via a hierarchy of defined Polycomb stations. 2012). Composite bam files having only uniquely aligned reads were used. The input-subtracted coverage (bigWig) files for each CHART experiment were generated using SPP software with a window of 500 bp and step size 100 bp (get.smoothed.tag.density). Coverage (bigWig) of input was normalized by FPM (Fragments Per Million mapped reads) scaling factor.
Genome_build: mm9
Supplementary_files_format_and_content: Input-subtracted coverage (bigWig) files generated by SPP. FPM-normalized coverage (bigWig) files are provided for input.


title: D7 ES JpxKD Hi-C rep1_1

description: processed data: d7.KD.combined.Hi-C.hic

data_processing:
Hi-C: Illumina adaptor-trimmed reads were further trimmed with the options "-a GATCGATC (MboI ligation junction) and -m 20." Individual reads of each pair were separately mapped to the mus (129S1/SvImJ) and cas (CAST/EiJ)  genomes (mm9) using Novoalign (v4.02.01) with the parameters "-F STDFQ -r None." Composite reads having only uniquely aligned reads were generated as described in CHART-seq data processing, and then merged into Hi-C summary files and filtered using HOMER (v4.10) with the parameters "makeTagDirectory -tbp1; makeTagDirectory -update -removePEbg -restrictionSite GATC -both -removeSelfLigation." To increase sequencing depth, HOMER tag directories from the two biological replicates were combined. To obtain the same number of valid contacts for control and Jpx-depleted cells, down-sampling of the larger HOMER tag file (control sample) was performed as follows. First, the linux command shuf (coreutils/8.27) was used to randomize tags. Then, because there are paired-tags in HOMER directory, both paired-tags were removed until the number of tags were reduced to the same size of the smaller tag file. As a result, we used the exact same number (898,009,206) of valid contacts for both control and Jpx KD Hi-C. Hi-C contact maps in "hic" format were generated using the command "Juicer.sh pre mm9" of Juicer tools (v1.5.3)(Durand et al., Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments. 2016).
Genome_build: mm9
Supplementary_files_format_and_content: Hi-C contact map in "hic" format.

extract_protocol: Hi-C ligated DNA were generated based on the in-situ Hi-C protocol (Rao et al., 2014) with minor modifications. The resulting in situ Hi-C DNA were sheared into fragments by sonication in microtube using a Covaris E220 (10 % duty cycle, 140 peak incident power, 200 cycles/burst, 110 s), subjected to double-size selection using AMPure beads (0.55X-0.8X) followed by biotin pull-down using 30 µL of Dynabeads MyOne Streptavidin C1 beads, and amplified with Illumina primers for 12 cycles of PCR to prepare for sequencing (paired-end 150bp).

treatment_protocol: LNA transfection: ES cells on day 7 of differentiation were trypsinized, transfected with scrambled LNA or Jpx LNA #1 by nucleofection, transferred to the gelatinized plates and harvested after incubation at 37°C  for 8 hr.

tag: transfection

value: Jpx LNA#1-transfected


title: D7 ES Control Hi-C rep1_1

description: processed data: d7.control.combined.Hi-C.hic

data_processing:
Hi-C: Illumina adaptor-trimmed reads were further trimmed with the options "-a GATCGATC (MboI ligation junction) and -m 20." Individual reads of each pair were separately mapped to the mus (129S1/SvImJ) and cas (CAST/EiJ) genomes (mm9) using Novoalign (v4.02.01) with the parameters "-F STDFQ -r None."  Composite reads having only uniquely aligned reads were generated as described in CHART-seq data processing, and then merged into Hi-C summary files and filtered using HOMER (v4.10) with the parameters "makeTagDirectory -tbp1; makeTagDirectory -update -removePEbg -restrictionSite GATC -both -removeSelfLigation." To increase sequencing depth, HOMER tag directories from the two biological replicates were combined. To obtain the same number of valid contacts for control and Jpx-depleted cells, down-sampling of the larger HOMER tag file (control sample) was performed as follows. First, the linux command shuf (coreutils/8.27) was used to randomize tags. Then, because there are paired-tags in HOMER directory, both paired-tags were removed until the number of tags were reduced to the same size of the smaller tag file. As a result, we used the exact same number (898,009,206) of valid contacts for both control and Jpx KD Hi-C. Hi-C contact maps in "hic" format were generated using the command "Juicer.sh pre mm9" of Juicer tools (v1.5.3)(Durand et al., Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments. 2016).
Genome_build: mm9
Supplementary_files_format_and_content: Hi-C contact map in "hic" format.

treatment_protocol: LNA transfection: ES cells on day 7 of differentiation were trypsinized, transfected with scrambled LNA or Jpx LNA#1 by nucleofection, transferred to the gelatinized plates and harvested after incubation at 37°C  for 8 hr.

value: Scrambled LNA-transfected


title: D7 ES JpxKD Hi-C rep2_2

description: processed data:d7.KD.combined.Hi-C.hic


title: D7 ES Jpx KD RAD21 ChIP-seq RAD21, rep1

description: processed data: d7.control.RAD21.combined.input_normalized_Spp.wig.bw

data_processing:
ChIP-Seq: ChIP-seq reads were subjected to the trimming of adapter sequence and removal of duplicates using Trim Galore! (v0.4.1) and cutadapt (v1.18) and then mapped to CAST/EiJ (Mus m. castaneus; cas) and 129S1/SvImJ (Mus m. musculus; mus) genomes using Novoalign (v4.02.01) with the parameters (-i300 100 -t180 -F STDFQ -rRandom -h180 180 -v180). From the independent mapping to cas and mus reads, we generated composite (sum of neutral, cas-specific and mus-specific) reads mapped back to the mm9 genome using a previously published pipeline (Pinter et al. Spreading of X chromosome inactivation via a hierarchy of defined Polycomb stations. 2012). Composite bam files having only uniquely aligned reads were used. Log2 fold-enrichment estimates (relative to input) coverage (bigWig) files for ChIP were generated using SPP software with a window of 150 bp and step size 25 bp (get.conservative.fold.enrichment.profile). Coverage (bigWig) of input was normalized by FPM (Fragments Per Million mapped reads) scaling factor. For RAD21 ChIP-seq, the bam files from two biologcal replicates were pooled to increase the sequencing depath, and then used to generate coverage files (bigWig).
Genome_build: mm9
Supplementary_files_format_and_content: Log2 fold-enrichment estimates (relative to input) coverage (bigWig) files generated by SPP. FPM-normalized coverage (bigWig) files for input.

extract_protocol: Nuclei chromatin was prepared from the cells crosslinked with 1% formaldehyde and sheared by sonication. RAD21 ChIP was performed using RAD21 antibody (Abcam, #ab992). Library construction was performed using NEBNext Ultra II DNA Library Prep Kit for Illumina (E7645S).

value: RAD21 ChIP-enriched DNA


title: D7 ES JpxKD Hi-C rep2_1

description: processed data:d7.KD.combined.Hi-C.hic

value: CAST/EiJ x 129S1


title: D7 ES Control Hi-C rep2_2

description: processed data:d7.control.combined.Hi-C.hic

data_processing:
Hi-C: Illumina adaptor-trimmed reads were further trimmed with the options "-a GATCGATC (MboI ligation junction) and -m 20." Individual reads of each pair were separately mapped to the mus (129S1/SvImJ) and cas (CAST/EiJ)  genomes (mm9) using Novoalign (v4.02.01) with the parameters "-F STDFQ -r None." Composite reads having only uniquely aligned reads were generated as described in CHART-seq data processing, and then merged into Hi-C summary files and filtered using HOMER (v4.10) with the parameters "makeTagDirectory -tbp1; makeTagDirectory -update -removePEbg -restrictionSite GATC -both -removeSelfLigation." To increase sequencing depth, HOMER tag directories from the two biological replicates were combined. To obtain the same number of valid contacts for control and Jpx-depleted cells, down-sampling of the larger HOMER tag file (control sample) was performed as follows. First, the linux command shuf (coreutils/8.27) was used to randomize tags. Then, because there are paired-tags in HOMER directory, both paired-tags were removed until the number of tags were reduced to the same size of the smaller tag file. As a result, we used the exact same number (898,009,206) of valid contacts for both control and Jpx KD Hi-C. Hi-C contact maps in "hic" format were generated using the command "Juicer.sh pre mm9" of Juicer tools (v1.5.3)(Durand et al., Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments. 2016).
Genome_build: mm9
Supplementary_files_format_and_content: Hi-C: Hi-C contact map in "hic" format.


title: Srandard TKS389A G4 Thymus KO input (replica 1)

source_name: SATB1 KO

extract_protocol:
For standard ChIP-seq, the protocol published by Kitagawa et al. (Nat Immunol 2017, 18, 173-183) was basically followed with minor modifications.   Thymocytes prepared from thymus of Satb1-/-  mice (P13) were cross-linked with 1% formaldehyde for 10 min at room temperature. After quenching cross-linking reaction (0.125M Gly at final), these cells were lysed in buffer (4% SDS, 50 mM Tris-HCl [pH 8.0], 10 mM EDTA, 100 mM NaCl) with Protease inhibitor (Roche) and RNase inhibitor. Cross-linked DNA was sonicated using Branson sonifier (20% power, 10 sec on and 30 sec off for 4-6 cycles) in sonication buffer (0.5% Na-laurylsarcosine, 0.1% DOC, 1mM EDTA, 0.5mM EGTA, 10mM Tris-HCl, 100mM NaCl) with Protease inhibitor and RNase inhibitor to generate fragment size 300-1,000bp. For chromatin-immunoprecipitation, 1 µg of an antibody of choice were added to 10 ~ 20 µg of sonicated solubilized chromatin in 350 µl in dilution buffer (1% Triton X-100, 0.01% SDS, 1 mM EDTA, 15 mM Tris-HCl, 100 mM NaCl) and incubated overnight at 4°C. The chromatin fragments bound to antibodies (after incubation overnight) were captured using 40 µl of protein-A or protein-G Dynabeads (Invitrogen; pre-washed with 0.1% BSA [Fraction V, Sigma), by 4 hrs incubation time. After beads washing and DNA elution from beads, ChIP DNAs was reverse-crosslinked at 65oC overnight, followed by RNase-A treatment and proteinase K treatments.  DNA was further purified with a QIAquick PCR purification kit (Qiagen), with elution in 15µl of Qiagen Elution Buffer (alternatively, Phenol-chloroform extraction and ethanol precipitation). The purified DNAs were subjected to ChIP-seq library construction.
Briefly for library construction,  DNA fragments were end-repaired and ligated to indexed sequencing adapters (NEB or Rubicon library kit) and amplified with 8-11 rounds of PCR, depending on the DNA amount.  Using SPRI beads (Beckmancoulter), small fragments (<200bp) were removed from the amplified library. The size-selected library was sequenced to 50bp single-end read lengths on an Illumina HiSeq4000 (Vincent J. Coates Genomic Sequencing Laboratory, UC Berkeley).

value: Thymus

value: SATB1 KO

value: Standard ChIP-seq


title: D7 ES Jpx KD RAD21 ChIP-seq input, rep2

description: processed data: d7.KD.RAD21.combined.input.comp.fpm.wig.bw

value: Differentiating mESC (day 7)

value: RAD21 Input DNA


title: D7 ES JpxKD Hi-C rep1_2

description: processed data:d7.KD.combined.Hi-C.hic


title: LNA#1:D7 ES Control ChIP-seq CTCF, rep1

data_processing:
ChIP-Seq: ChIP-seq reads were subjected to the trimming of adapter sequence and removal of duplicates using Trim Galore! (v0.4.1) and cutadapt (v1.2.1) and then mapped to CAST/EiJ (Mus m. castaneus; cas) and 129S1/SvImJ (Mus m. musculus; mus) genomes using Novoalign (v3.00.02) with the parameters (-i300 100 -t180 -F STDFQ -rRandom -h180 180 -v180). From the independent mapping to cas and mus reads, we generated composite (sum of neutral, cas-specific and mus-specific) reads mapped back to the mm9 genome using a previously published pipeline (Pinter et al. Spreading of X chromosome inactivation via a hierarchy of defined Polycomb stations. 2012). Composite bam files having only uniquely aligned reads were used. Log2 fold-enrichment estimates (relative to input) coverage (bigWig) files for ChIP were generated using SPP software with a window of 150 bp and step size 25 bp (get.conservative.fold.enrichment.profile). Coverage (bigWig) of input was normalized by FPM (Fragments Per Million mapped reads) scaling factor.
Genome_build: mm9
Supplementary_files_format_and_content: Log2 fold-enrichment estimates (relative to input) coverage (bigWig) files generated by SPP. FPM-normalized coverage (bigWig) files for input.

extract_protocol: Nuclei chromatin was prepared from the cells crosslinked with 1% formaldehyde and sheared by sonication. CTCF ChIP was performed using CTCF antibody (Cell Signaling, #2899S). Library construction was performed using  NEBNext® ChIP-Seq Library Prep Master Mix Set for Illumina.

treatment_protocol: LNA transfection: ES cells on day 7 of differentiation were trypsinized, transfected with Scrambled LNA or Jpx LNA#1 by nucleofection, transferred to the gelatinized plates and harvested after incubation at 37°C  for 8 hr.

value: CTCF ChIP-enriched DNA


title: D7 ES Jpx KD RAD21 ChIP-seq RAD21, rep2

description: processed data: d7.KD.RAD21.combined.input_normalized_Spp.wig.bw


title: D7 ES Control Hi-C rep2_1

data_processing:
Hi-C: Illumina adaptor-trimmed reads were further trimmed with the options "-a GATCGATC (MboI ligation junction) and -m 20." Individual reads of each pair were separately mapped to the mus (129S1/SvImJ) and cas (CAST/EiJ) genomes (mm9) using Novoalign (v4.02.01) with the parameters "-F STDFQ -r None." Composite reads having only uniquely aligned reads were generated as described in CHART-seq data processing, and then merged into Hi-C summary files and filtered using HOMER (v4.10) with the parameters "makeTagDirectory -tbp1; makeTagDirectory -update -removePEbg -restrictionSite GATC -both -removeSelfLigation." To increase sequencing depth, HOMER tag directories from the two biological replicates were combined. To obtain the same number of valid contacts for control and Jpx-depleted cells, down-sampling of the larger HOMER tag file (control sample) was performed as follows. First, the linux command shuf (coreutils/8.27) was used to randomize tags. Then, because there are paired-tags in HOMER directory, both paired-tags were removed until the number of tags were reduced to the same size of the smaller tag file. As a result, we used the exact same number (898,009,206) of valid contacts for both control and Jpx KD Hi-C. Hi-C contact maps in "hic" format were generated using the command "Juicer.sh pre mm9" of Juicer tools (v1.5.3)(Durand et al., Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments. 2016).
Genome_build: mm9
Supplementary_files_format_and_content: Hi-C: Hi-C contact map in "hic" format.


title: D7 ES Control RAD21 ChIP-seq input, rep1

description: processed data: d7.control.RAD21.combined.input.comp.fpm.wig.bw

treatment_protocol: LNA transfection: ES cells on day 7 of differentiation were trpysinized, transfected with scrambled LNA or Jpx LNA#1 by nucleofection, transferred to the gelatinized plates and harvested after incubation at 37°C  for 8 hr.


title: D7 ES Control RAD21 ChIP-seq RAD21, rep1

extract_protocol: Nuclei chromatin was prepared from the cells crosslinked with 1% formaldehyde and sheared by sonication. RAD21 ChIP was performed using RAD21 antibody (Abcam, #ab992). Library construction was performed using  NEBNext Ultra II DNA Library Prep Kit for Illumina (E7645S).


title: LNA#2:D7 ES Jpx KD ChIP-seq CTCF

data_processing:
ChIP-Seq: ChIP-seq reads were subjected to the trimming of adapter sequence and removal of duplicates using Trim Galore! (v0.4.1) and cutadapt (v1.18) and then mapped to CAST/EiJ (Mus m. castaneus; cas) and 129S1/SvImJ (Mus m. musculus; mus) genomes using Novoalign (v4.02.01) with the parameters (-i300 100 -t180 -F STDFQ -rRandom -h180 180 -v180). From the independent mapping to cas and mus reads, we generated composite (sum of neutral, cas-specific and mus-specific) reads mapped back to the mm9 genome using a previously published pipeline (Pinter et al. Spreading of X chromosome inactivation via a hierarchy of defined Polycomb stations. 2012). Composite bam files having only uniquely aligned reads were used. Log2 fold-enrichment estimates (relative to input) coverage (bigWig) files for ChIP were generated using SPP software with a window of 150 bp and step size 25 bp (get.conservative.fold.enrichment.profile). Coverage (bigWig) of input was normalized by FPM (Fragments Per Million mapped reads) scaling factor.
Genome_build: mm9
Supplementary_files_format_and_content: Log2 fold-enrichment estimates (relative to input) coverage (bigWig) files generated by SPP. FPM-normalized coverage (bigWig) files for input.

extract_protocol: Nuclei chromatin was prepared from the cells crosslinked with 1% formaldehyde and sheared by sonication. CTCF ChIP was performed using CTCF antibody (Cell Signaling, #2899S). Library construction was performed using NEBNext Ultra II DNA Library Prep Kit for Illumina (E7645S) for Illumina.

treatment_protocol: LNA transfection: ES cells on day 7 of differentiation were trypsinized, transfected with scrambled LNA or Jpx LNA#2 by nucleofection, transferred to the gelatinized plates and harvested after incubation at 37°C  for 8 hr.

value: Jpx LNA#2-transfected


title: D7 ES Jpx KD RAD21 ChIP-seq input, rep1

description: processed data:d7.control.RAD21.combined.input.comp.fpm.wig.bw

treatment_protocol: LNA transfection: ES cells on day 7 of differentiation were trypsinized, transfected with scrambled LNA or Jpx LNA #1 ny nucleofection, transferred to the gelatinized plates and harvested after incubation at 37°C  for 8 hr.


title: D7 ES Control Hi-C rep1_2

data_processing:
Hi-C: Illumina adaptor-trimmed reads were further trimmed with the options "-a GATCGATC (MboI ligation junction) and -m 20." Individual reads of each pair were separately mapped to the mus and cas genomes (mm9) using Novoalign (v4.02.01) with the parameters "-F STDFQ -r None." Composite reads having only uniquely aligned reads were generated as described in CHART-seq data processing, and then merged into Hi-C summary files and filtered using HOMER (v4.10) with the parameters "makeTagDirectory -tbp1; makeTagDirectory -update -removePEbg -restrictionSite GATC -both -removeSelfLigation." To increase sequencing depth, HOMER tag directories from the two biological replicates were combined. To obtain the same number of valid contacts for control and Jpx-depleted cells, down-sampling of the larger HOMER tag file (control sample) was performed as follows. First, the linux command shuf (coreutils/8.27) was used to randomize tags. Then, because there are paired-tags in HOMER directory, both paired-tags were removed until the number of tags were reduced to the same size of the smaller tag file. As a result, we used the exact same number (898,009,206) of valid contacts for both control and Jpx KD Hi-C. Hi-C contact maps in "hic" format were generated using the command "Juicer.sh pre mm9" of Juicer tools (v1.5.3)(Durand et al., Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments. 2016).
Genome_build: mm9
Supplementary_files_format_and_content: Hi-C contact map in "hic" format.


title: D7 ES Control RAD21 ChIP-seq input, rep2


title: D7 ES Control RAD21 ChIP-seq RAD21, rep2

extract_protocol: Same above


title: LNA#2:D7 ES Control ChIP-seq CTCF

extract_protocol: Nuclei chromatin was prepared from the cells crosslinked with 1% formaldehyde and sheared by sonication. CTCF ChIP was performed using CTCF antibody (Cell Signaling, #2899S). Library construction was performed using  NEBNext Ultra II DNA Library Prep Kit for Illumina (E7645S) for Illumina.


title: LNA#2:D7 ES Jpx KD RNA-seq, rep2

library_source: transcriptomic

data_processing:
RNA-seq: RNA-seq reads were adapter-trimmed using Trim Galore! (v0.4.1) and cutadapt (v1.18), and then aligned to the mm9 genome using TopHat2 (v2.0.10) (--mate-inner-dist 100 --mate-std-dev 100 --library-type fr-firststrand). Only uniquely mapped reads were selected and FPM-normalized coverage (bigWig) files were generated for forward or reverse strand.
Genome_build: mm9
Supplementary_files_format_and_content: FPM-normalized coverage (bigWig) files for forward or reverse strand.

molecule: total RNA

extract_protocol: Total RNA was extracted using TRIzol, depleted of ribosomal RNA and then treated with DNase. The rRNA-depleted RNA was selected by size greater than 200nt, fragmented to a mediam size of about 200nt and then subjected to RT reaction. The subsequent first-strand cDNA was subjected to second strand cDNA synthesis using NEBNext Ultra Directional RNA Second Strand Synthesis Module (NEB, #E7550S). Double-stranded DNA was subjected to library construction using NEBNext Ultra II DNA Library Prep Kit for Illumina (E7645S) for Illumina.

value: rRNA-depleted total RNA


title: LNA#2:D7 ES Jpx KD RNA-seq, rep1


title: LNA#2:D7 ES Jpx KD ChIP-seq input

value: Input DNA


title: LNA#2:D7 ES Control ChIP-seq input


title: LNA#2:D7 ES Control RNA-seq, rep1

extract_protocol: Total RNA was extracted using TRIzol, depleted of ribosomal RNA and then treated with DNase. The rRNA-depleted RNA was selected by size greater than 200nt, fragmented to a mediam size of about 200nt and then subjected to RT reaction. The subsequent first-strand cDNA was subjected to second strand cDNA synthesis using NEBNext Ultra Directional RNA Second Strand Synthesis Module (NEB, #E7550S).  Double-stranded DNA was subjected to library construction using  NEBNext Ultra II DNA Library Prep Kit for Illumina (E7645S) for Illumina.


title: LNA#2:D7 ES Control RNA-seq, rep2


title: D7 ES Jpx-AS CHART-seq, rep3

data_processing:
Library strategy: CHART-seq
CHART-Seq: CHART-seq reads were subjected to the trimming of adapter sequence and removal of duplicates using Trim Galore! (v0.4.1) and cutadapt (v1.18) and then mapped to CAST/EiJ (Mus m. castaneus; cas) and 129S1/SvImJ (Mus m. musculus; mus) genomes using Novoalign (v4.02.01) with the parameters (-i300 100 -t180 -F STDFQ -rRandom -h180 180 -v180) . From the independent mapping to cas and mus reads, we generated composite (sum of neutral, cas-specific and mus-specific) reads mapped back to the mm9 genome using a previously published pipeline (Pinter et al. Spreading of X chromosome inactivation via a hierarchy of defined Polycomb stations. 2012). Composite bam files having only uniquely aligned reads were used. The input-subtracted coverage (bigWig) files for each CHART experiment were generated using SPP software with a window of 500 bp and step size 100 bp (get.smoothed.tag.density). Coverage (bigWig) of input was normalized by FPM (Fragments Per Million mapped reads) scaling factor.
Genome_build: mm9
Supplementary_files_format_and_content: Input-subtracted coverage (bigWig) files generated by SPP. FPM-normalized coverage (bigWig) files are provided for input.

extract_protocol: CHART-seq: Cells were crosslinked with 1% formaldehyde and nuclei were further crosslinked with 3% formaldehyde. Nuclei chromatin was sheared by sonication to yield the majority of fragments with approximately 3kb. The resulting extracts were hybridized with either Jpx CHART probes (biotinylated DNA oligonucleotides that were complementary to Jpx) or Jpx AS CHART probes (the reverse complement of Jpx CHART probes) and then captured by streptavidin beads. After washes, DNA was eluted in the elution buffer with RNase H. No-RNaseH CHART was generated from Jpx CHART eluant in the absence of RNase H. CHART enriched DNA was further sonicated and subjected to library construction steps using NEBNext Ultra II DNA Library Prep Kit for Illumina (E7645S) for Illumina.

value: Untransfected

value: Jpx AS CHART-enriched DNA


title: D7 ES no-RNase H CHART-seq, rep3

value: DNA enriched by no-RNase H elution for Jpx CHART


title: D7 ES CHART-seq input, rep3

data_processing:
Library strategy: CHART-seq
CHART-Seq:  CHART-seq reads were subjected to the trimming of adapter sequence and removal of duplicates using Trim Galore! (v0.4.1) and cutadapt (v1.18) and then mapped to CAST/EiJ (Mus m. castaneus; cas) and 129S1/SvImJ (Mus m. musculus; mus) genomes using Novoalign (v4.02.01) with the parameters (-i300 100 -t180 -F STDFQ -rRandom -h180 180 -v180) .  From the independent mapping to cas and mus reads, we generated composite (sum of neutral, cas-specific and mus-specific) reads mapped back to the mm9 genome using a previously published pipeline (Pinter et al. Spreading of X chromosome inactivation via a hierarchy of defined Polycomb stations. 2012). Composite bam files having only uniquely aligned reads were used. The input-subtracted coverage (bigWig) files for each CHART experiment were generated using SPP software with a window of 500 bp and step size 100 bp (get.smoothed.tag.density). Coverage (bigWig) of input was normalized by FPM (Fragments Per Million mapped reads) scaling factor.
Genome_build: mm9
Supplementary_files_format_and_content: Input-subtracted coverage (bigWig) files generated by SPP. FPM-normalized coverage (bigWig) files are provided for input.


title: D7 ES CHART-seq input, rep2


title: D7 ES Jpx-AS CHART-seq, rep2


title: D3 ES CHART-seq input, rep2

value: Differentiating mESC (day 3)


title: D7 ES Jpx CHART-seq, rep2

value: Jpx CHART-enriched DNA


title: D3 ES no-RNase H CHART-seq, rep2


title: D3 ES Jpx CHART-seq, rep2


title: D0 ES no-RNase H CHART-seq, rep2

value: Undifferentiated mESC (day 0)


title: D3 ES Jpx-AS CHART-seq, rep2


title: D0 ES CHART-seq input, rep2


title: D0 ES Jpx-AS CHART-seq, rep2


title: Y334C MT Heart 3

status: Public on Nov 24 2021

city: Bonn

first: Ulrich

last: Schweizer

state: NRW

address: Nussallee 11

department: Institut für Biochemie und Molekularbiologie

country: Germany

institute: Universitätsklinikum Bonn

data_processing:
Sequence reads were trimmed with bbduk.sh following manufacturer's protocol. ref=/data/resources/polyA.fa.gz,/data/resources/truseq.fa.gz k=13 ktrim=r useshortkmers=t mink=5 qtrim=t trimq=10 minlength=20
Reads were aligned with STAR aligner following the manufacturer's protocol. STAR  --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1   --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.1 --alignIntronMin 20   --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMattributes NH HI NM MD  --outSAMtype BAM SortedByCoordinate --outFileNamePrefix
Amount of sequences aligned to transcripts was counted with STAR aligner
Genome_build: GRCm38.102
Supplementary_files_format_and_content: table with 2 columns in .tab format, column1: Ensemble Gene Accession Number, column2: corresponding counts

source_name: Heart

extract_protocol:
total RNA was extracted using RNeasy Plus Micro Kit (Qiagen, Hilden, Germany) recommended by manufacturer.
Libraries were prepared with the QuantSeq 3’ mRNA-Seq Fw. Library Prep Kit (Lexogen) and sequenced to 10M raw reads on an Illumina HiSeq 2500 machine, following the manufacturer’s protocols.
3' Poly(A) RNA-seq
RNA: total RNA was extracted using TRIzol Reagent (Invitrogen) recommended by manufacturer. Libraries were prepared with the QuantSeq 3’ mRNA-Seq Fw. Library Prep Kit (Lexogen) and sequenced to 10M raw reads on an Illumina HiSeq 2500 machine, following the manufacturer’s protocols.

tag: tissue

value: Heart

value: Y334C MT


title: D0 ES Jpx CHART-seq, rep2

value: CAST/EiJ x 129S1


title: Y334C MT Heart 2


title: Y334C WT Heart 1

extract_protocol:
total RNA was extracted using TRIzol Reagent (Invitrogen) recommended by manufacturer.
Libraries were prepared with the QuantSeq 3’ mRNA-Seq Fw. Library Prep Kit (Lexogen) and sequenced to 10M raw reads on an Illumina HiSeq 2500 machine, following the manufacturer’s protocols.
3' Poly(A) RNA-seq
RNA: total RNA was extracted using TRIzol Reagent (Invitrogen) recommended by manufacturer. Libraries were prepared with the QuantSeq 3’ mRNA-Seq Fw. Library Prep Kit (Lexogen) and sequenced to 10M raw reads on an Illumina HiSeq 2500 machine, following the manufacturer’s protocols.

value: Y334C WT


title: Y334C MT Cortex 1

source_name: Brain

value: Cortex


title: Y334C MT Cortex 2


title: Y334C WT Heart 2


title: Y334C WT Cortex 2


title: Y334C MT Cortex 3


title: D7 ES Jpx CHART-seq, rep3

value: Differentiating mESC (day 7)


title: Y334C WT Cortex 3


title: Y334C WT Cortex 1


title: Gxp4 MT Heart 4

value: Gxp4 MT


title: Gxp4 MT Heart 5


title: D7 ES no-RNase H CHART-seq, rep2


title: Gxp4 MT Heart 2


title: Gxp4 MT Heart 3


title: Gxp4 MT Heart 1


title: Gxp4 WT Heart 3

value: Gxp4 WT


title: Gxp4 WT Heart 2


title: Gxp4 WT Heart 1


title: Gxp4 MT Cortex 5


title: Gxp4 MT Cortex 4


title: Gxp4 MT Cortex 2


title: Gxp4 MT Cortex 3


title: Y334C WT Heart 3


title: Y334C MT Heart 1


title: Gxp4 WT Cortex 3


title: Liver Trit1 KO rep3 RPF

status: Public on Nov 17 2021

data_processing:
Sequence reads were trimmed with TrimGalore v0.6.5 and cutadapt v3.4 and size selected, reads with N>15 were used for further analysis
Ribosome profiling data was aligned using STAR Aligner v2.7.5c against rRNA and tRNA sequences retrieved from UCSC Table Browser, not matched reads were used for further analysis
Trimmed Ribo-seq (after tRNA and rRNA removal) data was aligned with STAR aligner v2.7.5c against UCSC mm10 RefSeq mouse transcriptome
Samtools v1.13 was used to sort and index the resulting files containing the aligned sequences
Amount of sequences aligned to transcripts was counted with STAR aligner
Genome_build: mm10
Supplementary_files_format_and_content: table with gene symbols as row names and gene counts for all samples in the columns in .csv-format

source_name: liver

extract_protocol:
50mg liver tissue powder was lysed in 1000 µl of ice-cold lysis buffer (10 mM Tris-Cl (pH 7.5), 300 mM KCl, 10 mM MgCl2, 1 mM DTT, 1% Triton X-100 and 10 U/ml DNAse I). Ribosome pellets were resuspended in Qiazol (Quiagen) after centrifugation of RNAseI digested monosomes (60 min at 25 °C and 1300 rpm on thermoblock) in 50% sucrose buffer, ribosome protected fragments were isolated using miRNAeasy kit (Quiagen) according to manufacturer protocol with modification to retain small RNAs. RPFs were electrophoresed on a 15% Tris-Borate-EDTA (TBE) Urea gel and RNA fragments between 15 and 40 nts in size were purified and incubated for 1 hout with T4 PNK according to manufacturers protocol.
Small RNA sequencing libraries were constructed by GenXPro with the TrueQuant smallRNA kit with a depth of 30 M reads on an Illumina NextSeq500 machine.
50mg liver tissue powder was lysed in 1000 µl of ice-cold lysis buffer (10 mM Tris-Cl (pH 7.5), 300 mM KCl, 10 mM MgCl2, 1 mM DTT, 1% Triton X-100 and 10 U/ml DNAse I). Ribosome pellets were resuspended in Qiazol (Quiagen) after centrifugation of RNAseI digested monosomes (60 min at 25 °C and 1300 rpm on thermoblock) in 50% sucrose buffer, ribosome protected fragments were isolated using miRNAeasy kit (Quiagen) according to manufacturer protocol with modification to retain small RNAs. RPFs were electrophoresed on a 15% Tris-Borate-EDTA (TBE) Urea gel and RNA fragments between 15 and 40 nts in size were purified and incubated for 1 hout with T4 PNK according to manufacturers protocol.
Small RNA sequencing libraries were constructed by GenXPro with the TrueQuant smallRNA kit with a depth of 30 M reads on an Illumina NextSeq500 machine.

tag: gender

value: male

value: liver

value: post natal day 150

value: Trit1 fl/fl; Alb-Cre pos


title: Liver Ctl rep3 RPF

value: Trit1 wt/fl; Alb-Cre neg


title: Liver Ctl rep1 RPF


title: Trit1 KO rep1 RPF


title: Liver Ctl rep2 RPF


title: Cell-specific Eftud2 heterozygous (control) embryos at E9.5 - rep3

status: Public on Sep 03 2021

city: Montreal

first: Loydie

last: Jerome-Majewska

state: QC

address: 1001 Decarie Blvd EM0.2210

department: Pediatrics

country: Canada

institute: McGill University Health Centre Glen Site

data_processing:
Reads were trimmed by length and quality using CutAdapt
Read quality was checked for each sample using MultiQC
Trimmed high-quality reads were then mapped with STAR aligner for each Sample
Number of reads associated with genes  were counted using featureCounts
Genome_build: mm10
Supplementary_files_format_and_content: Alignment file in binary format (BAM) for each Sample
Supplementary_files_format_and_content: Alignment index file (BAI) for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Neural crest cells at E9.5

growth_protocol: Embryos were collected and yolk sacs were used for genomic DNA extraction for genotyping.  For both stages (E9.0 and E9.5), the number of somites were counted under light microscope (Leica MZ6 Infinity1 stereomicroscope) at the time of dissection.  The head of the embryos were kept in RNA later at 4°C until RNA extraction.

extract_protocol:
RNA extraction from samples was performed using Qiagen RNeasy kit following manufacturer's protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: no treatment

value: Cranial nerve ganglia

tag: developmental stage

value: Embryonic day 9.5


title: Cell-specific Eftud2 homozygous (mutant) embryos at E9.5 - rep3


title: Cell-specific Eftud2 heterozygous (control) embryos at E9.5 - rep1


title: Cell-specific Eftud2 homozygous (mutant) embryos at E9.5 - rep2


title: Cell-specific Eftud2 homozygous (mutant) embryos at E9.5 - rep1


title: Gpx4 MT Cortex 1

value: Gpx4 MT


title: Cell-specific Eftud2 homozygous (mutant) embryos at E9.0 - rep3

source_name: Neural crest cells at E9.0

value: Embryonic day 9.0


title: Cell-specific Eftud2 heterozygous (control) embryos at E9.0 - rep2


title: Cell-specific Eftud2 homozygous (mutant) embryos at E9.0 - rep1


title: Gxp4 WT Cortex 2


title: RPL5DBA1

status: Public on Aug 31 2021

city: Bethesda

first: Jens

last: Lichtenberg

state: MD

address: 49 Convent Dr 3A19

department: National Human Genome Research Institute

institute: National Institutes of Health

data_processing:
Sequencing data was demultiplexed and aligned to the GRCh38 3.0.0 using the 10x Genomics Cell Ranger software (v3.0.1).
Cells meeting minimum unique molecular identifier (UMI) and detectable numbers of genes, as well as a maximum percentage of mitochondrial gene expression, were included. Genes expressed in at least 10 cells were included.
Batch correction, expression matrix construction, dimensionality reduction, and k-nearest neighbor clustering was performed in R.
Genome_build: GRCh38 3.0.0
Supplementary_files_format_and_content: UMI counts

molecule: polyA RNA

organism: Homo sapiens

source_name: CD34+ Lin- bone marrow

extract_protocol:
RNA was isolated and cDNA constructed using the 10x Genomics Single cell 3' Library and Gel Bead Kit according to the manufacturer's protocol.
Libraries were constructed using Chromium Single Cell 3’ library and Gel Bead Kits (10x Genomics) and sequencing performed either a NextSeq 550 (with a 26 base read for cell and molecule barcodes, an 8 base library index read, and a 98 base insert read) or a NovaSeq 6000 (with a 28 base read for cell and molecule barcodes, an 8 base library index read, and a 91 base insert read)

treatment_protocol: Frozen bone marrow aspirates were thawed and 12,000 - 15,000 CD34+ Lineage negative cells were isolated by FACS.

value: Bone marrow

value: CD34 enriched bone marrow

tag: disease state

value: DBA

tag: mutation


title: Cell-specific Eftud2 heterozygous (control) embryos at E9.0 - rep1


title: RPS19DBA3


title: LNA#1:D7 ES Jpx KD ChIP-seq input, rep2

value: CAST/EiJ x 129S1

value: Jpx LNA#1-transfected

value: Input DNA


title: RPS19DBA2


title: RPL11DBA1


title: Gpx4 WT Cortex 1

value: Cortex

value: Gpx4 WT


title: RPS19DBA1


title: Con3

value: Healthy donor

value: Control


title: RPL5DBA2


title: LNA#1:D7 ES Control ChIP-seq input, rep2

treatment_protocol: LNA transfection: ES cells on day 7 of differentiation were trypsinized, transfected with scrambled LNA or Jpx LNA#1, transferred to the gelatinized plates and harvested after incubation at 37°C  for 8 hr.

value: CAST/Ei x 129/Sv/Jae

value: Differentiating mESC (day 7)

value: Scrambled LNA-transfected


title: Liver Trit1 KO rep2 RPF

value: male

value: liver

value: post natal day 150

value: Trit1 fl/fl; Alb-Cre pos


title: Cell-specific Eftud2 heterozygous (control) embryos at E9.5 - rep2

value: Cranial nerve ganglia

value: Embryonic day 9.5


title: Con2

value: Bone marrow

value: CD34 enriched bone marrow


title: Cd_50 [S204-3_S8]

status: Public on Aug 18 2021

city: RALEIGH

first: Dereje

last: Jima

state: NC

address: 850 Main Campus Drive

department: CHHE

institute: NCSU

description:
S204-3_S8_L001_R1_001
F1 between C57BL/6 (mother) and CAST/EiJ (father)
C57BL/6J x CAST/EiJ hybrid
Gene expression in brain
Homogenized whole brain
Purified mRNA

data_processing:
Illumina Casava1.7 software used for basecalling.
The quality of raw RNA-seq data was assessed using the FastQC application and the initial 10 bases with poor quality were trimmed. Alignment was performed using STAR short read aligner to the respective mouse strain (C57BL/6J, CAST/EiJ) reference genomes. C57BL/6J and CAST/EiJ RNA-seq data were aligned to mm38 version 87 and CAST/EiJ version 1.86 reference genome downloaded from the Ensembl website, respectively. We used the WASP approach in STAR aligner to map one of the haplotype and supply the other haplotype variants as VCF file. The number of reads mapped to a genome feature was determined using htseq-count script from HTSeq python package. Independent analyses were conducted for the two strains. The two raw count data matrices were imported to R statistical computing environment for further analysis. Genes that had no count in more than 2/3 of the replicate samples were excluded from the analysis. Data normalization based on dispersion and differential analysis was conducted using the DESeq2 R package. A generalized linear model (~Treatment) was fitted between the expression count and a treatment group (0 ppm or 50 ppm maternal Cd exposure). Finally, a list of differentially expressed genes was generated between 50 ppm vs. 0 ppm maternal Cd exposure after applying Benjamini-Hochberg multiple testing correction (p adj <0.05).
Genome_build: mm38 version 87 and CAST/EiJ version 1.86
Supplementary_files_format_and_content: *_raw_readCount.csv: Comma-separated matrix tables with raw gene counts for every gene and every sample.

source_name: Brain Tissue

extract_protocol:
Whole brains were removed, flash frozen on dry ice, and kept at -80C until RNA was harvested using Qiagen AllPrep DNA/RNA/miRNA kit.
Purification of messenger RNA (mRNA) was performed using oligo-dT beads provided in the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs [NEB]). Complementary DNA (cDNA) libraries for Illumina sequencing were constructed using the NEBNext Ultra Directional RNA Library Prep Kit (NEB) and NEBNext Multiplex Oligos for Illumina (NEB) using the manufacturer-specified protocol. Following adapter ligation, the samples were selected for a final library size (adapters included) of 400–550 bp using sequential AMPure XP bead isolation (Beckman Coulter). Library enrichment was performed and indexes for each sample were added during the protocol-specified PCR amplification. Amplified library fragments were purified and checked for quality and final concentration using an Agilent 2200 Tapestation (D1000 chip, Agilent Technologies) combined with a Qubit fluorometer (ThermoFisher). Libraries were pooled in equimolar amounts for clustering and sequencing.
Illumina HiSeq 2500 DNA sequencer, utilizing a 125 bp single-end cycle sequencing kit.

treatment_protocol: Mothers were exposed to 0ppm or 50ppm CdCl2 in their drinking water prior to and during gestation, then pups were sacrificed within 24 hours of birth and whole brains were collected.

value: (C57BL/6 x CAST/EiJ) F1

value: whole brain

value: postnatal day 1

tag: Sex

value: female

tag: treatment

value: 50ppm CdCl2 in mother's H2O


title: Cd_0 [S180-2_S7]

description:
S180-2_S7_L001_R1_001
F1 between C57BL/6 (mother) and CAST/EiJ (father)
C57BL/6J x CAST/EiJ hybrid
Gene expression in brain
Homogenized whole brain
Purified mRNA

value: 0ppm CdCl2 in mother's H2O


title: Con1

value: Healthy donor

value: Control


title: Cd_50 [S175-6_S6]

description:
S175-6_S6_L001_R1_001
F1 between C57BL/6 (mother) and CAST/EiJ (father)
C57BL/6J x CAST/EiJ hybrid
Gene expression in brain
Homogenized whole brain
Purified mRNA


title: Cd_0 [S099-2_S2]

description:
S099-2_S2_L001_R1_001
F1 between C57BL/6 (mother) and CAST/EiJ (father)
C57BL/6J x CAST/EiJ hybrid
Gene expression in brain
Homogenized whole brain
Purified mRNA


title: Cd_0 [S106-2_S3]

description:
S106-2_S3_L001_R1_001
F1 between C57BL/6 (mother) and CAST/EiJ (father)
C57BL/6J x CAST/EiJ hybrid
Gene expression in brain
Homogenized whole brain
Purified mRNA


title: Cd_50 [S119-2_S5]

description:
S119-2_S5_L001_R1_001
F1 between C57BL/6 (mother) and CAST/EiJ (father)
C57BL/6J x CAST/EiJ hybrid
Gene expression in brain
Homogenized whole brain
Purified mRNA


title: Cell-specific Eftud2 heterozygous (control) embryos at E9.0 - rep3

value: Embryonic day 9.0


title: Cell-specific Eftud2 homozygous (mutant) embryos at E9.0 - rep2


title: Cd_50 [S116-2_S4]

description:
S116-2_S4_L001_R1_001
F1 between C57BL/6 (mother) and CAST/EiJ (father)
C57BL/6J x CAST/EiJ hybrid
Gene expression in brain
Homogenized whole brain
Purified mRNA


title: Cd_0 [S091-9_S1]

description:
S091-9_S1_L001_R1_001
F1 between C57BL/6 (mother) and CAST/EiJ (father)
C57BL/6J x CAST/EiJ hybrid
Gene expression in brain
Homogenized whole brain
Purified mRNA


title: MF1

status: Public on Jun 30 2020

description:
Myelofibrosis_patients.csv
All_aggregates.csv

data_processing:
Raw sequencing data were processed using the 10X Genomics Cell Ranger pipeline (version 2.0.0). Sequencing data in the binary base call (BCL) format were demultiplexed. Unique molecular identifier (UMI) counts for given genes were obtained by aligning FASTQ files to the human reference genome (GRCh38) using Cell Ranger software (version 2.0.0) from 10x Genomics. CellRanger “count” pipeline results from each of individual libraries from three patients and two healthy donors were then aggregated using default parameters to generate a gene count matrix based on CellRanger “aggr” standard pipeline. The UMI counts (> 1,000 and ≤ limited maximum UMIs), the number of detected genes (> 500 and ≤ limited maximum number of detected genes) and the percentage of mitochondrial gene expression (< 10%) per cell used as the cut-off criteria. We scaled UMI counts by the total library size multiplied by 10,000. The normalized expression values were then log transformed. We regressed out the unwanted source of variation (library size, percentage of mitochondrial genes and batches from patients and healthy donors) from gene expression values by applying the linear regression model using the limma package.
Genome_build: GRCh38
Supplementary_files_format_and_content: CSV files were generated from read counts of unique molecular identifiers

source_name: Myelofibrosis sample

extract_protocol:
Cryopreserved perhipheral blood mononuclear cells were thawed and CD34+ lineage negative cells isolated by FACS for single cell RNA sequencing using the 10x Genomics 3' single cell platform (v1).
Libraries were prepared as per the 10x Genomics Chromium Single Cell 3' Reagent kit user guide.

value: Myelofibrosis

value: CD34+ lineage negative peripheral blood HSPC


title: HD1

description:
Healthy_donors.csv
All_aggregates.csv

source_name: Healthy mobilized apheresis donor

value: Healthy control


title: MF2


title: MF3


title: MiddleCerebralArtery_MoyamoyaDisease#63_rep1 [MMD8]

status: Public on Oct 02 2020

type: RNA

city: Showa-ku, Nagoya

first: Kinya

last: Yokoyama

state: Aichi

address: Tsurumai 65

department: Neurosurgery

country: Japan

institute: Nagoya University Hospital

hyb_protocol: A Cy3-labeled amplified cDNA sample (2 µg), prepared without the fragmentation reaction, was used for hybridization (24 hours at 65 ℃) to the oligonucleotide spotted microarray slide (Human Whole Genome, SurePrint G3 Human GE v2 8×60K Microarray; Agilent Technologies). Subsequent washing and drying were performed according to the Agilent hybridization protocol.

scan_protocol: The slide was scanned with an Agilent Model G2505A DNA microarray scanner.

data_processing:
Signal intensity was quantified from the scanned image using Feature Extraction Software version 11.0.1.1 (Agilent Technologies).
We log-transformed the resulting signal intensities and normalized the data using the 75 percentile shift method as recommended in the Agilent 'One-Color Microarray-Based gene expressed Analysis' protocol.

source_name: Middle Crebral Artery, Adult Moyamoya Disease, Patient Number 63, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cDNA was prepared from 2ug cDNA using the SureTag DNA labeling kit (Agilent Technologies, Santa Clara, CA, USA) according to the manufacturer's instructions.  Dye incorporation and cDNA yield were checked with the NanoDrop One Spectrophotometer.

extract_protocol: Total RNA was extracted from each MCA specimen with an RNeasy Micro Kit (Qiagen). The purified total RNA was amplified with an Ovation PicoSL WTA System V2 kit (NuGEN Technologies, Bemmel, Netherlands)

treatment_protocol: We excised the vessel wall of the MCA following the reported procedure. Tissue samples were collected into RNAlater (Qiagen, Hilden, Germany) and stored at -80 °C.

value: Artery Wall

value: Female


title: MiddleCerebralArtery_MoyamoyaDisease#69_rep1 [MMD10]

source_name: Middle Crebral Artery, Adult Moyamoya Disease, Patient Number 69, replicate 1


title: MiddleCerebralArtery_MoyamoyaDisease#73_rep1 [MMD11]

source_name: Middle Crebral Artery, Adult Moyamoya Disease, Patient Number 73, replicate 1


title: MiddleCerebralArtery_MoyamoyaDisease#126_rep1 [MMD7]

source_name: Middle Crebral Artery, Adult Moyamoya Disease, Patient Number 126, replicate 1


title: MiddleCerebralArtery_InternalCarotidArteryAneurysm#91_rep1 [IA5]

source_name: Middle Crebral Artery, Internal Carotid Artery Aneurysm, Patient Number 91, replicate 1


title: MiddleCerebralArtery_InternalCarotidArteryAneurysm#106_rep1 [IA2]

source_name: Middle Crebral Artery, Internal Carotid Artery Aneurysm, Patient Number 106, replicate 1


title: MiddleCerebralArtery_MoyamoyaDisease#59_rep1 [MMD4]

source_name: Middle Crebral Artery, Adult Moyamoya Disease, Patient Number 59, replicate 1


title: HD2

description:
Healthy_donors.csv
All_aggregates.csv


title: MiddleCerebralArtery_Epilepsi#119_rep1 [EPI2]

source_name: Middle Crebral Artery, Epilepsi, Patient Number 119, replicate 1

value: Male


title: MiddleCerebralArtery_Epilepsi#116_rep1 [EPI1]

source_name: Middle Crebral Artery, Epilepsi, Patient Number 116, replicate 1


title: MiddleCerebralArtery_MoyamoyaDisease#120_rep1 [MMD5]

source_name: Middle Crebral Artery, Adult Moyamoya Disease, Patient Number 120, replicate 1


title: MiddleCerebralArtery_InternalCarotidArteryAneurysm#89_rep1 [IA6]

source_name: Middle Crebral Artery, Internal Carotid Artery Aneurysm, Patient Number 89, replicate 1


title: MiddleCerebralArtery_MoyamoyaDisease#84_rep1 [MMD1 ]

source_name: Middle Crebral Artery, Adult Moyamoya Disease, Patient Number 84, replicate 1

value: Fenale


title: MiddleCerebralArtery_InternalCarotidArteryAneurysm#114_rep1 [IA3]

source_name: Middle Crebral Artery, Internal Carotid Artery Aneurysm, Patient Number 114, replicate 1


title: MiddleCerebralArtery_InternalCarotidArteryAneurysm#115_rep1 [IA4]

source_name: Middle Crebral Artery, Internal Carotid Artery Aneurysm, Patient Number 115, replicate 1


title: MiddleCerebralArtery_MoyamoyaDisease#66_rep1 [MMD9]

source_name: Middle Crebral Artery, Adult Moyamoya Disease, Patient Number 66, replicate 1


title: MiddleCerebralArtery_MoyamoyaDisease#98_rep1 [MMD3]

source_name: Middle Crebral Artery, Adult Moyamoya Disease, Patient Number 98, replicate 1


title: MiddleCerebralArtery_Epilepsi#127_rep1 [EPI3]

source_name: Middle Crebral Artery, Epilepsi, Patient Number 127, replicate 1


title: MiddleCerebralArtery_InternalCarotidArteryAneurysm#104_rep1 [IA1]

source_name: Middle Crebral Artery, Internal Carotid Artery Aneurysm, Patient Number 104, replicate 1


title: MiddleCerebralArtery_MoyamoyaDisease#122_rep1 [MMD6]

source_name: Middle Crebral Artery, Adult Moyamoya Disease, Patient Number 122, replicate 1


title: MiddleCerebralArtery_MoyamoyaDisease#95_rep1 [MMD2]

source_name: Middle Crebral Artery, Adult Moyamoya Disease, Patient Number 95, replicate 1


title: B_Control_rep8

status: Public on Apr 08 2020

description:
B_Control_998.15_S25_M
1.25mm Punch of Placenta Junctional/Labyrinth Zone

data_processing:
Data analysis for RNA-Seq was performed by the Bioinformatics Core associated with Center for Human Health and Environment at NCSU. Briefly, quality control of read data was evaluated with FastQC. Alignment was preformed using STAR short read aligner(Dobin et al., 2013) to Rattus norvegicus (rn6) reference genome. The number of reads mapped to a genome features was determined using htseq-count script from HTSeq(Anders et al., 2015) python package and  count data was imported to R statistical computing environment for further analysis. Initially, genes that have no count in more than 1/4 of the replicate samples were excluded from the analysis. Data normalization based on dispersion and differential analysis were conducted using DESeq2(Love et al., 2014) package. We fitted a generalized linear model (~sex + Treatment) between the expression count. Finally, differential expression analysis was preformed between A_high vs B_control  dose.
Genome_build: ran6
Supplementary_files_format_and_content: Raw read count file .xlsx format from htseq-count

organism: Rattus norvegicus

source_name: Placenta

growth_protocol: Sacrifice on GD14 was performed four hours after final dosing (12:00h ± 60 minutes) to control for time post-exposure and time of collection.  All dams and fetuses were weighed and sacrificed by CO2 asphyxiation and rapid decapitation.  Placental dissection consisted of separating the decidua, myometrium, and mesometrium (referred to as the maternal side of the placenta) from the trophospongium and labyrinth zone (referred to as the fetal side of the placenta).  Frozen placentas were cryosectioned (Leica CM1900, Nubloch, Germany) at an orientation that produced a cross-section of each layer, and sliced to a depth approximately one-third of the way through the tissue, where we could see distinct layers, including the junctional and labyrinth zone, as well as the maternal arterial channel as reference landmarks for tissue collection.  Then two 1.25 mm punches were collected and stored in separate tubes at -80°C.  A single punch was used for RNA extractions for RNA-sequencing (high dose n = 5/sex, control n = 4/sex).

extract_protocol:
RNA extraction was performed with the Qiagen RNEasy Miniprep kit according to the manufacturer protocol (Qiagen, Cat. 74134).  RNA quality was determined using an Agilent 2100 Bioanalyzer and all samples, for both tissue types, were found to have an RNA integrity number (RIN) ≥ 10.  Sequencing libraries were prepared as described previously, using NEBNext Ultra Directional RNA Library Prep kit and NEBNext Poly(A) mRNA Magnetic Isolation Module (catalogs E7420 and E7490; New England Biolabs), to be compatible with Illumina sequencing.  Isolation, heat fragmentation, and priming was performed according to manufacturer’s instructions.  cDNA synthesis was followed by purification and size selection.  Finally, library clean-up was performed used AMPure XP beads (Beckman Coulter Genomics, Cat. A63881) and quality was assessed using the Agilent 2100 Bioanalyzer.  For each tissue library sequencing was performed using a 125-bp single-end protocol on a single lane of an Illumina HiSeq2500 sequencer.  Approximately, 27.4 million uniquely mapped reads were generated per placental library, and 23.7 million reads per fetal forebrain library.
Sequencing libraries were prepared using NEBNext Ultra Directional RNA Library Prep kit and NEBNext Poly(A) mRNA Magnetic Isolation Module (catalogs E7420 and E7490; New England Biolabs), to be compatible with Illumina sequencing.

treatment_protocol: Adult Wistar rats were obtained from Charles River at PND 70 – 90 (Raleigh, NC) in batches referred to as cohorts (cohort 1: n = 20 females and 10 males, PND 70; cohort 2: n = 10 females, PND 70; cohort 3: n = 40 females and 10 males, PND 90; cohort 4: n = 10 females, PND 90).  Two dams were paired with a single male during diestrus (as determined by vaginal cytology) to ensure they reached the proestrus/estrus (peak sexual receptivity) stage while with a male.  After 72 hours or detection of a sperm plug, males were removed and dams housed individually.  Gestational day (GD) 0 was defined 24 hours after separation or detection of a sperm plug.  Dams were weighed daily to monitor weight gain as an indicator of pregnancy.  If dams were not successfully impregnated dosing was terminated.  These dams were incorporated in the next cohort as part of the same dose group they were assigned originally after about a two-week period where they were not being dosed.  Therefore, the number of dams being dosed as part of cohort 1 was 20, cohort 2 was 13, cohort 3 was 43, and cohort 4 was 13.  Of the females being dosed 12 were successfully impregnated in cohort 1, 10 in cohort 2, 36 in cohort 3, and 12 in cohort 4.  Animals were maintained on Teklad 2020 (phytoestrogen-free) diet, then paired and monitored for the presence of a sperm plug.  Exposure was once per day for 14 days across GDs 1-14.  At the time of dosing 20 µl of each dosing solution was pipetted onto ¼ of a soy-free food treat pellet (apple flavored AIN-76A Rodent Diet Test Tabs, Test Diet, Richmond, IN) as we have done previously (Patisaul et al. 2013) resulting in the following exposure groups (animals randomly assigned): control (0 µg OPFRs) (Van Naarden Braun et al.), 500 µg OPFRs (2 mg/kg OPFR), 1,000 µg OPFRs (4 mg/kg OPFR), 2,000 µg OPFRs (8 mg/kg OPFR), and 1.25 mg 5-MT.  The food treat was administered once the solution was completely dry and consumption was monitored to ensure the dam ate the entire treat.  Dams were not dosed by individual weight but rather by an average colony (all female) weight of 250 g at conception producing exposures of approximately 0, 2, 4, and 8 mg/kg bw/day OPFRs and 5 mg/kg bw/day 5-MT (relative exposure likely decreased slightly across the 10 day window as body weight increased across pregnancy).

value: Wistar

value: vehicle

value: M


title: B_Control_rep7

description:
B_Control_998.14_S24_F
1.25mm Punch of Placenta Junctional/Labyrinth Zone

value: F


title: B_Control_rep9

description:
B_Control_999.02_S26_M
1.25mm Punch of Placenta Junctional/Labyrinth Zone


title: B_Control_Rep5

description:
B_Control_998.04_S22_M
1.25mm Punch of Placenta Junctional/Labyrinth Zone


title: A_High_rep9

description:
A_High_993.04_S16_F
1.25mm Punch of Placenta Junctional/Labyrinth Zone

value: 8mg/kg OPFRs


title: B_Control_rep6

description:
B_Control_998.12_S23_F
1.25mm Punch of Placenta Junctional/Labyrinth Zone


title: B_Control_rep10

description:
B_Control_999.08_S27_F
1.25mm Punch of Placenta Junctional/Labyrinth Zone


title: B_Control_rep4

description:
B_Control_982.12_S31_F
1.25mm Punch of Placenta Junctional/Labyrinth Zone


title: A_High_rep10

description:
A_High_993.1_S17_M
1.25mm Punch of Placenta Junctional/Labyrinth Zone


title: B_Control_rep3

description:
B_Control_982.09not06_S30_M
1.25mm Punch of Placenta Junctional/Labyrinth Zone


title: A_High_rep8

description:
A_High_972.1_S15_F
1.25mm Punch of Placenta Junctional/Labyrinth Zone


title: A_High_rep5

description:
A_High_951.02_S12_M
1.25mm Punch of Placenta Junctional/Labyrinth Zone


title: A_High_rep7

description:
A_High_972.06_S14_M
1.25mm Punch of Placenta Junctional/Labyrinth Zone


title: A_High_rep6

description:
A_High_951.03_S13_F
1.25mm Punch of Placenta Junctional/Labyrinth Zone


title: A_High_rep3

description:
A_High_7.11_S20_F
1.25mm Punch of Placenta Junctional/Labyrinth Zone


title: A_High_rep4

description:
A_High_7.12_S21_M
1.25mm Punch of Placenta Junctional/Labyrinth Zone


title: A_High_rep2

description:
A_High_1.1_S19_M
1.25mm Punch of Placenta Junctional/Labyrinth Zone


title: B_Control_rep2

description:
B_Control_09.09_S29_F
1.25mm Punch of Placenta Junctional/Labyrinth Zone


title: B_Control_rep1

description:
B_Control_09.01_S28_M
1.25mm Punch of Placenta Junctional/Labyrinth Zone


title: A_High_rep1

description:
A_High_01.02_S18_F
1.25mm Punch of Placenta Junctional/Labyrinth Zone


title: Control rep2 RPF

status: Public on Jul 26 2019

data_processing:
Library strategy: Ribo-Seq
Sequence reads were trimmed with TrimGalore v0.4.3 and cutadapt v1.12 and size selected, reads with N>20 were used for further analysis.
Ribosome profiling data was aligned using bowtie2 v2.2.5 against rRNA and tRNA sequences retrieved from UCSC Table Browser, not matched reads were used for further analysis.
Trimmed RNA-seq and Ribo-seq (after tRNA and rRNA removal) data was aligned with bowtie2 v2.2.5 against UCSC mm10 RefSeq mouse genome, retrieved from iGenomes (Illumina).
Samtools v1.5 was used to sort and index the resulting files containing the aligned sequences.
Amount of sequences aligned to transcripts was counted with HTSeq v0.6.0.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *_s_no_DESeq.txt: Tab-delimited tables with 2 columns in .txt format, column1: Gene symbols, column2: corresponding counts.

source_name: cortex

extract_protocol:
Tissue powder was lysed in lysis buffer (10 mM Tris-Cl (pH 7.5), 300 mM KCl, 10 mM MgCl2, 25 mg/ml cycloheximide, 100 mM DTT and 1% Triton X-100), ribosome pellets were resuspended in Qiazol (Qiagen) after centrifugation of RNaseI digested monosomes in 50% sucrose buffer, ribosome protected fragments were isolated using miRNeasy kit (Qiagen) according to manufacturer protocol with modification to retain small RNAs.
RPFs were electrophoresed on a 15% Tris-Borate-EDTA (TBE) Urea gel and RNA fragments between 20 and 40 nts in size were purified prior to the construction of libraries for deep-sequencing. Small RNA sequencing libraries were constructed using the NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs), according to the manufacturer's instructions.

tag: strain/background

tag: genotype/variation

value: Sbp2 wt/wt; Camk-Cre neg

value: male

value: brain cortex

value: postnatal day 34


title: Secisbp2 RQ rep2 RNA

data_processing:
Sequence reads were trimmed with TrimGalore v0.4.3 and cutadapt v1.12 and size selected, reads with N>20 were used for further analysis.
Ribosome profiling data was aligned using bowtie2 v2.2.5 against rRNA and tRNA sequences retrieved from UCSC Table Browser, not matched reads were used for further analysis.
Trimmed RNA-seq and Ribo-seq (after tRNA and rRNA removal) data was aligned with bowtie2 v2.2.5 against UCSC mm10 RefSeq mouse genome, retrieved from iGenomes (Illumina).
Samtools v1.5 was used to sort and index the resulting files containing the aligned sequences.
Amount of sequences aligned to transcripts was counted with HTSeq v0.6.0.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *_s_no_DESeq.txt: Tab-delimited tables with 2 columns in .txt format, column1: Gene symbols, column2: corresponding counts.

extract_protocol:
Qiazol (Qiagen) according to manufacturer protocol, Poly(A) Purist Mag kit (Ambion) was used to isolate polyA mRNA.
Randomly fragmented PolyA enriched total RNA was electrophoresed on a 15% Tris-Borate-EDTA (TBE) Urea gel and RNA fragments between 20 and 40 nts in size were purified prior to the construction of libraries for deep-sequencing. Small RNA sequencing libraries were constructed using the NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs), according to the manufacturer's instructions.

value: Sbp2 fl/R543Q; Camk-Cre pos


title: Secisbp2 RQ rep1 RNA


title: Control rep1 RNA


title: Control rep1 RPF


title: Control rep2 RNA


title: Secisbp2 RQ rep2 RPF


title: Child_low_cadmium 1808-04

status: Public on Dec 04 2018

description: Whole genome bisulfite sequencing

data_processing:
Bisulfite sequencing reads were aligned to the reference human genome (hg38) using BSMAP (Xi & Li 2009), which automatically trims adapters and low-quality sequence reads. For newborn cord blood samples, 460 and 535 million reads were generated for low and high Cd exposure groups, respectively, of which 61.5 % and 61.1 % were uniquely aligned to the reference genome, representing 13x and 15x coverage. For maternal blood samples, 201 million and 188 million reads were generated for low and high Cd exposure groups, respectively, of which 56.2 % and 59.5 % of reads were uniquely aligned to the reference genome, representing 5x and 6x coverage. The percentage of uniquely aligned reads is consistent with data reported in a separate study, in which four alignment tools for genome wide bisulfite sequencing data were compared and yielded 55.5 % uniquely mapped reads, on average (Chatterjee et al. 2012). Model Based Analysis of Bisulfite Sequencing (MOABS, V1.2.2) (Sun et al. 2014) was used to identify differentially methylated CpG dinucleotides and to call Differentially Methylated Regions (DMRs). MOABS uses a beta binomial hierarchical model to capture sampling and biological variation, and generates a credible methylation difference (CDIF) metric. This metric does not require the high coverage necessary for other approaches which mainly implement Fisher’s exact test and typically require >30x coverage. MOABS supports three models to call differentially methylated CpGs and DMRs: Fisher’s exact test, hidden Markov model and CDIF. We used CDIF in this study. DMRs were defined by a minimum of three methylated CpG dinucleotides within a maximum interval of 300 bp, each with an absolute methylation difference of at least 10 % in the same direction (i.e. lower or higher methylation) between low and high Cd exposed groups.
Genome_build: hg38

source_name: Blood (buffy coat)

extract_protocol:
Genomic DNA was isolated from the buffy coat from maternal and newborn cord blood samples using PureGene reagents (Qiagen, Inc., Valencia, CA). DNA was bisulfite converted using Epitect Bisulfite kits (Qiagen, Inc., Valencia, CA) according to manufacturer’s protocols. The bisulfite conversion rate was ~98.0 % across all samples.
Bisulfite converted maternal DNAs were pooled and converted to sequencing libraries using TruSeq DNA Methylation kits (Illumina, Inc., San Diego, CA) according to manufacturer’s protocols. Sequencing libraries from bisulfite converted newborn cord blood DNAs were prepared individually using TruSeq DNA Methylation kits, and index tagged using TruSeq DNA Methylation Index PCR Primers (Illumina, Inc.). The index tagged libraries were quantitated using the ddPCR Library Quantification Kit for Illumina TruSeq (Bio-Rad, Inc., Hercules, CA) according to manufacturer’s protocols, and a QX200 Droplet Digital PCR system at the North Carolina State University Genomic Sciences Laboratory (NCSU GSL). Normalized libraries were pooled, with 4 or 5 libraries per pool. Libraries were sequenced on an Illumina HiSeq 2500 instrument at the NCSU GSL, producing 100 bp single end reads.

treatment_protocol: Study participants were recruited between January 2009 and June 2011 as part of the ongoing Newborn Epigenetics STudy (NEST), a prospective cohort study of women and their children. Details of participant identification, enrollment and data and specimen collection procedures have been described elsewhere (Hoyo et al. 2014). Briefly, English- or Spanish-speaking pregnant women aged 18 years or older visiting Duke prenatal clinics were identified from logs of prenatal clinics in Durham County, NC, United States. From these, women who planned to relinquish custody of the child or had established HIV infection were excluded, as were those who received obstetric care at facilities other than Duke Obstetrics or Durham Regional Hospitals. By December of 2011, 1700 of the 2548 eligible women had been enrolled. From these 115 were excluded because of fetal demise and 281 refused further participation, could not be located for subsequent follow-up, were illiterate and could not reasonably provide informed consent, or were underage, leaving 1304 (77 %). The median gestational age at enrollment was 12 weeks (interquartile range (IQR): 7-14 weeks). The protocol was approved by Duke University, Durham Regional Hospital, and North Carolina State University. At enrollment, 10 ml of peripheral blood was obtained in EDTA vacutainers from all women, of which 1 ml was stored as whole blood in 200 µl aliquots. For the first 310 participants, one 200 µl aliquot was used to measure Cd using established solution-based ICP-MS methods that have been previously described (Vidal et al. 2015; Darrah et al. 2009; McLaughlin et al. 2011). Briefly, the 200 µl frozen samples were equilibrated at room temperature, homogenized and then pipetted into a trace-metal-clean test tube and verified gravimetrically using a calibrated mass balance. These samples were then spiked with internal standards comprising known quantities (10 and 1 ng/g, respectively) of indium and bismuth (SCP Science, Canada) used to correct for instrumental drift. Cd concentrations were measured using a Perkin Elmer DRC II (Dynamic Reaction Cell) axial field ICP-MS at the University of Massachusetts, Boston. The method detection limit (83 pg/g parts per trillion) was calculated using the t99SLLMV method (USEPA, 1993) at 99 % CI (t = 3.71). The limit of detection and the limit of quantification estimated according to (Long & Winefordner 1983) were less than 43 pg/g, and 51 pg/g, respectively. In the current study, we analyzed specimens from 20 pregnant women and their offspring, 10 with the highest blood Cd concentrations in the first trimester of pregnancy and 10 who were selected from the majority of women with blood concentrations close to zero. Participants were selected to minimize confounding by matching on factors shown either to be directly associated with CpG methylation and thus provide a potential explanation for associations observed, or to modify associations between Cd or other toxic metals and CpG methylation. By matching on these factors individuals in the high and low Cd exposure groups were comparable with respect to advanced maternal age, pre-pregnancy obesity, gestational age at delivery and race/ethnicity, among other factors. In this population, only one woman had gestational diabetes, a factor that may also influence CpG methylation.

value: Newborn cord blood


title: Mother_high_cadmium DASE.fastq.gz

description: Whole genome bisulfite sequencing

value: Maternal blood


title: Child_low_cadmium 1751-04

description: Whole genome bisulfite sequencing


title: Child_low_cadmium 1753-04

description: Whole genome bisulfite sequencing


title: Child_low_cadmium 1807-04

description: Whole genome bisulfite sequencing


title: Mother_low_cadmium DASC.fastq.gz

description: Whole genome bisulfite sequencing


title: Child_low_cadmium 1825-04

description: Whole genome bisulfite sequencing


title: Child_low_cadmium 1809-04

description: Whole genome bisulfite sequencing


title: Child_low_cadmium 1747-04

description: Whole genome bisulfite sequencing


title: Child_low_cadmium 1464-04

description: Whole genome bisulfite sequencing


title: Child_low_cadmium 1725-04

description: Whole genome bisulfite sequencing


title: Child_high_cadmium 2164-04

description: Whole genome bisulfite sequencing


title: MiddleCerebralArtery_AdultMoyamoyaDisease#73_rep1

status: Public on Feb 29 2020

description: MCA MMD 4

data_processing: Signal intensity was quantified from the scanned image using Feature Extraction Software version 11.0.1.1 (Agilent Technologies).

source_name: Middle Cerebral Artery, Adult Moyamoya Disease, Patient Number 73, replicate 1

extract_protocol: Total RNA was extracted from each MCA and STA specimen with an RNeasy Micro Kit (Qiagen). The purified total RNA was amplified with an Ovation PicoSL WTA System V2 kit (NuGEN Technologies, Bemmel, Netherlands)

treatment_protocol: We excised the vessel wall of the MCA following the reported procedure, and also obtained a small piece of the STA. Tissue samples were collected into RNAlater (Qiagen, Hilden, Germany) and stored at -80 °C.

tag: condition

value: Adult Moyamoya Disease

tag: individual

value: Patient Number 73

value: Artery Wall (MCA)


title: MiddleCerebralArtery_AdultMoyamoyaDisease#69_rep1

description: MCA MMD 3

source_name: Middle Cerebral Artery, Adult Moyamoya Disease, Patient Number 69, replicate 1

value: Patient Number 69

value: Female

tag: age


title: MiddleCerebralArtery_InternalCarotidArteryAneurysm#115_rep1

description: MCA IA 4

source_name: Middle Cerebral Artery, Internal Carotid Artery Aneurysm, Patient Number 115, replicate 1

value: Internal Carotid Artery Aneurysm

value: Patient Number 115


title: MiddleCerebralArtery_InternalCarotidArteryAneurysm#104_rep1

description: MCA IA 1

source_name: Middle Cerebral Artery, Internal Carotid Artery Aneurysm, Patient Number 104, replicate 1

value: Patient Number 104


title: MiddleCerebralArtery_InternalCarotidArteryAneurysm#114_rep1

description: MCA IA 3

source_name: Middle Cerebral Artery, Internal Carotid Artery Aneurysm, Patient Number 114, replicate 1

value: Patient Number 114


title: MiddleCerebralArtery_InternalCarotidArterylAneurysm#106_rep1

description: MCA IA 2

source_name: Middle Cerebral Artery, Internal Carotid Artery Aneurysm, Patient Number 106, replicate 1

value: Patient Number 106


title: Child_high_cadmium 2188-04

description: Whole genome bisulfite sequencing


title: Child_high_cadmium 1453-04

description: Whole genome bisulfite sequencing


title: Child_high_cadmium 1088-04

description: Whole genome bisulfite sequencing


title: Child_high_cadmium 1241-04

description: Whole genome bisulfite sequencing


title: Secisbp2 RQ rep1 RPF


title: Child_high_cadmium 1993-04

description: Whole genome bisulfite sequencing


title: Child_high_cadmium 1187-04

description: Whole genome bisulfite sequencing


title: Child_high_cadmium 1013-04

description: Whole genome bisulfite sequencing


title: MiddleCerebralArtery_AdultMoyamoyaDisease#66_rep1

description: MCA MMD 2

source_name: Middle Cerebral Artery, Adult Moyamoya Disease, Patient Number 66, replicate 1

value: Patient Number 66

value: Male


title: MiddleCerebralArtery_AdultMoyamoyaDisease#63_rep1

description: MCA MMD 1

source_name: Middle Cerebral Artery, Adult Moyamoya Disease, Patient Number 63, replicate 1

value: Patient Number 63


title: High_rep2

status: Public on Feb 28 2018

description:
Gene Expression in fetal forebrains
S17F_S77_L007_R1_001

data_processing:
The read quality was evaluated with FastQC. Alignment was performed using STAR short read aligner to Rattus norvegicus (rn6) reference genome. The number of reads mapped to genome features was determined using htseq-count script from HTSeq python package and count data was imported to R statistical computing environment for further analysis. Initially, genes that had no counts in more than 2/3 of the replicate samples were excluded from the analysis.
Genome_build: rn6
Supplementary_files_format_and_content: Raw read count csv format

source_name: Brain tissue_high dose FM550

growth_protocol: Sacrifice occurred on GD 18, four hours after final dosing (12:00h ± 60 minutes) to control for time post-exposure and time of collection.  All dams and fetuses were weighed and sacrificed by CO2 asphyxiation and rapid decapitation. A single paw was collected from each fetus to determine sex. Whole fetal heads were collected, flash frozen, and then cryosectioned (Leica CM 1900) from the rostral end in order to isolate forebrain via microdissection.  Anatomical landmarks were identified with the assistance of a developing mouse brain atlas, with all forebrain tissue from plates 48-57 obtained via microdissection, placed in an Eppendorf tube, and stored at -80°C to use for RNA extractions for RNA-sequencing (n = 3 per sex per group). The RNA samples were sequenced using  an Illumina HiSeq2500 sequencer.

extract_protocol:
RNA extraction was performed with the Qiagen RNEasy Miniprep kit according to the manufacturer protocol (Qiagen, Cat. 74134).  RNA quality was determined using an Agilent 2100 Bioanalyzer and all samples, for both tissue types, were found to have an RNA integrity number (RIN) ≥ 10.  Sequencing libraries were prepared as described previously, using NEBNext Ultra Directional RNA Library Prep kit and NEBNext Poly(A) mRNA Magnetic Isolation Module (catalogs E7420 and E7490; New England Biolabs), to be compatible with Illumina sequencing.  Isolation, heat fragmentation, and priming was performed according to manufacturer’s instructions.  cDNA synthesis was followed by purification and size selection.  Finally, library clean-up was performed used AMPure XP beads (Beckman Coulter Genomics, Cat. A63881) and quality was assessed using the Agilent 2100 Bioanalyzer.  For each tissue library sequencing was performed using a 125-bp single-end protocol on a single lane of an Illumina HiSeq2500 sequencer.  Approximately,  23.7 million reads per fetal forebrain library.
Sequencing libraries were prepared using NEBNext Ultra Directional RNA Library Prep kit and NEBNext Poly(A) mRNA Magnetic Isolation Module (catalogs E7420 and E7490; New England Biolabs), to be compatible with Illumina sequencing.

treatment_protocol: Briefly, adult Wistar rats (n = 48 females and 26 males) were maintained on Teklad 2020 (phytoestrogen-free) diet, then paired and monitored for the presence of a sperm plug; designated gestational day (GD) 0.  Exposure was once per day for 10 days across GDs 9-18. At the time of dosing 20 µl of each dosing solution was pipetted onto ¼ of a soy-free food treat pellet (chocolate flavored AIN-76A Rodent Diet Test Tabs, Test Diet, Richmond, IN) as we have done previously resulting in the following exposure groups (animals randomly assigned): 0 µg FM 550 (vehicle) [49], 300 µg FM 550 (low), and 1,000 µg FM 550 (high).  Dams were not dosed by individual weight but rather by an average colony (all female) weight of 300 g at conception producing exposures of approximately 0, 1 and 3.3 mg/kg bw per day FM 550 (relative exposure likely decreased slightly across the 10 day window as body weight increased across pregnancy).

value: Forebrain

tag: strain

value: Wistar

value: male


title: High_rep1

description:
Gene Expression in fetal forebrains
S15F_S75_L007_R1_001


title: Control_rep2

description:
Gene Expression in fetal forebrains
S7F_S71_L007_R1_001

source_name: Brain tissue_control


title: VEHICLE_24h_rep23

status: Public on Feb 22 2018

description:
targeted RNA
Gene Expression at 24 hours in iPSC Cardiomyocytes
processed data file column header: 262_S262_L001_R1_001.fastq.gz

data_processing:
Library strategy: TempOSeq
Detailed in https://github.com/demis001/temposeqcount
Temposeqcount is a pipeline that accepts the probe manifest file (included on the series record) and generates the probe fasta file, indexes it, maps the fastq file against the indexed probe fasta file using the STAR aligner and calculates the read count.
Supplementary_files_format_and_content: txt file with raw read counts

source_name: induced PSCs

growth_protocol: iCell cardiomyocytes were plated and maintained according to the  manufacturer’s recommendations (Cellular Dynamics International, Madison, WI) and in accordance with  previously published protocols with minor adjustments (Sirenko et al. 2017; Grimm et al. 2016; Grimm et  al. 2015; Sirenko, Cromwell, et al. 2013; Sirenko, Crittenden, et al. 2013). Individual units of   cardiomyocytes were thawed for 4 min in a 37 °C water bath and subsequently resuspended in 10 ml of   cardiomyocyte plating medium containing 1:500 penicillin/streptomycin solution. Following microscopic   cell counting using the trypan blue exclusion method, the cell density was adjusted to a final plating   density of 2x105 cells/ml. 25μl of cell suspension were then transferred per well to a 384-well microplate,   yielding a final cell density of 5000/well. Tissue-culture treated microplates (cat.no.: 353962, Corning   Life Sciences, Corning, NY) were gelatinized for 2 hours at 37 °C with 25μl 0.1% gelatin in water before   cardiomyocytes were plated. After disposal of the gelatin solution and addition of the cell suspension,   microplates were kept at room temperature for 30 min. Cells were then incubated at 37 °C and 5% CO2   for 48 hours. The plating medium was then exchanged with 40μl of maintenance medium containing   1:500 penicillin/streptomycin solution per well. Maintenance medium was replaced every 48-72 hours   until day 13 post-plating. The maintenance medium was then exchanged with 50μl fresh medium per well   and incubated overnight.

extract_protocol:
RNA was isolated from cells using TRIzol reagent (Invitrogen) and further purified by RNeasy MinElute Cleanup (Qiagen).Differential gene expression patterns and  concentration-response relationships were analyzed using TempO-Seq™ (BioSpyder Technologies, Inc.,  Carlsbad, CA) (Yeakley et al. 2017), a targeted RNA sequencing technology 119 focused on a surrogate  transcriptome panel comprising 2982 transcripts, as described previously (Grimm et al. 2016).
The  sequencing library was prepared according to the manufacturer’s guidelines and as previously described  (Grimm et al. 2015). In brief, RNA in 2μl of each cell lysate were hybridized with the provided detector  oligo pool mix (2μl per sample) using the following thermocycler settings: 10 min at 70°C, followed by  gradual decrease to 45°C over 49 min, and ending with 45°C for 1 min. Subsequent steps included  nuclease digestion (90 min at 37°C) ligation step (60 min at 37°C, followed by heat denaturation at 80°C  for 30 min) following addition of 24μl nuclease mix and 24μl ligation mix. 10μl of each ligation product  were then transferred to a 96-well amplification microplate containing 10μl of PCR mix per well. The  ligation products were then uniquely labeled during product amplification, when well-specific,  “barcoded” primer pairs were introduced to templates. Sequence-based barcoding is an essential step  allowing for correct identification and recognition of transcript-specific sequencing counts. 5μl of sample  amplicons from each well were subsequently pooled into a single sequencing library. The TempO-Seq  library was further processed using a PCR clean-up kit (Clontech, Mountain View, CA) prior to  sequencing at Texas A&M University Genomics & Bioinformatics Services. Sequencing was achieved  using a 50 single-end read mode in a rapid flow cell (2 sequencing lanes for increased sequencing depth)  on a HiSeq 2500 Ultra-High-Throughput Sequencing System (Illumina, San Diego, CA). Sequencing  readouts were demultiplexed to generate FASTQ files, and passed all internal quality controls.

treatment_protocol: Cells were treated the next morning (day 14 post-plating) with 12.5μl 5x  chemical solutions in 0.5% DMSO (v/v) in media (vehicle) in addition to untreated or vehicle-treated  negative control wells, and incubated at 37 °C and 5% CO2. Following 24 hours of incubation, the cell  medium was discarded, and cardiomyocytes were lysed with 10μl 1x lysis buffer provided in the TempO  Seq assay kit (BioSpyder Technologies, Carlsbad, CA). Lysate-containing micro-plates were agitated at  300 rpm using a benchtop microplate shaker and stored at -80°C until further use.

tag: cell type

value: Beating Cardiomyocytes

value: Vehicle

tag: dose um


title: VEHICLE_24h_rep21

description:
targeted RNA
Gene Expression at 24 hours in iPSC Cardiomyocytes
processed data file column header: 252_S252_L001_R1_001.fastq.gz


title: Child_high_cadmium 1460-04

description: Whole genome bisulfite sequencing

value: Newborn cord blood


title: High_rep3

description:
Gene Expression in fetal forebrains
S19F_S79_L007_R1_001


title: Control_rep1

description:
Gene Expression in fetal forebrains
S2F_S70_L007_R1_001


title: Control_rep3

description:
Gene Expression in fetal forebrains
S12F_S74_L007_R1_001


title: VEHICLE_24h_rep24

description:
targeted RNA
Gene Expression at 24 hours in iPSC Cardiomyocytes
processed data file column header: 264_S264_L001_R1_001.fastq.gz


title: VEHICLE_24h_rep19

description:
targeted RNA
Gene Expression at 24 hours in iPSC Cardiomyocytes
processed data file column header: 248_S248_L001_R1_001.fastq.gz


title: VEHICLE_24h_rep16

description:
targeted RNA
Gene Expression at 24 hours in iPSC Cardiomyocytes
processed data file column header: 110_S110_L001_R1_001.fastq.gz


title: VEHICLE_24h_rep13

description:
targeted RNA
Gene Expression at 24 hours in iPSC Cardiomyocytes
processed data file column header: 098_S98_L001_R1_001.fastq.gz


title: VEHICLE_24h_rep18

description:
targeted RNA
Gene Expression at 24 hours in iPSC Cardiomyocytes
processed data file column header: 114_S114_L001_R1_001.fastq.gz


title: VEHICLE_24h_rep14

description:
targeted RNA
Gene Expression at 24 hours in iPSC Cardiomyocytes
processed data file column header: 100_S100_L001_R1_001.fastq.gz


title: Propranolol_24h_dose_10

description:
targeted RNA
Gene Expression at 24 hours in iPSC Cardiomyocytes
processed data file column header: 024_S24_L001_R1_001.fastq.gz

value: Proprenolol


title: VEHICLE_24h_rep20

description:
targeted RNA
Gene Expression at 24 hours in iPSC Cardiomyocytes
processed data file column header: 250_S250_L001_R1_001.fastq.gz


title: Propranolol_24h_dose_0.1

description:
targeted RNA
Gene Expression at 24 hours in iPSC Cardiomyocytes
processed data file column header: 020_S20_L001_R1_001.fastq.gz


title: Nifedipine_24h_dose_1

description:
targeted RNA
Gene Expression at 24 hours in iPSC Cardiomyocytes
processed data file column header: 010_S10_L001_R1_001.fastq.gz

value: Nifedepine


title: Nifedipine_24h_dose_10

description:
targeted RNA
Gene Expression at 24 hours in iPSC Cardiomyocytes
processed data file column header: 012_S12_L001_R1_001.fastq.gz


title: VEHICLE_24h_rep22

description:
targeted RNA
Gene Expression at 24 hours in iPSC Cardiomyocytes
processed data file column header: 260_S260_L001_R1_001.fastq.gz


title: VEHICLE_24h_rep17

description:
targeted RNA
Gene Expression at 24 hours in iPSC Cardiomyocytes
processed data file column header: 112_S112_L001_R1_001.fastq.gz


title: VEHICLE_24h_rep15

description:
targeted RNA
Gene Expression at 24 hours in iPSC Cardiomyocytes
processed data file column header: 102_S102_L001_R1_001.fastq.gz


title: MEDIA_24h_rep9

description:
targeted RNA
Gene Expression at 24 hours in iPSC Cardiomyocytes
processed data file column header: 108_S108_L001_R1_001.fastq.gz

value: Media


title: MEDIA_24h_rep11

description:
targeted RNA
Gene Expression at 24 hours in iPSC Cardiomyocytes
processed data file column header: 256_S256_L001_R1_001.fastq.gz


title: Nifedipine_24h_dose_0.1

description:
targeted RNA
Gene Expression at 24 hours in iPSC Cardiomyocytes
processed data file column header: 008_S8_L001_R1_001.fastq.gz


title: MEDIA_24h_rep8

description:
targeted RNA
Gene Expression at 24 hours in iPSC Cardiomyocytes
processed data file column header: 106_S106_L001_R1_001.fastq.gz


title: Isoproterenol_24h_dose_0.1

description:
targeted RNA
Gene Expression at 24 hours in iPSC Cardiomyocytes
processed data file column header: 002_S2_L001_R1_001.fastq.gz

value: Isopreterenol


title: Isoproterenol_24h_dose_10

description:
targeted RNA
Gene Expression at 24 hours in iPSC Cardiomyocytes
processed data file column header: 006_S6_L001_R1_001.fastq.gz


title: MEDIA_24h_rep12

description:
targeted RNA
Gene Expression at 24 hours in iPSC Cardiomyocytes
processed data file column header: 258_S258_L001_R1_001.fastq.gz


title: MEDIA_24h_rep10

description:
targeted RNA
Gene Expression at 24 hours in iPSC Cardiomyocytes
processed data file column header: 254_S254_L001_R1_001.fastq.gz


title: VEHICLE_24h_rep12

description:
targeted RNA
Gene Expression at 24 hours in iPSC Cardiomyocytes
processed data file column header: 287_S287_L001_R1_001.fastq.gz


title: VEHICLE_24h_rep8

description:
targeted RNA
Gene Expression at 24 hours in iPSC Cardiomyocytes
processed data file column header: 279_S279_L001_R1_001.fastq.gz


title: VEHICLE_24h_rep9

description:
targeted RNA
Gene Expression at 24 hours in iPSC Cardiomyocytes
processed data file column header: 281_S281_L001_R1_001.fastq.gz


title: MEDIA_24h_rep7

description:
targeted RNA
Gene Expression at 24 hours in iPSC Cardiomyocytes
processed data file column header: 104_S104_L001_R1_001.fastq.gz


title: Propranolol_24h_dose_1

description:
targeted RNA
Gene Expression at 24 hours in iPSC Cardiomyocytes
processed data file column header: 022_S22_L001_R1_001.fastq.gz


title: VEHICLE_24h_rep5

description:
targeted RNA
Gene Expression at 24 hours in iPSC Cardiomyocytes
processed data file column header: 135_S135_L001_R1_001.fastq.gz


title: VEHICLE_24h_rep6

description:
targeted RNA
Gene Expression at 24 hours in iPSC Cardiomyocytes
processed data file column header: 137_S137_L001_R1_001.fastq.gz


title: VEHICLE_24h_rep4

description:
targeted RNA
Gene Expression at 24 hours in iPSC Cardiomyocytes
processed data file column header: 133_S133_L001_R1_001.fastq.gz