title: HEK293T_totalRNA_nostress_shortRT_plusDM_rep2

status: Public on Mar 13 2022

city: Chicago

first: Christopher

middle: D

last: Katanski

state: Illinois

department: Biochemistry

institute: The University of Chicago

data_processing:
Libraries were sequenced on Illumina Hi-Seq or Nova-seq platform. First, paired end reads were split by barcode sequence using Je demultiplex with options BPOS=BOTH BM=READ_1 LEN=4:6 FORCE=true C=false 6. BM and LEN options were adjusted for samples with a 3 nt barcode instead of 4, and for samples where the barcode is located in read 2
Next read 2 files were used to map with bowtie2 with the following parameters: -q -p 10 --local —no-unal. Reads were mapped to curated list of non-redundant tRNA genes with tRNAScane score >40; mRNA was mapped to hg38 transcriptome
Bowtie2 output sam files were converted to bam files, then sorted using samtools. Next IGV was used to collapse reads into 1 nt window. IGV output .wig files were reformatted using custom python scripts (available on GitHub at https://github.com/ckatanski/MSRR-seq).
The bowtie2 output Sam files were also used as input for a custom python script using PySam, a python wrapper for SAMTools ( https://github.com/pysam-developers/pysam) to sum all reads that mapped to each gene
Data was visualized with custom R scripts (available on GitHub at https://github.com/ckatanski/MSR-seq)
Assembly: Hg19; hg38

source_name: RNA extracted from HEK293T cell culture, with AlkB demethylase treatment

growth_protocol: HEK293T cells were cultured with complete DMEM medium under standard conditions according to ATCC. Briefly, HEK293T cells were grown in Hyclone DMEM medium (GE Healthcare Life Sciences, SH30022.01) with 10% FBS and 1% Pen-Strep (Penicillin-Streptomycin) to 80% confluency and passaged. Cells were collected and total RNA was extracted using TRIzol (ThermoFisher, 15596026) by following the manufacturer’s protocol when cells reached 80-90% confluency. MCF7 cells were cultured in EMEM medium (ATCC, 30-2003) with 10% FBS (ThermoFisher, 10082147), 0.01 mg/ml bovine insulin (Sigma-Aldrich, I0516), and 10 nM β-estradiol (Sigma- Aldrich, E2758) to 80% confluency and passaged at ratios of 1:3. Total RNA were extracted using TRIzol.

extract_protocol:
Cells were collected and total RNA was extracted using TRIzol (ThermoFisher, 15596026) by following the manufacturer’s protocol when cells reached 80-90% confluency. Poly(A)-selection was done with NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, E7490S) according to manufacturer’s instructions: 1 µg of input polyA+ RNA samples and 100 ng polysome polyA+ RNA samples were used to build sequencing libraries. The RNA fragmentation and end repair steps are the same as the CMC sequencing libraries construction. Briefly, polyA+ RNA in 18 µl were added to PCR tubes and 2 µl Magnesium RNA fragmentation buffer (NEB, E6150S) was added to each tube. The tubes were incubated at 94°C in a thermocycler for 5 mins to fragment the RNA to ~200 nt. The tubes were transferred to ice and 2 µl RNA fragmentation stop solution was then added to each tube to stop the fragmentation. Samples were spun down and diluted to 50 µl using sterile H2O. The fragmented RNA was purified using Zymo RNA clean and concentrator columns and eluted in 16 µl sterile H2O. 2 µl T4 PNK buffer and 2 µl T4 PNK were added to the tubes and the tubes were incubated at 37 °C for 30 mins to repair the ends of the fragmented RNA. MSR-seq method was then used to build sequencing libraries with the fragmented RNA. Slight modifications were made to the MSR-Seq protocol. After the first ligation step, ligation reaction was quenched by adding 50 mM EDTA. Samples were combined and ligation products over 200nt long was purified using Zymo RNA clean and concentrator columns twice. Target cDNA products were purified using AMPure
Total RNA was prepared for library construction by first deacylating in a solution of 100 mM Tris-HCl, pH 9.0 at 37 °C for 30 minutes, then neutralized by addition of sodium acetate, pH 4.8 to a final concentration of 180 mM. Deacylated RNA was then ethanol precipitated and resuspended in water, or desalted using a Zymo Research Oligo Clean-and-Concentrator spin column. First bar-code ligation: Depending on the nature of the experiment described in the main text, input RNA or total nucleic acid samples were either deacylated or had undergone one-pot deacylation and β-elimination as described above. Up to 1 µg of total RNA input was used in a ligation reaction of 50 µL with the following components: 1 U/µL T4 RNA ligase I (NEB), 1x NEB T4 RNA ligase I buffer, 15% PEG 8000, 50 µM ATP, 1 mM hexaamine cobalt chloride, and 5% DMSO. After adding the ligation mix to the sample, the capture hairpin oligo (CHO, Table S5) was added to a final concentration of 1 µM and the samples were incubated at 16 °C overnight (12+ hours). Binding to Dynabeads: The ligation mixture was diluted by adding an equal volume of water to reduce the viscosity of the solution. Next, streptavidin-coated MyOne C1 Dynabeads (ThermoFisher) were added to each sample in a 1.2:1 excess over CHO (for example, a 50 µL reaction had 50 pmol capture hairpin oligo; beads were supplied at 10 mg/ml and had binding capacity of 500 pmol biotinylated oligo per mg, so use 12 µL beads). The bead-sample mixture was incubated at room temperature for 15 minutes. After binding, supernatants were removed, and the beads washed once with high salt wash buffer (1 M NaCl, 20 mM Tris-HCl, pH 7.4) and once with low salt wash buffer (100 mM NaCl, 20 mM Tris-HCl, pH 7.4). After washing, multiple individually barcoded samples can be combined for downstream steps. At this stage, enzymatic or chemical treatments can be incorporated to the library preparation protocol such as AlkB demethylase reaction or CMC treatments (see below).Dephosphorylation: A 50 µL dephosphorylation mix containing the following was added to the multiplexed sample on bead: 0.04 U/µL calf intestine phosphatase (Roche), 10 mM MgCl2, 0.5 mM ZnCl2, 20 mM HEPES, pH 7.3. The sample was incubated at 37 °C for 30 minutes. The sample was then washed once with high salt wash buffer and once with low salt wash buffer, then resuspended in 20 µL water. Reverse transcription: 5 µL of SuperScript IV VILO 5x master mix (ThermoFisher) was added to the dephosphorylated sample (final volume of 25 µL) and then incubated at 55 °C for 10 minutes. The sample was then washed once with high salt wash buffer and once with low salt wash buffer. Identical results were obtained upon extending the reaction time to 60 minutes. For overnight reverse transcription, after the initial 10 min incubation at 55 °C, the samples are further incubated at 35 °C overnight. RNase H digestion: Beads were then resuspended into 50 µL of RNase H master mix containing 0.4 U/uL RNase H (NEB) and 1x NEB RNase H buffer and incubated at 37 °C for 15 minutes. The sample was then washed once with high salt wash buffer and once with low salt wash buffer. The sample was then resuspended in 40 µL water. Periodate oxidation: 10 µL of 250 mM freshly prepared sodium periodate, 0.5 M sodium acetate, pH 5 were added to the RNase H digested sample and incubated at room temperature for 30 minutes. Afterwards, ribose was added to a final concentration of 167 mM to quench excess periodate at room temperature for 5 minutes. The sample was then washed once with high salt wash buffer and once with low salt wash buffer. Second ligation: Beads were resuspended into 50 µL of a ligation master mix with the following components: 2U/µL T4 RNA ligase I (NEB), 1x NEB T4 RNA ligase I buffer, 2 µM second ligation oligo (Table S5), 25% PEG 8000, 50 µM ATP, 7.5% DMSO, and 1 mM hexaamine cobalt chloride. After incubation at room temperature overnight (12+ hours), the reaction was diluted with 50 µL water to reduce viscosity, washed once with high salt wash buffer and once with low salt wash buffer, and then resuspended in water. The amount of water was 6 µL per sample in the first ligation reaction, before pooling the barcoded samples. For example, if the second ligation mixture contains a pool of 6 samples, the amount of water used for resuspension would be 36 µL. Samples can be stored at 4 °C or frozen at -20 °C; both can be used for the next PCR step. PCR: A 50 µL PCR reaction was run using 5-10% of the bead slurry products from the second ligation reaction using Q5 DNA polymerase (NEB) and following the manufacturer’s instructions: 0.02 U/µL Q5 DNA polymerase, 1x Q5 reaction buffer, 0.2 mM dNTPs, 0.5 µM Illumina index primer (Table S5), and 0.5 µM Illumina multiplex primer (Table S5). Typical PCR cycles were 9-15 cycles at 10 seconds at 98 °C, 15 seconds at 55 °C, and 72 °C for 20 seconds. PCR reactions were then processed through the DNA Clean and Concentrate kit (Zymo Research). TBE-PAGE gel extraction: Following desalting, PCR products were run on 10% non-denaturing TBE gel with dsDNA size markers; lanes were cut according to the desired product size, mashed by pipette tip, and then resuspended in crush-and-soak buffer (500 mM sodium acetate, pH 5.0). The gel fragments were extracted overnight and then ethanol precipitated.
MSR-seq, mRNA-seq, DM-tRNA-seq

treatment_protocol: HEK293T cells were cultured in DMEM medium (GE Healthcare Life Sciences, SH30022.01) with 10% FBS and 1% Pen–Strep (Penicillin–Streptomycin). Twenty-four 15-cm plates of HEK293T cells (5 × 106 cells each) were seeded three days before collection. On the day of polysome profiling, 6 plates of cells (2 plates for 1 sample) were treated with different stress conditions: (1) unstressed control; (2) 42 C heat shock, 1h; (3) 0.6 mM H2O2, 2h; (4) 300 µM NaAsO2, 2h. Polysome profiling was immediately performed after stress treatment. Demethylase buffer conditions were modified from Li et al 2. Three stock solutions are made fresh immediately before reaction: L-ascorbic acid 200 mM, 2-ketogluterate 3 mM, and ammonium iron sulfate 5 mM. The final reaction mixture contained 2 mM L-ascorbic acid, 1 mM 2-ketogluterate, 0.3 mM ammonium iron sulfate, 100 mM KCl, 50 mM MES pH 6, 50 ng/µL BSA, 4 µM wild-type AlkB, and 4 µM AlkB-D135S. 50 µL of the reaction mixture was added to 5-20 µL of decanted streptavidin bead slurry after ligation, immobilization, and washing. Reaction continued for 30 min at 37 C. Following the reaction, beads were washed once with high salt wash buffer (1 M NaCl, 20 mM Tris-HCl pH 7.4) and once with low salt wash buffer (100 mM NaCl, 20 mM Tris-HCl pH 7.4). MCF7 total RNA sequencing libraries were constructed as follows. Small RNA (<200nt) was first removed from 1 μg MCF7 total RNA using spin columns (Zymo Research RNA Clean & Concentrator-5, R1016) and the large RNA (>200 nt) was eluted with 18 μl sterile H2O in a microcentrifuge tube. The RNA was transferred to PCR tubes and 2 μl Magnesium RNA fragmentation buffer (NEB, E6150S) was added to each tube and the tubes were incubated at 94 C in a thermocycler for 5 minutes to fragment the RNA to ~200 nt. 2 μl RNA fragmentation stop solution was then added to each tube. The samples were diluted to 50 μl with H2O and Zymo Research spin columns were used to purify the fragmented RNA; the RNA were eluted in 16 μl sterile H2O in a microcentrifuge tube. For 3’ end repair of the RNA fragments, 2 μl 10x T4 PNK buffer and 2 μl T4 PNK at 10U/μl (ThermoFisher, EK0032) were added and the mixture incubated at 37C for 30 minutes. The fragmented, end-repaired RNA was used to build sequencing libraries using the msRNA-seq protocol described above with the following modifications. The fragmented RNA was ligated to bar-coded capture hairpin oligonucleotides and bound to streptavidin beads. The samples were then pooled, mixed and split into two parts for ±CMC (N-cyclohexyl-N′-(2-morpholinoethyl)carbodiimide) treatment (+CMC:-CMC=1.5 : 1 ratio). 12 μl sterile H2O and 24 µl TEU buffer (50 mM Tris-HCl (pH 8.3), 4 mM EDTA, 7 M urea) were first added to each tube, then 4 µl freshly prepared 1M CMC in TEU buffer was added to +CMC samples and 4 µl sterile H2O was added -CMC samples. The samples were incubated at 30 C for 16 hours at 1400 rpm on an Eppendorf ThermoMixer. The samples were washed twice with high salt buffer and once with low salt buffer. The samples were then resuspended with 40 µl of 50 mM sodium carbonate and 2 mM EDTA (pH 10.4) buffer and incubated at 37 C for 6 hours at 1400 rpm. The beads were washed twice with high salt buffer and once with low salt buffer and then proceeded to the msRNA-seq steps such as phosphatase treatment and reverse transcription. Polysome profiling procedures were adapted from reference 3. Briefly, cells were treated with 100 µg/ml cycloheximide (CHX) in DMEM for 7 mins right after stress treatments. DMEM medium was removed. Cells were then collected using 10 ml ice-cold PBS with 100 µg/ml CHX and cell lifter. Cells were pelleted by centrifugation at 3000 RPM for 5 minutes. Cell pellet was washed twice with 5 ml ice-cold PBS with 100 µg/ml CHX. Cells from two plates were combined for one sample. Cells were resuspended in 1 ml ice-cold PBS and transferred to microcentrifuge tubes. 200 µl cell suspension from each sample was saved as input. Cells were pelleted by centrifugation at 3000 RPM for 5 mins. For input cells samples, 500 µl TRIzol reagent was added to extract the total RNA. For polysome cells samples, cell pellet was resuspended by 4 volumes of lysis buffer (20 mM HEPES, pH 7.6, 100 mM KCl, 5 mM MgCl2, 1% Triton X-100, 100 µg/ml CHX, freshly added 1 × protease inhibitor (11873580001, Roche), 40 U/µl RNase inhibitor (AM2696, Thermo)). Cells were rotated and lysed at 4 C cold room for 30 mins. Lysed samples were centrifuged at 16000g for 15 mins to collect the clear lysate (~600-700 µl). 4 ul Turbo DNase was added to each lysate and the samples were incubated at room temperature for 15 mins. The samples were centrifuged again at 16000g for 15 mins to get clear lysate. Absorbance at 260 nm of each sample was measured. Samples were adjusted to the same absorbance using lysis buffer. 5%-50% sucrose gradient (20 mM HEPES, pH 7.6, 100 mM KCl, 5 mM MgCl2, 100 µg/ml CHX, freshly added 1 × protease inhibitor, 40 U/µl RNase inhibitor) was perpared using a Biocomp gradient station. 600 µl gradient buffer was removed from the top of the balanced sucrose gradient. 600 µl lysate was loaded onto the top of the gradient slowly while gently rotating the tube. The samples were centrifuged at 28000 RPM for 3 hours at 4 C using a Beckman SW28.1 rotor. After centrifugation, fractions were collected and measured using Biocomp gradient station (30 fractions total). Fractions were flash frozen and stored at –80 C before RNA extraction and library construction. For polysome RNA extraction, fractions from disome and higher were combined and 2 volumes of TRIzol reagent was added to extract the RNA. PolyA+ RNA was extracted from the input and polysome RNA using polyA+ RNA extraction kit from Promega (Z5310) or NEB (E7490S), respectively.

tag: fraction

value: Total RNA

tag: enzyme/chemical treatment

value: AlkB demethylase treated

tag: rt condition

value: Short RT


title: HEK293T_totalRNA_nostress_shortRT_plusDM_rep1

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: strain


title: HEK293T_totalRNA_nostress_shortRT_minusDM_rep1

source_name: RNA extracted from HEK293T cell culture, without AlkB demethylase treatment


title: HEK293T_totalRNA_nostress_shortRT_minusDM_rep3


title: HEK293T_totalRNA_nostress_shortRT_plusDM_rep3


title: HEK293T_totalRNA_nostress_shortRT_minusDM_rep2


title: Infected + 6'SLN-CD

status: Public on Dec 19 2021

city: Geneva

first: Ilya

last: Kolpakov

state: GE

address: 9 Ch. des MInes

department: Health 2030 Genome Center`

country: Switzerland

institute: Fondation Campus Biotech Geneva

data_processing:
1. Demultiplexing performed with bcl2fastq v2.20
2. Analysis of single-cell RNA-seq fastqs using Cell Ranger v3.1 (single "count" command) essentially consisting of the following steps.
2.A RNA-seq read mapping on GRCh38.p10 / gencode v29  joined with Influenza A reference (GCA_001343785.1). Viral transcrpts are prefixed with "InfluenzaA_".
2.B Resolution and filtering of cell barcodes and per-cell unique molecular identifiers (UMIs).
3.C Construction of  (sparse) count matrices containing per-gene UMI counts for each valid cell barcode.
Genome_build: GRCh38
Supplementary_files_format_and_content: Per-cell per-gene UMI counts in 10X HDF5 feature barcode matrix format. The HDF file contains a single group named "matrix" which contains the cell barcodes and UMI counts in compressed sparse column format (CMC).

molecule: polyA RNA

source_name: Ex vivo reconstuted airway epithelia

growth_protocol: Human Airway Epithelia were purchased from Epithelix Sàrl, Geneva

extract_protocol:
Tissues were dissociated using TiplE, live cells were sorted and captured using the 10x Chromium Technology (Illumina)
Libraries were prepared according to the  10x Chromium Technology (Illumina) manufacturer's instructions
Single cell RNA-seq, v3.1 Next GEM Chemistry

treatment_protocol: Tissues were infected or not apically, with Infleunza A virus, and then administered or not apically with 6'SLN-CD, or basally with IFN lambda

tag: donors

value: Healthy donors

tag: infection

value: Influenza A virus

tag: treatment


title: Infected + 6'SLN-CD + IFN lambda

value: 6'SLN-CD and IFN lambda


title: 8037 HA

status: Public on May 26 2022

city: Los Angeles

first: Joshua

middle: Evan

last: Burda

state: CA

address: 127 S San Vicente Blvd

department: Biomedical Sciences, Center for Neural Science and Medicine

institute: Cedars Sinai Medical Center

description: DEA_refSeq_SMARCA4cKO_SCI_vs_SMARCA4cKO_Uninj_Complete_geneList_EdgeR

data_processing:
genome alignment: STAR aligner (v.2.4.0j)
Read counting: HT-seq (v.0.6.0)
data normalization and differential expression: EdgeR (v.3.28.0)
Assembly: mm10
Supplementary files format and content: xlsx; Gene ID; Log2FC; raw and normalized read counts

organism: Mus musculus

source_name: thoracic spinal cord

extract_protocol:
Astrocyte ribosome-associated mRNA isolation: Fourteen days after complete crush SCI or 24 hours following IP injection of LPS, spinal cords of wild-type, Stat3-astro-cKO or Smarca4-astro-cKO mice were perfused with ice cold saline and spinal cords rapidly dissected and frozen on dry ice. For SCI samples, the central 3 mm of the lower thoracic lesion including the lesion core and 1 mm rostral and caudal were then rapidly removed and snap frozen in liquid nitrogen. Anatomically equivalent regions of spinal cord were taken from mice treated with LPS or from genotype-matched healthy controls. Frozen tissue samples were processed either for RiboTag analysis via haemagglutinin (HA) immunoprecipitation and purification of astrocyte ribosome-associated mRNA using standard methods.
Astrocyte RNA Integrity was analysed by a 2100 Bioanalyzer (Agilent) using the RNA Pico chip, RIN ≥ 8.9 for all samples. cDNA was generated from 10 ng of RNA using the Universal plus mRNA-Seq Kit (Nugen).
Multiplexed sequencing was performed with a NovaSeq 6000 sequencer (Illumina) on a NovaSeq S2 flow cell to produce 50 base-pair paired-end reads.

tag: tissue

value: thoracic spinal cord

tag: genotype

value: Crush SCI at T10


title: Infected Untreated


title: glamblia_directRNA_rep2

status: Public on Mar 09 2022

city: Aurora

first: Olivia

last: Rissland

state: CO

address: 12801 East 17th Ave

department: BMG

institute: University of Colorado Denver

data_processing:
3'-end Seq libraries were sequenced at the Genomics and Microarray Shared Resource at the University of Colorado Denver Cancer Center on an Illumina MiSeq (MSQ-M01247R). Basecalling was completed with RTA version 1.18.54.0 and demultiplexing was done with bcl2fastq version 1.8.4
Adaptors were trimmed from 3'-end reads using Cutadapt v2.3. Libraries were aligned to the G. lamblia genome release 50 (2020-12-15) using STAR 2.5.2a (Dobin et al., 2013)
Downstream analyses were then performed with Python version 3.7.4, using in-house scripts.
Genome_build: G. lamblia release-50 https://giardiadb.org/giardiadb/app/downloads/release-50/GintestinalisAssemblageAWB/
Supplementary_files_format_and_content: BED file containing the coordinates of predicted cleavage sites based on assignment to the nearest open reading frame
Direct RNA Seq libraries were sequenced on a FLO-MIN106 flow-cell with a minION (MIN-101B) device in the Rissland lab at the University of Colorado Anschutz campus. Basecalling was completed by Guppy on the minKNOW software (Oxford Nanopore Technologies)
Reads were mapped by minimap2 (Li, 2018) to the G. lamblia genome release 50 (2020-12-15) obtained from GiardiaDB.org
Poly(A) tails were measured with the nanopolish software version 0.11.1 (Loman et al., 2015)
Mapped nanopore reads were assigned to their corresponding gene using featureCounts version 2.0.0 (Liao et al., 2014)
Genome_build: G. lamblia release-50 https://giardiadb.org/giardiadb/app/downloads/release-50/GintestinalisAssemblageAWB/
Supplementary_files_format_and_content: Tab separated values files containing poly(A) tail lengths for all reads

organism: Giardia duodenalis

source_name: Trophozoite

growth_protocol: G. lamblia trophozoites were grown in filtered modified TYI-S-33 medium in 10ml polystyrene tubes at 37°C

extract_protocol:
Total RNA was used to generate libraries with Oxford Nanopore's Direct RNA sequencing kit according to manufacturer's protocol and sequenced on a minION device
RNA was extracted from trophozoites with hot acid phenol as described in Collart & Oliviero, Current protocols in molecular biology (1993)
See SAMPLES section

treatment_protocol: Cells were untreated

tag: developmental stage

value: Trophozoite


title: Infected + IFN lambda

value: IFN lambda


title: glamblia_directRNA_rep1


title: Mock Steady State


title: sra9993 test on prod

status: Public on Sep 24 2021

city: qq

first: Pierre

middle: X

last: Ledoux

address: qq

institute: werty

data_processing: asdfasdf

source_name: liver

extract_protocol: sdfasdf

value: ddfdfdf


title: MSK_UM03_PRIMARY_TUMOR

status: Public on Aug 05 2021

city: NEW YORK

first: Ashley

middle: M

last: Laughney

state: New York

address: 413 East 69th Street

department: Physiology, Biophysics, and Systems Biology

institute: Weill Cornell Medicine

description:
Barcoded single cells
UvMel3_dense.csv

data_processing:
The Sequence Quality Control (SEQC) package was utilized to process the data, constructing a count matrix from raw reads, including de-multiplexing, alignment, error-correction, and the generation of a raw digital expression matrix by collapsing groups of reads with the same unique molecular identifier (UMI), cell barcode and gene annotation. Alignment to the hg38 annotation was restricted to transcribed, polyadenylated RNA of length > 200 nucleotides (gene biotypes accessible by 3’ mRNA sequencing technologies) to increase mapping specificity.
Genome_build: hg38
Supplementary_files_format_and_content: CSV files containing raw gene expression matrices of cells by gene. The multi-level index contains basic metadata and all columns are genes.
Supplementary_files_format_and_content: An h5ad file containing raw, normalized, and imputed count matrices for the final, merged and processed dataset.

source_name: Uveal Melanoma

extract_protocol:
Primary uveal melanomas were obtained from patients undergoing enucleation surgery at Memorial Sloan Kettering Cancer Center (MSKCC, New York, NY) after obtaining informed consent. Samples were collected from 6 patients spanning prognostic gene expression profiles (GEP1 and GEP2). Immediately after enucleation, a sclera window was made and tumor was removed (with a freer elevator) and sent for DecisionDx for bulk GEP classification and for scRNAseq processing. Tissue samples were immediately placed in RPMI media (Corning) or Hypothermosol on ice and dissociated using both mechanical and enzymatic digestion (Human Tumour Dissociation Kit #130-095-929, Miltenyi Biotec), generally within 1 hour of surgical resection. Tissues were minced with a razor blade in the Miltenyi enzyme mix according to the manufacturer’s specifications and transferred to a Gentle MACS Octo Dissociator with heaters (# 30-096-427, 37°C) for further mechanical dissociation. Upon completion, cell suspensions were passed through a 70 µm filter and washed twice with FACS buffer (2% heat-inactivated FBS, 1 mM EDTA and Pen/Strep in PBS without Ca or Mg). Red blood cells were lysed in Red Blood Cell Lysis Solution (ACK lysis buffer) once or twice depending on red blood cell content, and final single-cell suspensions were made in Hanks’ Balanced Salt Solution (HBSS). For scRNA-seq, the remaining cell suspensions were subsequently flow sorted with a BD FACSAria II cell sorter fitted with a 100 µM nozzle to enrich for viable, single cells according to forward and side scattering, and DAPI exclusion. Cells were sorted directly into RPMI media with 10% FBS, washed thrice and re-suspend in PBS with 0.04% BSA for single cell encapsulation. Final cell concentrations were determined with a hemocytometer.
Barcoded hydrogel bead synthesis, single cell encapsulation and library construction were done following a modified inDrops protocol. Zilionis, R., et al. Single-cell barcoding and sequencing using droplet microfluidics. Nature protocols 12, 44-73 (2017).

tag: individual

value: patient UM03

value: uveal melanoma

tag: stage of tumor progression

value: Primary Tumor

tag: decisiondx bulk diagnosis


title: 3DhiPSCCM.3

status: Public on Aug 31 2021

city: Charleston

first: Charles

middle: Matthew

last: Kerr

state: SC

address: 68 President St

department: Molecular Cell Biology and Pathobiology

institute: Medical University of South Carolina

description: biological replicate 3

data_processing:
equenced reads (fastq files) were mapped to reference genome (HG19) using STAR genome aligner
Using HOMER, tag directories were created using the mapped .BAM files
The tag directories from the previous step was used generate count data for gene-level differential expression analyses using HOMER
Secondary analysis were performed using R studio.  In particular, the package, bioconductor was used to perform principal component analysis and differential gene expression (DESeq2)
Genome_build: HG19

source_name: hiPSC-CM donor 01434, exp#50

growth_protocol: 3D hiPSC-CM were pre-culture for 4 (D-4 to D0) days followed by 10 days (D0 to D10), changing FujiFilm iCell CM Maintenance Media every 2 days

extract_protocol:
30-35 spheroids were collected immediately out of culture and put in lysis buffer on D10 (2 days after last media change) Total RNA was extracted with an Omega bio-tek E.Z.N.A Total RNA kit
Illumina‚Äôs Truseq mRNA non-stranded library protocol with 100 ng of RNA was used to prepare sequencing libraries following the manufacture‚Äôs protocol with the exception of using half reactions

tag: tag

value: tissue:cardiac spheroid

value: developmental stage:experimental Day 14 (2 days after media change)

value: concentration:normoxia, 300um diameter


title: MSK_UM05_PRIMARY_TUMOR

description:
Barcoded single cells
UvMel5_dense.csv

value: patient UM05


title: MSK_UM06_PRIMARY_TUMOR

description:
Barcoded single cells
UvMel6_dense.csv

value: patient UM06


title: MSK_UM04_PRIMARY_TUMOR

description:
Barcoded single cells
UvMel4_dense.csv

value: patient UM04


title: 3DhiPSCCM.1

description: biological replicate 1


title: MSK_UM01B_PRIMARY_TUMOR

description:
Barcoded single cells
UvMel1B_dense.csv

value: patient UM01


title: MSK_UM02_PRIMARY_TUMOR

description:
Barcoded single cells
UvMel2_dense.csv

value: patient UM02


title: MSK_UM01A_PRIMARY_TUMOR

description:
Barcoded single cells
UvMel1A_dense.csv


title: Mock + 6'SLN-CD + IFN lambda

value: Healthy donors

value: 6'SLN-CD and IFN lambda


title: 201025_FTLD_240_snRNA-C12

status: Public on Jul 09 2021

city: Cambridge

first: Myriam

last: Heiman

state: Massachusetts

address: 77 Massachusetts Ave., Bldg 46-4285

department: Brain and Cognitive Sciences

institute: Massachusetts Institute of Technology

data_processing:
Basecalls converted to FASTQ with Cellranger v4.0.
FASTQ files were aligned, demultiplexed, and sorted with Cellranger v4.0 using pre-mRNA annotated GRCh38 reference.
Counts were filtered and annotated using ACTIONet R package.
Genome_build: GRCh38
Supplementary_files_format_and_content: MTX files of filtered count matrices. TSV files of row and column annotations and metadata (for MTX file) per individual.

source_name: Motor Cortex

extract_protocol:
Tissue was homogenized in 700 µL of homogenization buffer (320 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 0.1% NP-40, 1 mM β-mercaptoethanol, and 0.4 U/µL RNase inhibitor) with a 2 mL tissue grinder. Tissue was filtered through a 40 µm cell strainer and mixed with 450 µL solution of 50% OptiPrep density gradient medium, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], and 1 mM β-mercaptoethanol.  The mixture was then pipetted onto an OptiPrep density gradient containing 750 µL of 30% OptiPrep Solution (134 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 1 mM β-mercaptoethanol, 0.04% NP-40, and 0.17 U/µL RNase Inhibitor) on top of 300 µL of 40% OptiPrep Solution inside a microcentrifuge tube. Nuclei were pelleted at the interface of the OptiPrep density gradient by centrifugation. Nuclei were washed three times with 2% BSA and the nuclear pellet was re-suspended in 100 µL of 2% BSA.
Libraries were constructed according to the 10x Genomics Single Cell Expression v3 User Manual.
Molecules barcoded with 10x Gene Expression 3' kit v3.

value: Motor Cortex

tag: ID

tag: disease state


title: organoid-day 15

status: Public on Jul 19 2021

city: East Lansing

first: Aitor

last: Aguirre

state: MI

address: 775 Woodlot Dr

department: Biomedical Engineering

institute: Michigan State University

description: >200 bp RNA

data_processing:
Qualiy control using FASTQC
alignment was performed with HISAT2
Reads were counted with featurecounts
Differential expression analysis was performed with EdgeR
Genome_build: hg38
Supplementary_files_format_and_content: Excel files containing counts per million

growth_protocol: Specific differentiation protocol conditions can be found in Israeli et al., 2020

extract_protocol:
Qiagen RNAeasy Kit
Libraries were prepared according to Illumina Truseq protocols

treatment_protocol: Each sample represents a mean pool of 3 6-wells of a 6-well plate for monolayer samples, and 5-8 organoids for organoid samples

tag: cell line

tag: cell type

value: human induced pluripotent stem cells derived from a healthy patient

tag: experimental condition

value: cells differentiated using heart organoid protocol


title: organoid-day 19

description: >200 bp RNA


title: organoid-day 17

description: >200 bp RNA


title: 201025_FTLD_239_snRNA-C11


title: 201025_FTLD_237_snRNA-C9


title: 3DhiPSCCM.2

description: biological replicate 2


title: 201019_ALS_113_snRNA-B7


title: 201019_ALS_106_snRNA-B5

value: sALS


title: 201025_FTLD_232_snRNA-C5


title: 201019_ALS_108_snRNA-B6


title: 201019_ALS_101_snRNA-B1


title: 201019_ALS_102_snRNA-B2


title: 201025_FTLD_234_snRNA-C6


title: 201019_PN_311_snRNA-B8

description: Pathologically normal

value: PN


title: 200721_FTLD_210_snRNA-A11


title: 200721_PN_302_snRNA-B4

description: Pathologically normal


title: 191114_PN_328_snRNA-F9

description: Pathologically normal


title: 200721_FTLD_214_snRNA-A12


title: 191114_PN_325_snRNA-F8

description: Pathologically normal


title: 191114_PN_324_snRNA-F7

description: Pathologically normal


title: 191114_PN_322_snRNA-F5

description: Pathologically normal


title: 201025_FTLD_238_snRNA-C10


title: 191114_PN_317_snRNA-F2

description: Pathologically normal


title: 191114_PN_318_snRNA-F3

description: Pathologically normal


title: 191114_PN_319_snRNA-F4

description: Pathologically normal


title: 191114_PN_309_snRNA-F1

description: Pathologically normal


title: 191114_PN_308_snRNA-E12

description: Pathologically normal


title: 191114_PN_307_snRNA-E11

description: Pathologically normal


title: 201025_FTLD_235_snRNA-C7


title: 191114_PN_306_snRNA-E10

description: Pathologically normal


title: 201019_ALS_103_snRNA-B3


title: 201019_ALS_104_snRNA-B4


title: 191114_PN_304_snRNA-E9

description: Pathologically normal


title: 191114_PN_303_snRNA-E8

description: Pathologically normal


title: 200721_FTLD_229_snRNA-B2


title: 191114_PN_301_snRNA-E7

description: Pathologically normal


title: 200721_FTLD_206_snRNA-A10

value: sFTLD


title: 191113_FTLD_226_snRNA-E4


title: 191113_FTLD_229_snRNA-E6


title: 191113_FTLD_225_snRNA-H5


title: 191113_FTLD_228_snRNA-E5


title: 191113_FTLD_216_snRNA-H3


title: 191113_FTLD_224_snRNA-E2


title: 191113_FTLD_222_snRNA-E1


title: 191113_FTLD_218_snRNA-H4


title: 191113_FTLD_217_snRNA-D11


title: 191114_PN_323_snRNA-F6

description: Pathologically normal


title: 191113_FTLD_209_snRNA-D6


title: 191113_FTLD_211_snRNA-D7


title: 191113_FTLD_214_snRNA-D9


title: 191113_FTLD_207_snRNA-D5


title: 191112_ALS_130_snRNA-A5


title: 191113_FTLD_202_snRNA-D3


title: 191112_ALS_128_snRNA-A7


title: 191112_ALS_127_snRNA-A4


title: 191113_FTLD_204_snRNA-D4


title: 191112_ALS_126_snRNA-A6


title: 191112_ALS_124_snRNA-A3


title: 191112_ALS_129_snRNA-A2


title: 191112_ALS_118_snRNA-C4


title: 191112_ALS_122_snRNA-D2


title: 191112_ALS_117_snRNA-C3


title: 191112_ALS_115_snRNA-C1


title: 191112_ALS_120_snRNA-A1


title: 191112_ALS_114_snRNA-B12


title: 191112_ALS_116_snRNA-C2


title: 191112_ALS_111_snRNA-B10


title: 191112_ALS_110_snRNA-B9


title: mice ID: ER73 [LPS]

status: Public on Jun 25 2021

city: Montpellier

first: Nicole

last: Hannemann

address: 80 Avenue Augustin Fliche

department: IRMB

country: France

institute: INSERM U1183

description:
Fra1_LPS.annot.txt
Raw data not available for this record.

library_source: genomic

data_processing:
Quality filtering with FASTX Toolkit 0.0.14 fastq_quality_filter (-q 30 -p 50).
Sdapter clipping with FASTX Toolkit 0.0.14 fastx_clipper (-a GATCGGAAGAGCACACGTCTGAACTCCAGTCAC -n -C).
End trimming with FASTX Toolkit 0.0.14 fastx_trimmer (-f 7 -l 98).
Alignment to the mm10 reference with bwa mem v0.7.14.
Peak calling with macs v1.3.7.1 (--gsize 1870000000).
Determining intersect of peaks of all 3 samples for every treatment group using bedtools intersect.
Genome_build: (GRCm38) mm10
Supplementary_files_format_and_content: *.txt: Tab-separated text files containing intersected macs peaks.

molecule: genomic DNA

source_name: peritoneal elicited macrophages

growth_protocol: The mice were bred and maintained on a 129/C57Bl6 background. All experiments were performed with male or female mice at the age of 8 weeks. Animals were housed in standardized conditions following the guidelines of the German Animal Welfare Act. Animals were kept in a standard diet and water ad libitum and kept with a 12 hour day/night cycle. All experiments with animals are authorized by the local ethics committee.

extract_protocol:
ChIP was performed as described previously: Carey MF, Peterson CL, and Smale ST. Chromatin immunoprecipitation (ChIP). Cold Spring Harbor protocols. 2009;2009(9):pdb.prot5279.
Libraries are prepared using the Illumina TruSeq ChIP Sample Preparation Kit. After quantification and profiling ChIP DNA >5 ng ChIP-enriched fragmented input DNA is used to repair the ends of fragments. After adenylation of the 3' ends indexed paired-end adapters are ligated. After purification of ligated products and PCR amplification a QC is performed in order to normalize and pool the indexed libraries. The indexed libraries are the sequenced as single read 1x100 bp fragments on the HiSeq-2500.

treatment_protocol: Thioglycollate-elicited macrophages were generated by injecting mice i.p. with 2.5 ml of 4% (w/v) Brewer’s thioglycollate medium. Peritoneal cavity cells were harvested 72 h later by lavage. Cells were washed and plated in RPMI-1640 supplemented with 10% (v/v) FCS and 1% (v/v) penicillin/streptomycin. Cells were incubated overnight, and adherent cells were stimulated with 1 μg/ml LPS (Sigma-Aldrich), or ACs (with a 1:5 ratio).

value: Peritoneal macrophages

value: LPS

tag: precipitated for

tag: mice id


title: Ctrl

status: Public on Jun 06 2021

city: Chengdu

first: Yu

last: Shi

state: Sichuan

address: NO.14 South Renmin Road

country: China

institute: Sichuan University

data_processing:
Sample demultiplexing, barcode processing and UMI counting were performed by using the official 10x Genomics pipeline Cell Ranger v2.1.0 (https://support.10xgenomics.com).  Briefly, FASTQs generated from Illumina sequencing output were aligned to the mouse reference genome (mm10). Next, Gene-Barcode matrices were generated for each individual sample by counting unique molecular identifiers (UMIs) and filtering non-cell associated barcodes. Finally, we generated a gene-barcode matrix containing the barcoded cells and gene expression counts.
Genome_build: mm10

source_name: metaphyseal mesenchymal progenitors

growth_protocol: This is a mouse work and cells were freshly isolated.

extract_protocol:
Cells from the cancellous bone region of the femur were isolated as follows.  Upon removal of the epiphysis, the metaphyseal bone region extending about 5 mm below the growth plate was dissected and crushed with mortar and pestle in FACS Buffer, followed by digestion with 0.25% collagenase type I (C0130, Sigma-Aldrich) in PBS (Gibco) for 20 min at 37 °C with gentle shaking. The cells were then centrifuged and re-suspended with FACS Buffer and filtered with a 70-μm cell strainer.  The tdTomato+CD31-CD45-Ter119- cells were sorted with Navios EX (Beckman Coulter).  Cell viability and number were determined with a cell counter (Biorad).
10x Genomics Chromium platform was used to capture and barcode cells to generate single-cell Gel Beads-in-Emulsion (GEMs) by following the manufacturer’s protocol.  The oligonucleotides coating the gel beds enable mRNA capture by 30 bp oligo-dT and provide barcodes to index cells (16 bp) as well as transcripts (10 bp unique molecular identifier; UMI).  Following reverse transcription, cDNAs with both barcodes were amplified, and a library was constructed using the Single Cell 3’ Reagent Kit (v2 chemistry) for each sample.  The resulting libraries were sequenced on an Illumina NovaSeq 6000 System.

treatment_protocol: Gli1-CreERT2; Ai9 mice at 1 month of age were administrated Tamoxifen for three consecutive days once daily followed by three daily injections of teriparatide or vehicle.

value: Bone mesenchymal progenitor

tag: strain

value: Mix background

value: Vehicle


title: Raw264.7-uvCLAP-GFP-rep2

status: Public on Mar 31 2021

city: Beijing

first: Meiling

last: Piao

address: Shuangqing Road 30

department: Life Science

institute: Tsinghua University

data_processing:
Library strategy: uvCLAP
Calculate smartSHAPE score from smartSHAPE sequencing data:
1) The 3’ adaptor is removed with Cutadapt
2) Duplicated reads were collapsed with custom script;
3) The first 10nt were removed using trimmomatic
4) Clean reads were mapped to human rRNA with Bowtie2
5) Un-mapped reads were mapped to the human (hg38) or mouse (mm10) genome using STAR
6) Sam files were convert into .tab files using icSHAPE-pipe sam2tab;
7) The smartSHAPE score was calculated using icSHAPE-pipe calcSHAPENoCont
For uvCLAP data:
Raw reads were trimmed by Cutadapt and collapsed to remove duplicated reads. The clean reads were mapped to mouse rRNA by Bowtie2, and the remaining un-mapped reads were re-mapped to mouse genome (mm10) by STAR. Peaks were called out by Piranha with Reg1 group as response sample and GFP group as covariate sample. The bin size was set to 50 with -z 50.
For RNA-Seq data:
Raw reads were trimmed by Cutadapt. The trimmed reads were mapped to mouse rRNA by bowtie2, and the remaining un-mapped reads were re-mapped to mouse genome (mm10) by STAR. We set parameter --quantMode TranscriptomeSAM GeneCounts to generate the read count file. The RNA-Seq differentail expression analysis is carried by DESeq2.
Genome_build: hg38 and mm10
Supplementary_files_format_and_content: .shape format: tab-seperated file, each row represent a transcript. The meaning of each column: transcript_id, length, a star symbol, reactivity score for each base

source_name: Raw264.7 cell line

growth_protocol: HEK293T cells, iBMDM and Raw264.7 cells were cultured were maintained in DMEM (Gibco) medium with high glucose, supplemented with 10% FBS and 1% Penicillin-Streptomycin at 37°C with 5% CO2.

extract_protocol:
For smartSHAPE and RNA-Seq, RNAs were isolated with Trizol reagents.
For smartSHAPE, cells were treated with NAI-N3 or DMSO and RNAs were isolated with Trizol followed by rRNA removal. RNAs were reverse transcribed with random primers, and RNase I digestion was performed at 37 °C for 30 min. Enrichment was performed using MyOne C1 beads. After elution, cDNAs were ligated with biotinylated 3’ adaptor using CircLigase and immobilized with MyOne C1 beads. Second strand synthesis and 5’ligation was performed on the beads. smartSHAPE libraries were generated by amplification of ligation products. RNA seq libraries of Reg1 KO and WT iBMDMs were generated with KAPA RNA Hyper Prep kit. uvCLAP libraries were generated as published protocol (PMID: 29559621).

treatment_protocol: For structure probing, cells were treated with NAI-N3 or DMSO at 37°C for 5min and quenched by adding 500 µl Trizol. For RNA seq, cells were treated with 100 ng/ml LPS for 0 h or 3 h before RNA isolation. For uvCLAP, cells were maintained in media supplied with 50 µM biotin overnight and treated with 100 ng/mL LPS for 3 h.


title: Raw264.7-uvCLAP-Reg1-rep2


title: PTH

value: Teriparatide 400ng/g body weight i.p. injection for 3 dyas


title: Lumbar/Sacral_F_rep3

status: Public on Feb 27 2021

city: Bethesda

first: Claire

middle: E

last: LE PICHON

state: MD

address: 35A Convent Drive, 2D933

department: NICHD

institute: National Institutes of Health

description:
Sex: 4 female
lumbar_8

data_processing:
Reads were aligned and assigned to Ensembl GRm38 transcript definitions using the CellRanger v3.1.0 pipeline (10X Genomics)
Outlier identification and removal based on number of expressed genes and mitochondrial proportions (Seurat)
Data normalization and scaling (Seurat)
Batch correction by data integration (Seurat)
PCA, clustering, and UMAP projection (Seurat)
Differential expression analysis (Seurat, DESeq2)
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Tar archives include raw_feature_bc_matrix files (barcodes.tsv, features.tsv, matrix.mtx).
Supplementary_files_format_and_content: csv file includes annotations for the single nucleus RNAseq data.

source_name: Lumbar and sacral spinal cord

extract_protocol:
Spinal cords were rapidly extruded from reporter mice and subdissected by spinal cord level. Tissue was homogenized and nuclei were isolated (see protocol) prior to FACS sorting for GFP+ nuclei. Samples were processed on a Sony SH800 Cell Sorter with a 100 mm sorting chip and GFP+/DRAQ5+ nuclei were collected.
Libraries were constructed according to the manufacturer’s instructions (10X Genomics).

value: Chat-iCre:+/wt; SUN-SfGFP:+/wt

tag: Sex

value: female

tag: age

value: 8 weeks


title: Thoracic_F_rep3

description:
Sex: 4 female
thoracic_2

source_name: Thoracic spinal cord


title: Cervical_F_rep3

description:
Sex: 4 female
cervical_5

source_name: Cervical spinal cord


title: Thoracic_M_rep2

description:
Sex: 4 male
thoracic_1

value: male


title: Cervical_M_rep2

description:
Sex: 4 male
cervical_4


title: Thoracic_M+F_rep1

description:
Sex: 2 male + 2 female
thoracic_3

value: pooled male and female


title: Lumbar/Sacral_M+F_rep1

description:
Sex: 2 male + 2 female
lumbar_9


title: Cervical_M+F_rep1

description:
Sex: 2 male + 2 female
cervical_6


title: P-extra 2 Post

status: Public on Oct 06 2020

city: Hangzhou

first: Junqing

last: Wu

address: Yuhangtang Road 866

institute: Zhejiang University

data_processing:
Base-calls were performed with Illumina bcl2fastq
Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular (UMI) barcode sequences using Drop-seq_tools-1.12. The reads quality under 10 were removed.
ScRNA-seq reads were aligned to the Homo_sapiens GRCh38 genome assembly using STAR version (2.5.2a)  with default configurations.
Next, merge the STAR alignment tagged bam SAM to recover cell /molecular barcodes and the reads are annotated with exon tags.
Last, we demultiplexed all cell barcodes taken into consideration for the analysis from the exon-tagged bam files to get a digital expression matrix based on UMI counts.
Genome_build: Homo_sapiens GRCh38 genome
Supplementary_files_format_and_content: Tab-delimited text files of digital expression matrix (dge) based on raw UMI counts ,columns are cells, and rows are genes.

organism: Homo

source_name: BMMC

extract_protocol:
Cells were isolated from bone marrow aspirates by Ficoll Hypaque Solution.
Library preparations were performed according to the Microwell-seq protocol

value: BMMC

tag: tumor stage

value: de novo AML

tag: gender

value: F

value: acute myeloid leukemia


title: P-extra 2 Pre


title: P-extra 1 Pre

value: M


title: P-extra 1 Post


title: P37


title: P39


title: P36


title: P40


title: Raw264.7-uvCLAP-Reg1-rep1


title: P34


title: P32


title: Lumbar/Sacral_M_rep2

description:
Sex: 4 male
lumbar_7

tag: genotype


title: P30


title: Raw264.7-uvCLAP-GFP-rep1


title: P38


title: P25


title: P26


title: P27


title: 191112_ALS_112_snRNA-D1

tag: tissue

value: Motor Cortex

value: sALS


title: P20


title: P24


title: P23


title: P17


title: P21


title: P20-POST

value: post regimen


title: P19


title: P31


title: P13


title: P15


title: P11


title: P07


title: P08


title: P16


title: P33


title: P35


title: P12


title: P29


title: P10


title: P28


title: N03

value: Normal


title: P06


title: P14


title: P22


title: N01


title: P05


title: P04-POST


title: P03


title: P04


title: P02


title: P18


title: Placenta female IA rep2

status: Public on Sep 23 2020

city: BOSTON

first: CHANG

last: CAO

state: MA

address: 185 CAMBRIDGE ST.

department: CENTER FOR GENOMIC MEDICINE

institute: Mass General Brigham

data_processing:
Image analysis and base calling were conducted by the HiSeq Control Software. Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification.
Reads were trimmed by trimmomatic v0.39 and high-quality reads were aligned to mouse reference genome (GRCm38.p6) using STAR 2.7.2b.
The reads counts were calculated by featureCounts software.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: placenta

extract_protocol:
At E12.5, dams were sacrificed and their placentas removed, placed in RNAlater overnight, and extracted using Qiagen Rneasy plus mini kit (cat. no. 73404). NEBNext Ultra RNA Library Prep Kit for Illumina (cat. no. E7770) was used for the construction of sequencing libraries following manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard illumina protocols

treatment_protocol: At wean, female mouse littermates were randomized to ID or IA diet and were maintained on their respective diets throughout the study.

value: placenta

tag: treatment

value: iron adequate

value: embryonic day 12.5


title: Placenta female IA rep3


title: P01


title: N02


title: Placenta male IA rep3


title: P09


title: Placenta male ID rep3

value: iron deficient


title: Placenta male IA rep1


title: Placenta female IA rep1


title: Placenta female ID rep1


title: Placenta male ID rep2


title: Placenta male ID rep1


title: CTRL002 H3K27me3 ChIP-seq

status: Public on Sep 05 2020

city: Milan

first: Chiara

last: Lanzuolo

address: Via Francesco Sforza 35

country: Italy

institute: CNR and Istituto Nazionale Genetica Molecolare

data_processing:
Reads were aligned to the hg38-noalt reference human genome available in the bcbio-nextgen pipeline, using bwa aln (version 0.7.12) with options -n 2 -k 2 and saved the results in sam format with bwa samse.
The sam files were converted to bam and name sorted with samtools (version 1.3.1). We marked PCR duplicates using the biobambam2 toolset (version 2.0.54). We discarded reads mapping to non-autosomal chromosomes, PCR duplicates, qcfail, multimapping and unmapped reads with samtools.
We calculated the genome wide IP - input signal for all samples, using the SPP package (version 1.15.4). We imported bam files into the R (version 3.3.1) statistical environment, and selected informative reads with the get.binding.characteristics and select.informative.tags functions, removed anomalous positions with extremely high number of reads using the remove.local.tag.anomalies function, and calculated the differential signal, smoothed by a Gaussian kernel, using the get.smoothed.tag.density function with the default bandwidth and tag.shift parameters.
We called H3K27me3 ChIP-seq peaks with the get.broad.enrichment.clusters function of SPP on the preprocessed data with window.size = 2000 and z.thr = 3, tag.shift = ((cross correlation peak position) / 2) parameters.
Genome build: hg38-noalt
Supplementary_files_format_and_content: bed: H3K27me3 peak coordinates for a specific sample. bigWig: genome wide IP - input signal for a specific sample, smoothed by a Gaussian kernel.

source_name: skin fibroblast

growth_protocol: Primary fibroblast cell lines were cultured in DMEM High glucose with glutamax supplemented with 15% FBS and 1% Pen/Strep.

extract_protocol:
Cells were cross-linked with 1% HCHO for 12 minutes at room temperature, lysed and chromatin sheared using Covaris M220 focused-ultrasonicator. IP were performed overnight on a wheel at 4° with 2 micrograms of H3K27me3 antibody (07-449, Millipore). The following day, antibody-chromatin immunocomplexes were loaded onto Dynal G magnetic beads (Invitrogen 10004D); the bound complexes were washed once in Low Salt Solution (0,1% SDS, 2mM EDTA, 1% Triton X-100, 20mM Tris pH 8, 150 mM NaCl), once in High Salt Solution (0,1% SDS, 2mM EDTA, 1% Triton X-100, 20mM Tris pH 8, 500 mM NaCl), once again in Low Salt Solution and once in Tris/EDTA 50 mM NaCl. Crosslinking was reversed at 65°C overnight in Elution Buffer (50 mM Tris pH 8, 10 mM EDTA, 1% SDS). DNA purified by standard phenol/chloroform extraction, precipitated and resuspended in 30 μl of 10 mM Tris pH 8. ChIP efficiency was tested by qPCR reactions, performed in triplicate (precipitated DNA samples as well as input DNA) using QuantiTect SYBR Green master mix (Qiagen) on a StepOnePlus™ Real-Time PCR System (Applied Biosystems). Relative enrichment was calculated as ChIP / Input ratio.
Libraries for sequencing were created using NEBNext Ultra II DNA Library Prep Kit (NEB), then qualitatively and quantitatively checked using Agilent High Sensitivity DNA Kit (Agilent Technologies, 5067-4627) on a Bioanalyzer 2100 (Agilent Technologies). Libraries with distinct adapter indexes were multiplexed and, after cluster generation on FlowCell, were sequenced for 50bp in the single read mode on a HiSeq 2000 sequencer (Illumina).

value: patient derived skin fibroblast

tag: passage

tag: chip antibody

value: 07-449, Millipore


title: Placenta female ID rep3


title: CTRL002 H3K9me3 ChIP-seq

data_processing:
We trimmed reads, using Trimmomatic61 (version 0.32) in single end mode.
Reads were aligned to the hg38-noalt reference human genome available in the bcbio-nextgen pipeline, using bwa aln (version 0.7.12) with options -n 2 -k 2 and saved the results in sam format with bwa samse.
The sam files were converted to bam and name sorted with samtools (version 1.3.1). We marked PCR duplicates using the biobambam2 toolset (version 2.0.54). We discarded reads mapping to non-autosomal chromosomes, PCR duplicates, qcfail, multimapping and unmapped reads with samtools.
We calculated the genome wide IP - input signal for all samples, using the SPP package (version 1.15.4). We imported bam files into the R (version 3.3.1) statistical environment, and selected informative reads with the get.binding.characteristics and select.informative.tags functions, removed anomalous positions with extremely high number of reads using the remove.local.tag.anomalies function, and calculated the differential signal, smoothed by a Gaussian kernel, using the get.smoothed.tag.density function with the default bandwidth and tag.shift parameters.
We used the Enriched Domain Detector (EDD) tool to call H3K9me3 peaks, with the following options: --fdr 0.1 –gap-penalty 10 –bin-size 100 –write-log-ratios –write-bin-scores and also excluding blacklisted genomic regions containing telomeric, centromeric, and certain heterochromatic regions. We also changed the required_fraction_of_informative_bins parameter to 0.98.
Genome build: hg38-noalt
Supplementary_files_format_and_content: bed: H3K9me3 peak coordinates for a specific sample. bigWig: genome wide IP - input signal for a specific sample, smoothed by a Gaussian kernel.

extract_protocol:
Cells were cross-linked with 1% HCHO for 12 minutes at room temperature, lysed and chromatin sheared using Branson Digital Sonifier. IP were performed overnight on a wheel at 4° with 2.4 micrograms of H3K9me3 antibody (ab8898, Abcam). The following day, antibody-chromatin immunocomplexes were loaded onto Dynal G magnetic beads (Invitrogen 10004D); the bound complexes were washed once in Low Salt Solution (0,1% SDS, 2mM EDTA, 1% Triton X-100, 20mM Tris pH 8, 150 mM NaCl), once in High Salt Solution (0,1% SDS, 2mM EDTA, 1% Triton X-100, 20mM Tris pH 8, 500 mM NaCl), once again in Low Salt Solution and once in Tris/EDTA 50 mM NaCl. Crosslinking was reversed at 65°C overnight in Elution Buffer (50 mM Tris pH 8, 10 mM EDTA, 1% SDS) and DNA extracted from beads by standard phenol/chloroform extraction, precipitated and resuspended in 30 μl of 10 mM Tris pH 8. ChIP efficiency was tested by qPCR reactions, performed in triplicate (precipitated DNA samples as well as input DNA) using QuantiTect SYBR Green master mix (Qiagen) on a StepOnePlus™ Real-Time PCR System (Applied Biosystems). Relative enrichment was calculated as ChIP / Input ratio. Libraries for sequencing were created using the automation instrument Biomek FX (Beckman Coulter), then qualitatively and quantitatively checked using Agilent High Sensitivity DNA Kit (Agilent Technologies, 5067-4627) on a Bioanalyzer 2100 (Agilent Technologies).
Libraries with distinct adapter indexes were multiplexed and, after cluster generation on FlowCell, were sequenced for 50bp in the single read mode on a HiSeq 2000 sequencer at the IEO Genomic Unit in Milan.

value: ab8898, Abcam


title: Placenta female ID rep2


title: CTRL002 RNA-seq

data_processing:
Transcript level quantification was done with Kallisto (version 0.43.0) to estimate transcript level read counts and TPM (Transcripts Per Million) values. The GENCODE v27 annotation was used to build the transcriptome index. Kallisto was run with the --bias option to perform sequence based bias correction on each sample.
Genome build: GENCODE v27
Supplementary_files_format_and_content:tsv: length, effective length, estimated read count and TPM for transcripts from the GENCODE v27 annotation.

extract_protocol:
cDNA libraries were prepared from total RNA, extracted with Trizol.
We constructed libraries by using Illumina TruSeq Stranded Total RNA Kit with Ribo-Zero GOLD. cDNA fragments of ~300 bp were purified from each library and were sequenced for 125bp, using an Illumina HiSeq 2500 instrument according to manufacturer’s instructions (Illumina).


title: CTRL002 S4 fraction

data_processing:
Library strategy: SAMMY-Seq
Reads were aligned to the hg38-noalt reference human genome available in the bcbio-nextgen pipeline, using bwa aln (version 0.7.12) with options -n 2 -k 2 and saved the results in sam format with bwa samse.
The sam files were converted to bam and name sorted with samtools (version 1.3.1). We marked PCR duplicates using the biobambam2 toolset (version 2.0.54). We discarded reads mapping to non-autosomal chromosomes, PCR duplicates, qcfail, multimapping and unmapped reads with samtools.
We calculated the genome wide IP - input signal for all samples, using the SPP package (version 1.15.4). We imported bam files into the R (version 3.3.1) statistical environment, and selected informative reads with the get.binding.characteristics and select.informative.tags functions, removed anomalous positions with extremely high number of reads using the remove.local.tag.anomalies function, and calculated the differential signal, smoothed by a Gaussian kernel, using the get.smoothed.tag.density function with the default bandwidth and tag.shift = 0 parameters.
We used the Enriched Domain Detector (EDD) tool to select significantly enriched SAMMY-seq domains by comparing less accessible fractions to more accessible ones (S3 vs S2, S4 vs S3 and S4 vs S2 comparisons) in each sample, with the following options: --gap-penalty 25 --bin-size 50 --write-log-ratios --write-bin-scores and also excluding blacklisted genomic regions containing telomeric, centromeric, and certain heterochromatic regions62. We also changed the required_fraction_of_informative_bins parameter to 0.98.
Genome build: hg38-noalt
Supplementary_files_format_and_content: bed: SAMMY-seq enriched domain coordinates for a specific sample. bigWig: genome wide IP - input signal for a specific sample, smoothed by a Gaussian kernel.

extract_protocol:
10 million fibroblasts were washed in PBS 1X, and extracted in cytoskeleton buffer (CSK: 10 mM PIPES pH 6,8; 100 mM NaCl; 1 mM EGTA; 300 mM Sucrose; 3 mM MgCl2; 1X protease Inhibitors by Roche Diagnostics; 1 mM PMSF) supplemented with 1 mM DTT and 0,5% Triton X-100. After 5 min at 4°C the cytoskeletal structure was separated from soluble proteins by centrifugation at 3000 rpm for 3 min, and the supernatant was labeled as S1 fraction. The pellets were washed with an additional volume of cytoskeleton buffer. Chromatin was solubilized by DNA digestion with 25U of RNase–free DNase (Invitrogen) in CSK buffer for 60 min at 37°C. To stop digestion, ammonium sulphate was added in CSK buffer to a final concentration of 250 mM and, after 5 min at 4°C samples were pelleted at 5000 rpm for 3 min at 4°C and the supernatant was labeled as S2 fraction. After a wash in CSK buffer, the pellet was further extracted with 2M NaCl in CSK buffer for 5 min at 4°C, centrifuged at 5000 rpm 3 min at 4°C and the supernatant was labeled as S3 fraction. This treatment removed the majority of histones from chromatin. After 2 washing in NaCl 2M CSK, the pellets were solubilized in 8M urea buffer to remove any remaining protein component by applying highly denaturing conditions. This remaining fraction was labeled as S4.
For DNA fractionation, we took an aliquot corresponding to 30% of volume of S2, S3, S4 fractions and added TE buffer to reach a final volume of 300μL. After incubation with RNAse A (Roche) (90 minutes at 37°) and Proteinase K (Sigma) (150 minutes at 55°), DNA was extracted from beads by standard phenol/chloroform extraction, precipitated and resuspended in 25μl milliQ H2O. After Nanodrop (260/280 = 1,7-1,9; 260/230 ≥ 2) and Qubit HS DNA quantification, we added H2O to a final volume of 105μL. Then samples were transferred to 96 well plates and sonicated 4 times with Bioruptor sonicator (10 minutes 30 seconds ON - 30 seconds OFF, High Power). The DNA profiles were finally checked by capillary electrophoresis (Agilent 2100 Bioanalyzer). Finally, DNA libraries were prepared by using NuGEN Ovation Ultralow Library Prep System kit and then sequenced using an Illumina HiSeq 2500 instrument according to manufacturer’s instructions (Illumina).


title: CTRL001 H3K27me3 ChIP-seq


title: CTRL002 S2 fraction


title: CTRL002 input H3K9me3


title: Placenta male IA rep2


title: CTRL002 S3 fraction


title: SW131 NN4:cervical mucosa from cancer-free normal control

status: Public on Aug 06 2020

type: genomic

city: Baltimore

first: Thomas

last: Pisanic

address: Shaffer Hall 200D, 3400 N Charles St

department: Institute for NanoBioTechnology

institute: Johns Hopkins University

description:
Sentrix Position: R01C01
SW131 NN4

hyb_protocol: Bisulfite-treated (BST-) DNA was analyzed using Illumina’s Infinium Human MethylationEPIC BeadChip Kit (WG-317-1002) by following manufacturer’s manual.

scan_protocol: Polymer-coated chips were image-processed in Illumina’s iScan scanner.

data_processing: R Version 3.6.1, minfi R package version 1.30.0

label: Cy5 and Cy3

label_protocol: DNA bisulfite conversion was carried out using EZ DNA Methylation Kit (Zymo Research) by following manufacturer’s manual with modifications for Illumina Infinium Methylation Assay. Briefly, 400 ng of genomic DNA was first mixed with 5 µl of M-Dilution Buffer and incubate at 37˚C for 15 minutes and then mixed with 100 µl of CT Conversion Reagent prepared as instructed in the kit’s manual. Mixtures were incubated in a thermocycler with 16 thermal cycles at 95˚C for 30 seconds and 50˚C for one hour. Bisulfite-converted DNA samples were loaded onto 96-column plates provided in the kit for desulphonation and purification.

extract_protocol: For all samples, genomic DNA was extracted and purified by QIAamp FFPE DNA tissue kit (Qiagen, Hilden, Germany).

treatment_protocol: All samples were of fresh-frozen tissue obtained from women undergoing surgery for malignant or benign gynecological diseases.

tag: uniqueid

tag: histology

tag: tissue type

value: fresh-frozen

tag: race

value: B

value: Female

tag: grade

tag: sample group


title: SW0213 T4:endometrial endometrioid carcinoma

description:
Sentrix Position: R07C01
SW0213 T4

source_name: endometrial endometrioid carcinoma

value: endometrial endometrioid carcinoma


title: FM403T:uterine serous carcinoma

description:
Sentrix Position: R08C01
FM403T

source_name: uterine serous carcinoma

value: uterine serous carcinoma


title: SW0145 T1:endometrial endometrioid carcinoma

description:
Sentrix Position: R07C01
SW0145 T1

value: W


title: 376 TCS1:high-grade serous ovarian carcinoma

description:
Sentrix Position: R05C01
376 TCS1

source_name: high-grade serous ovarian carcinoma

value: high-grade serous ovarian carcinoma


title: SW156 NN1:endometrial mucosa from cancer-free normal control

description:
Sentrix Position: R02C01
SW156 NN1


title: HM --> 863TCS:endometrial endometrioid carcinoma

description:
Sentrix Position: R04C01
HM --> 863TCS

value: A


title: 7070 T:high-grade serous ovarian carcinoma

description:
Sentrix Position: R06C01
7070 T


title: 221 TCS --> 307 TS: poorly differentiated ovarian tumor

description:
Sentrix Position: R05C01
221 TCS --> 307 TS

source_name: poorly differentiated ovarian tumor

value: poorly differentiated ovarian tumor


title: SW201 NN2:cervical mucosa from cancer-free normal control

description:
Sentrix Position: R03C01
SW201 NN2


title: SY --> 8544TCS:uterine serous carcinoma

description:
Sentrix Position: R04C01
SY --> 8544TCS


title: 900TDNA:uterine serous carcinoma

description:
Sentrix Position: R08C01
900TDNA


title: 993TCS:uterine serous carcinoma

description:
Sentrix Position: R08C01
993TCS


title: PAP45:endometrial endometrioid carcinoma

description:
Sentrix Position: R07C01
PAP45

value: O


title: SW94N4:cervical mucosa from cancer-free normal control

description:
Sentrix Position: R03C01
SW94N4


title: PAP43:endometrial endometrioid carcinoma

description:
Sentrix Position: R04C01
PAP43


title: SW159 NN3:endometrial mucosa from cancer-free normal control

description:
Sentrix Position: R01C01
SW159 NN3


title: 121 T:high-grade serous ovarian carcinoma

description:
Sentrix Position: R06C01
121 T


title: SW173 NN4:fallopian tube mucosa from cancer-free normal control

description:
Sentrix Position: R03C01
SW173 NN4


title: FM474T:uterine serous carcinoma

description:
Sentrix Position: R08C01
FM474T


title: 1028 T (should be 1208 T):high-grade serous ovarian carcinoma

description:
Sentrix Position: R06C01
1028 T (should be 1208 T)


title: SW96 N2:endometrial mucosa from cancer-free normal control

description:
Sentrix Position: R02C01
SW96 N2


title: 125 T (FM342):high-grade serous ovarian carcinoma

description:
Sentrix Position: R06C01
125 T (FM342)


title: SW 190T1:uterine serous carcinoma

description:
Sentrix Position: R04C01
SW 190T1


title: SW147 NN2:fallopian tube mucosa from cancer-free normal control

description:
Sentrix Position: R03C01
SW147 NN2


title: SW160 NN2:cervical mucosa from cancer-free normal control

description:
Sentrix Position: R02C01
SW160 NN2


title: 792 TCS2:high-grade serous ovarian carcinoma

description:
Sentrix Position: R05C01
792 TCS2


title: PAP44:endometrial endometrioid carcinoma

description:
Sentrix Position: R07C01
PAP44


title: SW150 NN4:endometrial mucosa from cancer-free normal control

description:
Sentrix Position: R01C01
SW150 NN4


title: 600 TCS1:high-grade serous ovarian carcinoma

description:
Sentrix Position: R05C01
600 TCS1


title: SW160 NN1:endometrial mucosa from cancer-free normal control

description:
Sentrix Position: R02C01
SW160 NN1


title: 340TS:uterine serous carcinoma

description:
Sentrix Position: R08C01
340TS


title: SW189 NN1:endometrial mucosa from cancer-free normal control

description:
Sentrix Position: R01C01
SW189 NN1


title: SW136 NN2:cervical mucosa from cancer-free normal control

description:
Sentrix Position: R01C01
SW136 NN2


title: SW95 N16:cervical mucosa from cancer-free normal control

description:
Sentrix Position: R03C01
SW95 N16


title: SW95 N2:fallopian tube mucosa from cancer-free normal control

description:
Sentrix Position: R03C01
SW95 N2


title: 7491 TS2:high-grade serous ovarian carcinoma

description:
Sentrix Position: R05C01
7491 TS2


title: PAP52:endometrial endometrioid carcinoma

description:
Sentrix Position: R08C01
PAP52


title: 366TS:uterine serous carcinoma

description:
Sentrix Position: R08C01
366TS


title: 1027 T (FM312):high-grade serous ovarian carcinoma

description:
Sentrix Position: R06C01
1027 T (FM312)


title: SW 274T1:endometrial endometrioid carcinoma

description:
Sentrix Position: R04C01
SW 274T1


title: 120 T1:high-grade serous ovarian carcinoma

description:
Sentrix Position: R06C01
120 T1


title: 6407 TCS: poorly differentiated ovarian tumor

description:
Sentrix Position: R05C01
6407 TCS


title: SW0114 T2:endometrial endometrioid carcinoma

description:
Sentrix Position: R07C01
SW0114 T2


title: SW0143 T1:endometrial endometrioid carcinoma

description:
Sentrix Position: R07C01
SW0143 T1


title: OY --> none:endometrial endometrioid carcinoma

description:
Sentrix Position: R04C01
OY --> none


title: SW150 NN2:cervical mucosa from cancer-free normal control

description:
Sentrix Position: R03C01
SW150 NN2


title: 713:high-grade serous ovarian carcinoma

description:
Sentrix Position: R06C01
713


title: PAP54:endometrial endometrioid carcinoma

description:
Sentrix Position: R04C01
PAP54


title: SW130 NN1:fallopian tube mucosa from cancer-free normal control

description:
Sentrix Position: R02C01
SW130 NN1

value: H


title: SW0084 T2:endometrial endometrioid carcinoma

description:
Sentrix Position: R07C01
SW0084 T2


title: SW108N10:endometrial mucosa from cancer-free normal control

description:
Sentrix Position: R01C01
SW108N10


title: SW108 N14:cervical mucosa from cancer-free normal control

description:
Sentrix Position: R01C01
SW108 N14


title: 541 AT:high-grade serous ovarian carcinoma

description:
Sentrix Position: R06C01
541 AT


title: 562 TS2:high-grade serous ovarian carcinoma

description:
Sentrix Position: R05C01
562 TS2


title: USC 6:high-grade serous ovarian carcinoma

description:
Sentrix Position: R05C01
USC 6

value: no data


title: KK --> PAP 51:endometrial endometrioid carcinoma

description:
Sentrix Position: R04C01
KK --> PAP 51


title: SW94 N12:endometrial mucosa from cancer-free normal control

description:
Sentrix Position: R02C01
SW94 N12


title: SW156 NN5:fallopian tube mucosa from cancer-free normal control

description:
Sentrix Position: R02C01
SW156 NN5


title: 64212 T (JH626) --> SW0372 T1:high-grade serous ovarian carcinoma

description:
Sentrix Position: R06C01
64212 T (JH626) --> SW0372 T1


title: 810 TCS (FM417):high-grade serous ovarian carcinoma

description:
Sentrix Position: R07C01
810 TCS (FM417)


title: 906 T:high-grade serous ovarian carcinoma

description:
Sentrix Position: R07C01
906 T


title: PAP50:endometrial endometrioid carcinoma

description:
Sentrix Position: R08C01
PAP50


title: SW116 N7:endometrial mucosa from cancer-free normal control

description:
Sentrix Position: R01C01
SW116 N7


title: 650 AS:high-grade serous ovarian carcinoma

description:
Sentrix Position: R05C01
650 AS


title: PAP48:endometrial endometrioid carcinoma

description:
Sentrix Position: R08C01
PAP48


title: SW112 N3:fallopian tube mucosa from cancer-free normal control

description:
Sentrix Position: R01C01
SW112 N3


title: 1120:high-grade serous ovarian carcinoma

description:
Sentrix Position: R06C01
1120


title: SW156 NN4:cervical mucosa from cancer-free normal control

description:
Sentrix Position: R03C01
SW156 NN4


title: Control organoid 3

status: Public on Apr 14 2020

first: Gary

last: Hardiman

address: 135 Cannon Street

department: Medicine

description:
control biological replicate 3
Organoid_Infarction_vs_Control_deseq_124360_1337.txt

data_processing:
Illumina bcl2fastq conversion software v2.17.1.14 used for basecalling.
Sequenced reads (fastq files) were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Secondary analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform (OnRamp Bioinformatics, San Diego, CA). OnRamp’s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data, including data validation and quality control and read alignment to the human genome (hg19) using blastx
The resulting SAM files were sorted and inputted into the Python package HTSeq to generate count data for gene-level differential expression analyses.
Transcript count data from DESeq2 analysis of the samples were sorted according to their adjusted p-value or q-value, which is the smallest false discovery rate (FDR) at which a transcript is called significant.
Genome_build: HG19
Supplementary_files_format_and_content: tab-delimited .txt files include DESEQ2 output for each Comparison ...

source_name: hiPSC-CM donor 01434, exp# 43

growth_protocol: organoids were pre-culture for 4 (D-4 to D0) days followed by 10 days (D0 to D10), changing cell ratio media every 2 days

extract_protocol:
30-35 organoids were collected immediately out of culture and put in lysis buffer on D11 (1 day after last media change) Total RNA was extracted with a RNeasy Mini Kit by Qiagen
Illumina’s Truseq mRNA non-stranded library protocol with 100 ng of RNA was used to prepare sequencing libraries following the manufacture’s protocol with the exception of using half reactions

treatment_protocol: infarct organoids were grown in 10% oxygen with 1uM norepinephrine added to culture media starting at D0

value: cardiac organoid

tag: developmental stage

value: experimental Day 11 (1 day after media change)

tag: concentration

value: normoxia, 300um diameter, 50% CMs + 50%(4:2:1 ratio) FB:HUVEC:ADSC, cell ratio media


title: SW150 NN1:fallopian tube mucosa from cancer-free normal control

description:
Sentrix Position: R02C01
SW150 NN1


title: SW159 NN1:cervical mucosa from cancer-free normal control

description:
Sentrix Position: R02C01
SW159 NN1


title: 514 TCS: poorly differentiated ovarian tumor

description:
Sentrix Position: R06C01
514 TCS


title: DM851T:uterine serous carcinoma

description:
Sentrix Position: R04C01
DM851T


title: SW101 N2:fallopian tube mucosa from cancer-free normal control

description:
Sentrix Position: R03C01
SW101 N2


title: Control organoid 2

description:
control biological replicate 2
Organoid_Infarction_vs_Control_deseq_124360_1337.txt


title: SW137 NN3:cervical mucosa from cancer-free normal control

description:
Sentrix Position: R01C01
SW137 NN3


title: ST:endometrial endometrioid carcinoma

description:
Sentrix Position: R05C01
ST


title: PAP49:endometrial endometrioid carcinoma

description:
Sentrix Position: R08C01
PAP49


title: PAP53:endometrial endometrioid carcinoma

description:
Sentrix Position: R05C01
PAP53


title: RNA_T24_NSD_T0N3

status: Public on Nov 13 2019

city: Lausanne

first: Maxime

last: Jan

state: Suisse

address: University of Lausanne

department: CIG

institute: University of Lausanne

description: Quantification of total RNA in mouse cortex (12:12 Light-Dark). Control sample with ad libitum sleep. (Time: 24  CTime: 0 )

data_processing:
RNA-seq data were processed using the Illumina Pipeline Software version 1.82. All RNA-seq samples passed FastQC quality thresholds (version 0.10.1) and could thus be used in subsequent analysis.
Transcript abundance was quantified by kallisto version 0.43.0 (56) using the GRCm38 reference transcriptome (mm10) and the parameters --single -l 100 -s 20 -b 100. The abundances were processed as follows using sleuth version 0.29.0: transcript abundances were merged into gene counts in transcripts per million (TPM), after which we applied a detection cutoff of 5.5 on the mean gene counts across samples in the time series. Batch effects were corrected by ComBat.Transcript abundance was quantified by kallisto version 0.43.0 (56) using the GRCm38 reference transcriptome (mm10) and the parameters --single -l 100 -s 20 -b 100. The abundances were processed as follows using sleuth version 0.29.0: transcript abundances were merged into gene counts in transcripts per million (TPM), after which we applied a detection cutoff of 5.5 on the mean gene counts across samples in the time series. Batch effects were corrected by ComBat.
ATAC-seq reads were aligned to the mouse genome (mm10) using bowtie2 in paired-end mode, with the parameters recommended for open chromatin (--very-sensitive --maxins 2000 --no-mixed --no-discordant). Duplicatesequences were removed using samtools rmdup.
ATAC-seq data files were processed before peak calling as follows. Alignment files were converted into bed files and tags were extracted using bedtools version 2.26.0. Each tag position was shifted +4 base pairs on the positive strand and - 5 base pairs on the negative strand to center tags on transposase binding events.
The peak calling was performed on pooled tags for replicates using Macs2 version 2.1.1 [--nomodel --shift -75 --extsize 150], and peaks were filtered using a 0.05 FDR cutoff for a local random Poisson distributed background noise, captured by Macs2.
Peak boundaries were merged between time points and conditions in order to build a common peak mapping reference covering all samples. Finally, peak coverage was quantified using HTSeq version 0.6.1 for each sample, using the common mapping reference. We filtered low coverage peaks using a minimum mean threshold of 10 reads per peak.
Genome_build: mm10
Supplementary_files_format_and_content: Chromatin accessibility (peak coverage) [CPM], Coordinate of ATAC peaks, Gene expression [log2 TPM]

source_name: Cerebral cortex tissue

growth_protocol: Mice were housed under standard conditions according to the Swiss Animal Protection Act, under a 12h:12h light/dark cycle, with food accessible ad libitum at all times.

extract_protocol:
Mice were anesthetized with isoflurane prior to decapitation. Cortex was rapidly dissected and flash frozen in liquid nitrogen. Frozen cortex of each individual was ground in liquid nitrogen and stored at -80°C until further use. Tissue from each mouse was distributed to the two protocols (RNAseq and ATAC-seq), such that both datasets originate from the exact same set of individuals.
Total RNA was extracted using the miRNeasy kit (Qiagen; Hilden, Germany) following the manufacturer's instructions. RNA-seq libraries were prepared using 1000 ng of total RNA and the Illumina TruSeq Stranded mRNA reagents (Illumina; San Diego, CA, USA) on a Sciclone liquid handling robot (PerkinElmer; Waltham, MA, USA) using a PerkinElmerdeveloped automated script. Libraries were sequenced on the Illumina HiSeq 2500 sequencer, producing >36 million (median 55 million) mappable single-end 100 bp reads. ATAC-seq was performed as followed, 100'000 nuclei were treated with 2.5 μl Tagment DNA enzyme (Nextera DNA Sample Preparation Kit, Illumina) in transposition buffer (10mM Tris Base, 5mM MgCl2, 10% DMSO, pH 7.6) at 37°C for 30 minutes, followed by cleanup on a Qiagen Minelute column. Fragments >1kb in size were removed using 0.6X, then 1X, volumes of AmpureXP beads (Beckman Coulter Life Sciences; Indianapolis, IN, USA). DNA fragments were subjected to 11 cycles of PCR amplification with Nextera dual index primers (Illumina) and the NEBNext High Fidelity 2X PCR Master Mix (New England Biolabs; Ipswich, MA, USA). PCR reactions were cleaned up with one volume AmpureXP beads, quantified by Qubit (ThermoFisher Scientific; Waltham, MA, USA) and quality controlled by Fragment Analyzer (Advanced Analytical Technologies; Ankeny, IA, USA). Libraries were sequenced on the Illumina HiSeq 2500 sequencer, producing >25 million (median 41 million) mappable 50 bp paired-end reads per sample after removal of duplicate and mitochondrial sequences.

treatment_protocol: Mice for tissue collection were divided into two experimental cohorts, sleep deprived (SD) and non-sleep deprived (controls, Ctr). After a one-week habituation to the experimental setting, at the age of 11-12 weeks, the SD mice were sleep-deprived by gentle handling for 6 hours starting at light onset (zeitgeber time ZT0-ZT6), and allowed to recover according to the tissue collection schedule.

tag: ztime

tag: time

tag: condition

value: NSD

tag: batch

tag: 7 days after sd

tag: strain

value: male


title: PAP47:endometrial endometrioid carcinoma

description:
Sentrix Position: R08C01
PAP47

value: fresh-frozen

tag: age

tag: gender


title: RNA_T0_NSD_T0N2

description: Quantification of total RNA in mouse cortex (12:12 Light-Dark). Control sample with ad libitum sleep. (Time: 0  CTime: 0 )


title: RNA_T30_SD_T30S4

description: Quantification of total RNA in mouse cortex (12:12 Light-Dark). Sample taken after sleep deprivation. (Time: 30  CTime: 6 )

value: SD


title: RNA_T0_NSD_T0N1


title: 702TS:uterine serous carcinoma

description:
Sentrix Position: R04C01
702TS

value: Female


title: 633 TCS:high-grade serous ovarian carcinoma

description:
Sentrix Position: R07C01
633 TCS


title: RNA_T30_SD_T30S3


title: RNA_T24_NSD_T0N5


title: RNA_T6_NSD_T6N4

description: Quantification of total RNA in mouse cortex (12:12 Light-Dark). Control sample with ad libitum sleep. (Time: 6  CTime: 6 )


title: RNA_T6_NSD_T6N3


title: RNA_T6_NSD_T6N2


title: RNA_T78_SD_T78S4

description: Quantification of total RNA in mouse cortex (12:12 Light-Dark). Sample taken after sleep deprivation. (Time: 78  CTime: 6 )


title: RNA_T78_SD_T78S3


title: Control organoid 1

description:
control biological replicate 1
Organoid_Infarction_vs_Control_deseq_124360_1337.txt

tag: tissue


title: RNA_T24_NSD_T0N9


title: RNA_T72_SD_T72S4

description: Quantification of total RNA in mouse cortex (12:12 Light-Dark). Sample taken after sleep deprivation. (Time: 72  CTime: 0 )


title: RNA_T72_SD_T72S3


title: SW197 NN1:endometrial mucosa from cancer-free normal control

description:
Sentrix Position: R03C01
SW197 NN1

tag: uniqueid


title: SW288 T1:endometrial endometrioid carcinoma

description:
Sentrix Position: R04C01
SW288 T1

tag: histology

value: endometrial endometrioid carcinoma


title: RNA_T66_SD_T66S3

description: Quantification of total RNA in mouse cortex (12:12 Light-Dark). Sample taken after sleep deprivation. (Time: 66  CTime: 18 )


title: RNA_T0_NSD_T0N8


title: RNA_T66_SD_T66S5


title: RNA_T66_SD_T66S2


title: RNA_T27_SD_T27S5

description: Quantification of total RNA in mouse cortex (12:12 Light-Dark). Sample taken after sleep deprivation. (Time: 27  CTime: 3 )


title: RNA_T27_SD_T27S3


title: RNA_T3_NSD_T3N4

description: Quantification of total RNA in mouse cortex (12:12 Light-Dark). Control sample with ad libitum sleep. (Time: 3  CTime: 3 )


title: RNA_T27_SD_T27S2


title: RNA_T3_NSD_T3N3


title: RNA_T3_NSD_T3N2


title: 199 TCS:high-grade serous ovarian carcinoma

description:
Sentrix Position: R07C01
199 TCS

tag: tissue type


title: PAP46 --> SW0382 T1:endometrial endometrioid carcinoma

description:
Sentrix Position: R08C01
PAP46 --> SW0382 T1

tag: race


title: RNA_T54_SD_T54S2

description: Quantification of total RNA in mouse cortex (12:12 Light-Dark). Sample taken after sleep deprivation. (Time: 54  CTime: 6 )


title: SW108 N3:fallopian tube mucosa from cancer-free normal control

description:
Sentrix Position: R01C01
SW108 N3

value: B

tag: grade


title: RNA_T78_SD_T78S2


title: RNA_T48_SD_T48S1

description: Quantification of total RNA in mouse cortex (12:12 Light-Dark). Sample taken after sleep deprivation. (Time: 48  CTime: 0 )


title: RNA_T48_SD_T48S4


title: RNA_T60_SD_T60S4

description: Quantification of total RNA in mouse cortex (12:12 Light-Dark). Sample taken after sleep deprivation. (Time: 60  CTime: 12 )


title: RNA_T18_NSD_T18N8

description: Quantification of total RNA in mouse cortex (12:12 Light-Dark). Control sample with ad libitum sleep. (Time: 18  CTime: 18 )


title: RNA_T54_SD_T54S4


title: RNA_T18_NSD_T18N7


title: RNA_T42_SD_T42S6

description: Quantification of total RNA in mouse cortex (12:12 Light-Dark). Sample taken after sleep deprivation. (Time: 42  CTime: 18 )


title: SW96 N5:cervical mucosa from cancer-free normal control

description:
Sentrix Position: R03C01
SW96 N5

tag: sample group


title: RNA_T18_NSD_T18N3


title: RNA_T54_SD_T54S1


title: RNA_T42_SD_T42S4


title: RNA_T18_NSD_T18N4


title: SW131 NN1:endometrial mucosa from cancer-free normal control

description:
Sentrix Position: R02C01
SW131 NN1


title: RNA_T36_SD_T36S4

description: Quantification of total RNA in mouse cortex (12:12 Light-Dark). Sample taken during sleep deprivation. (Time: 36  CTime: 12 )


title: RNA_T30_SD_T30S1


title: RNA_T72_SD_T72S2


title: RNA_T12_NSD_T12N5

description: Quantification of total RNA in mouse cortex (12:12 Light-Dark). Control sample with ad libitum sleep. (Time: 12  CTime: 12 )


title: RNA_T12_NSD_T12N4


title: 126 T (FM343):high-grade serous ovarian carcinoma

description:
Sentrix Position: R07C01
126 T (FM343)

value: W


title: RNA_T12_NSD_T12N2


title: RNA_T12_NSD_T12N1


title: RNA_T42_SD_T42S2


title: RNA_T36_SD_T36S1


title: RNA_T198_SD_J76S3

description: Quantification of total RNA in mouse cortex (12:12 Light-Dark). Sample taken after sleep deprivation. (Time: 198  CTime: 6 ) . Group sampled 7 days after sleep deprivation [SD]


title: RNA_T198_SD_J76S1


title: RNA_T6_NSD_J76N2

description: Quantification of total RNA in mouse cortex (12:12 Light-Dark). Control sample with ad libitum sleep. (Time: 6  CTime: 6 ). Group sampled 7 days after sleep deprivation [Control]

value: Control


title: RNA_T198_SD_J76S2


title: RNA_T18_NSD_T18N2


title: RNA_T6_NSD_J76N1


title: RNA_T48_SD_T48S3


title: RNA_T192_SD_J70S3

description: Quantification of total RNA in mouse cortex (12:12 Light-Dark). Sample taken after sleep deprivation. (Time: 192  CTime: 0 ). Group sampled 7 days after sleep deprivation [SD]


title: RNA_T192_SD_J70S2


title: RNA_T60_SD_T60S3


title: SW95 N4:endometrial mucosa from cancer-free normal control

description:
Sentrix Position: R03C01
SW95 N4


title: RNA_T60_SD_T60S2


title: RNA_T0_NSD_J70N1

description: Quantification of total RNA in mouse cortex (12:12 Light-Dark). Control sample with ad libitum sleep. (Time: 0  CTime: 0 ). Group sampled 7 days after sleep deprivation [Control]


title: RNA_T192_SD_J70S1


title: SW159 NN2:fallopian tube mucosa from cancer-free normal control

description:
Sentrix Position: R02C01
SW159 NN2


title: RNA_T24_NSD_J70N2

description: Quantification of total RNA in mouse cortex (12:12 Light-Dark). Control sample with ad libitum sleep. (Time: 24  CTime: 0 ). Group sampled 7 days after sleep deprivation [Control]


title: SW148NN2:fallopian tube mucosa from cancer-free normal control

description:
Sentrix Position: R02C01
SW148NN2


title: MT --> SW0157 T1:endometrial endometrioid carcinoma

description:
Sentrix Position: R05C01
MT --> SW0157 T1

value: A


title: 415 TCS2 --> 304 TSA:high-grade serous ovarian carcinoma

description:
Sentrix Position: R06C01
415 TCS2 --> 304 TSA

value: high-grade serous ovarian carcinoma


title: KO3

status: Public on Apr 02 2019

city: Tampa

first: Paulo

middle: Cesar

last: Rodriguez

address: 12902 Magnolia Drive, MRC2067E

institute: Moffitt Cancer Center

description:
sample name in processed data file:
006_RNA_Rodriguez_CICPT_1239.counts

data_processing:
Sequencing reads were subjected to adaptor trimming, series of quality assessment before being aligned with Tophat v2.0.13 against mouse reference genome mm10.
Quantification of read counts aligned to the region associated with each gene was performed using HTSeq v0.6.1 based on National Center for Biotechnology information (NCBI) RefSeq gene model.
Read counts of all samples were normalized using the median-of-ratios method implemented in R/Bioconductor package DESeq2 v1.6.3.
Differential expression analysis between the two groups was performed by serial dispersion estimation and statistical model fitting procedures implemented in DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: Text file of normalized gene abundance

source_name: Primary CD8 T cell

growth_protocol: Splenic cells were grown in complete RPMI media at 37°C in 5% CO2

extract_protocol:
Total RNA was extracted using the RNAeasy Mini Kit (Qiagen). Next, RNA was quantified by NanoDrop 1000 spectrophotometer and the RNA quality was assessed by Agilent 2100 Bioanalyzer.
The libraries were sequenced on the Illumina NextSeq 500 v2 sequencer with 75-base single-end run in order to generate approximately 60 million reads per sample.

treatment_protocol: Spleens from wildtype and Ddit3 -/- P-mel mice were homogenated and splenic cells were seeded and treated with 1 µg/ml gp10025-33 for 48 hours, then primed CD8+ T cells were isolated by negative enrichment

tag: surface markers

tag: cell type

value: CD8 T cell

value: spleen

tag: genotype

value: Ddit3 KO


title: KO1

description:
sample name in processed data file:
004_RNA_Rodriguez_CICPT_1239.counts


title: WT2

description:
sample name in processed data file:
002_RNA_Rodriguez_CICPT_1239.counts

value: WT


title: WT1

description:
sample name in processed data file:
001_RNA_Rodriguez_CICPT_1239.counts


title: WT3

description:
sample name in processed data file:
003_RNA_Rodriguez_CICPT_1239.counts


title: lib5022 [TN09_9004933_0]

status: Public on Feb 28 2019

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

institute: Benaroya Research Institute

data_processing:
Base-calling was performed automatically by Illumina real time analysis software and demultiplexing was performed on Illumina BaseSpace.
Hard trimming was performed in Galaxy; 1 3'-end base was removed from all reads using the FASTQ Trimmer tool (v1.0.0)
Quality-based trimming was performed in Galaxy; reads were trimmed from both ends using the FASTQ Quality Trimmer tool (v1.0.0) until minimum base quality for each read was >= 30.
Reads were aligned in Galaxy using bowtie and TopHat (Tophat for Illumina tool, v.1.5.0)
Read counts per Ensembl gene ID were estimated in Galaxy using htseq-count (htseq-count tool, v.0.4.1).
Sequencing, alignment, and quantitation metrics were obtained for FASTQ, BAM/SAM, and count files in Galaxy using FastQC, Picard, TopHat, Samtools, and htseq-count.
Genome_build: GRCh38
Supplementary_files_format_and_content: T1D_placebos_raw_counts.csv is a comma-delimited matrix. The first column ("ensgene") contains Ensembl gene IDs. The remaining columns include raw read counts assigned for each library. All samples that passed SNP-based identity checks are included, with 3 samples of uncertin provenance excluded. Data have not otherwise been filtered or normalized.

source_name: whole blood

extract_protocol:
RNA was isolated from whole blood samples preserved in Tempus blood RNA tubes (Applied Biosystems, CA) using the Total RNA Isolation chemistry on an ABI Prism 6100 (Applied Biosystems, CA) or a Thermo Scientific KingFisher (Thermo Fisher Scientific, MA).
Samples were globin-reduced with the GLOBINclear kit (Ambion, CA), and libraries were constructed from globin-reduced RNA using the Illumina TruSeq RNA Sample Preparation kit v2. Libraries were clustered on flow cells using the TruSeq Single Read Cluster Kit v3.

tag: subject

tag: rate of c-peptide change

tag: visit day

tag: age at enrollment

tag: Sex

value: female

value: White

tag: ethnicity

value: Not Hispanic or Latino

tag: library batch

tag: lymphocyte percent

tag: neutrophil percent


title: lib5149 [TN09_9043244_27]

value: male


title: lib5137 [TN09_9025230_0]


title: lib5152 [TN09_9009983_27]


title: lib5073 [TN09_9043569_27]

value: Hispanic or Latino


title: lib5144 [TN09_9085527_4]


title: lib5066 [TN09_9088780_0]


title: lib5105 [TN09_9000192_0]


title: lib6851 [T1DAL_00110202_15]


title: lib5107 [TN09_9022468_4]


title: lib4711 [TN02_9028156_11]


title: lib5145 [TN09_9033420_4]


title: lib5070 [TN09_9004933_4]


title: lib5069 [TN09_9099432_4]


title: lib5037 [TN09_9023648_27]


title: lib5027 [TN09_9040341_4]

value: Black or African American


title: lib5026 [TN09_9033420_0]


title: lib4710 [TN02_9015338_2]


title: lib5020 [TN09_9081868_0]


title: lib5109 [TN09_9081868_27]


title: lib5111 [TN09_9029938_27]


title: RNA_T36_SD_T36S2

tag: ztime

tag: time

tag: condition

value: SD

tag: batch

tag: 7 days after sd

tag: strain

tag: gender


title: lib4704 [TN02_9071282_11]

tag: race


title: lib5139 [TN09_9009711_0]

tag: subject


title: lib4702 [TN02_9065086_29]

tag: rate of c-peptide change


title: lib4703 [TN02_9024813_23]

tag: visit day


title: RNA_T12_NSD_T12N6

value: NSD


title: lib4705 [TN02_9019151_11]

tag: age at enrollment


title: lib4849 [START_010005_0]

tag: Sex


title: lib4707 [TN02_9076280_17]

tag: ethnicity


title: lib5063 [TN09_9086478_0]

value: White; Other

tag: library batch


title: lib4696 [TN02_9025240_23]

tag: lymphocyte percent


title: lib4699 [TN02_9025380_2]

tag: neutrophil percent


title: lib5059 [TN09_9098612_4]


title: lib5061 [TN09_9022468_0]


title: lib4846 [START_008003_11]


title: lib4700 [TN02_9035402_2]


title: lib5099 [TN09_9006235_0]


title: lib5098 [TN09_9053436_4]


title: lib4847 [START_008003_0]


title: lib5068 [TN09_9081868_4]


title: lib4708 [TN02_9025380_11]


title: lib4701 [TN02_9058753_29]


title: lib4698 [TN02_9053329_2]


title: lib5104 [TN09_9000192_4]


title: SW103 N8:endometrial mucosa from cancer-free normal control

description:
Sentrix Position: R01C01
SW103 N8

tag: uniqueid

tag: histology

tag: tissue type

value: fresh-frozen

tag: age

value: W

value: Female

tag: grade

tag: sample group


title: lib4848 [START_010005_11]


title: lib5157 [TN09_9088780_4]


title: lib5166 [TN09_9086478_27]


title: lib5160 [TN09_9021857_4]

value: Other


title: lib4697 [TN02_9001542_17]


title: lib5165 [TN09_9043569_4]


title: lib4709 [TN02_9058753_2]


title: lib5153 [TN09_9085527_0]


title: lib4706 [TN02_9019475_2]


title: lib5019 [TN09_9003145_27]


title: lib5154 [TN09_9025127_0]


title: lib5013 [TN09_9099432_0]


title: lib5011 [TN09_9040341_0]


title: lib5007 [TN09_9015041_4]


title: lib5123 [TN09_9065335_4]


title: lib5124 [TN09_9023648_0]


title: lib5115 [TN09_9086478_4]


title: lib5122 [TN09_9010400_4]


title: lib4983 [TN09_9025230_4]


title: lib4920 [TN09_9006235_27]


title: lib4918 [TN09_9008090_27]


title: lib4959 [TN09_9070242_27]


title: lib5009 [TN09_9053436_0]


title: lib5132 [TN09_9085527_27]


title: lib4957 [TN09_9081360_27]


title: lib5093 [TN09_9025230_27]


title: lib5127 [TN09_9075373_4]


title: lib4954 [TN09_9006235_4]


title: lib4914 [TN09_9043661_0]


title: lib5017 [TN09_9075373_27]


title: lib5086 [TN09_9070242_0]


title: lib4994 [TN09_9000192_27_1]


title: lib4986 [TN09_9070242_4]


title: lib4993 [TN09_9098612_0]


title: lib5083 [TN09_9043661_4]


title: lib4923 [TN09_9009711_27]


title: lib5057 [TN09_9099432_27]


title: lib5056 [TN09_9004933_27]


title: lib4912 [TN09_9043569_0]


title: ZM --> PAP 55: poorly differentiated ovarian tumor

description:
Sentrix Position: R04C01
ZM --> PAP 55

value: poorly differentiated ovarian tumor

value: A

tag: gender


title: lib4985 [TN09_9025127_4]

tag: race


title: lib5041 [TN09_9010400_0]

tag: subject


title: lib4909 [TN09_9089197_0]

tag: rate of c-peptide change


title: lib4910 [TN09_9009983_0]

tag: visit day


title: lib4953 [TN09_9008090_0]

tag: age at enrollment


title: lib5042 [TN09_9075373_0]

tag: Sex


title: lib4952 [TN09_9008090_4]

tag: ethnicity


title: lib4908 [TN09_9003145_0]

tag: library batch


title: lib5004 [TN09_9029938_4]

tag: lymphocyte percent


title: lib4898 [TN09_9021857_27_1]

tag: neutrophil percent


title: lib4896 [TN09_9001125_0]


title: lib4879 [START_008008_11]


title: lib4899 [TN09_9021857_27_2]


title: lib4876 [START_008008_17]


title: lib4895 [TN09_9045965_0]


title: lib4979 [TN09_9040341_27]


title: lib5044 [TN09_9081360_4]


title: lib4878 [START_008008_0]


title: lib4842 [START_002010_0]


title: lib4877 [START_002019_11]

value: Asian; White


title: lib5002 [TN09_9065335_0]


title: lib4759 [TN02_9040657_11]


title: lib4843 [START_001005_0]


title: lib4906 [TN09_9081360_0]


title: lib4936 [TN09_9010400_27]


title: lib4935 [TN09_9009711_4]


title: lib4845 [START_003004_0]


title: lib4880 [START_013007_14]


title: lib4929 [TN09_9001125_4]


title: lib4752 [TN02_9076280_23]


title: lib4844 [START_003004_11]


title: lib4977 [TN09_9025127_27]


title: lib4817 [TN02_9001825_11]


title: lib4924 [TN09_9089197_4]


title: lib4753 [TN02_9076428_17]


title: lib4976 [TN09_9000192_27_2]


title: lib4852 [START_002003_17]


title: lib4853 [START_002003_14]


title: lib4850 [START_001005_17]


title: lib4890 [TN09_9009983_4]


title: lib4814 [TN02_9065329_11]

value: Asian


title: lib4886 [TN09_9015041_0]


title: lib4889 [TN09_9043244_0]


title: lib4681 [TN02_9071282_17]


title: lib4680 [TN02_9054059_17]

value: female


title: lib4815 [TN02_9098296_29]

value: White


title: lib4719 [TN02_9071282_29]

value: Not Hispanic or Latino


title: lib4816 [TN02_9081451_23]


title: lib4718 [TN02_9079286_23]

value: male


title: lib4717 [TN02_9039335_23]

value: Unknown or Not Reported


title: lib4715 [TN02_9001542_2]


title: lib4682 [TN02_9071282_23]


title: lib4713 [TN02_9076428_11]


title: lib4714 [TN02_9025240_11]


title: lib4887 [TN09_9045965_4]


title: lib4851 [START_001005_14]


title: lib4683 [TN02_9041386_11]

value: Hispanic or Latino


title: lib4716 [TN02_9043986_11]


title: lib4712 [TN02_9063227_17]


title: lib4870 [START_002010_17]


title: lib4749 [TN02_9040657_23]


title: lib4869 [START_002007_17]


title: lib4866 [START_002007_14]


title: lib4784 [TN02_9057024_2]


title: lib4783 [TN02_9081451_2]


title: lib4781 [TN02_9013178_2]


title: lib4782 [TN02_9064544_2]


title: lib4861 [START_001005_11]


title: lib4860 [START_013007_11]


title: lib4867 [START_002012_14]


title: lib4859 [START_013003_11]


title: lib4858 [START_013007_0]


title: lib4776 [TN02_9016861_2]


title: lib4695 [TN02_9015338_23]


title: lib4813 [TN02_9081777_11]


title: lib4811 [TN02_9001825_29]


title: lib4812 [TN02_9064544_11]


title: lib4694 [TN02_9053642_17]


title: lib4810 [TN02_9064544_29]


title: lib4751 [TN02_9001542_23]


title: lib4685 [TN02_9024813_17]


title: lib4809 [TN02_9098713_29]


title: lib4808 [TN02_9019475_23]


title: lib4750 [TN02_9028256_23]


title: lib4868 [START_002019_14]


title: lib4724 [TN02_9066885_17]


title: lib4721 [TN02_9093772_2]


title: lib4722 [TN02_9075533_23]


title: lib4723 [TN02_9057024_17]


title: lib4720 [TN02_9028256_11]


title: lib4786 [TN02_9075533_2]


title: lib4757 [TN02_9043986_17]


title: lib4755 [TN02_9058753_11]


title: lib4780 [TN02_9028256_17]


title: lib4693 [TN02_9053329_23]


title: lib4754 [TN02_9025240_17]


title: lib4684 [TN02_9019475_17]


title: lib4790 [TN02_9076280_11]


title: lib4787 [TN02_9019151_2]


title: lib4785 [TN02_9076280_2]


title: lib4747 [TN02_9039335_11]


title: lib4744 [TN02_9098713_23]


title: lib4791 [TN02_9028156_2]


title: lib4788 [TN02_9054059_23]


title: lib4789 [TN02_9025240_2]


title: lib4690 [TN02_9098713_11]


title: lib4689 [TN02_9065329_2]


title: lib4726 [TN02_9079286_11]


title: lib4727 [TN02_9052681_11]


title: lib4778 [TN02_9053329_29]


title: lib4688 [TN02_9066885_2]


title: lib4758 [TN02_9015338_11]


title: lib4777 [TN02_9054059_29]


title: lib4748 [TN02_9079286_17]


title: lib4818 [TN02_9064544_17]


title: lib4692 [TN02_9063227_2]


title: lib4725 [TN02_9016861_11]


title: lib4819 [TN02_9015755_23]


title: lib4687 [TN02_9043986_2]


title: lib4746 [TN02_9093772_11]


title: lib4820 [TN02_9013178_29]


title: lib4745 [TN02_9028156_17]


title: lib4821 [TN02_9081451_29]


title: lib4793 [TN02_9028156_29]


title: lib4794 [TN02_9063227_29]


title: lib4856 [START_010005_17]


title: lib4871 [START_002012_17]


title: lib4884 [START_013007_17]


title: lib4854 [START_002010_14]


title: lib4686 [TN02_9039335_17]


title: lib4864 [START_002007_11]


title: lib4795 [TN02_9081777_2]


title: lib4885 [START_002019_17]


title: lib4797 [TN02_9001825_2]


title: lib4862 [START_002012_0]


title: lib4865 [START_002019_0]


title: lib4863 [START_002012_11]


title: lib4796 [TN02_9081451_11]


title: lib4799 [TN02_9063227_11]


title: lib4822 [TN02_9015755_29]


title: lib4741 [TN02_9019151_17]


title: lib4800 [TN02_9071282_2]


title: lib4743 [TN02_9063227_23]


title: lib4798 [TN02_9098296_2]


title: lib4881 [START_013003_14]


title: lib4742 [TN02_9019475_11]


title: lib4883 [START_013003_17]


title: lib4855 [START_003004_14]


title: lib4691 [TN02_9028256_2]


title: lib4792 [TN02_9057024_29]


title: lib4873 [START_008003_14]


title: lib4857 [START_013003_0]


title: lib4774 [TN02_9066885_23]


title: lib4772 [TN02_9075533_29]


title: lib4769 [TN02_9035402_17]


title: lib4770 [TN02_9093772_17]


title: lib4775 [TN02_9016861_17]


title: lib4875 [START_008003_17]


title: lib4874 [START_008008_14]