title: [DDB_PD_087]_[SDT288_WT]_[Fed-batch]_[13h]_[R1]


title: Myometrium from fibroid patient (MyoF), patient MP345

status: Public on Jun 01 2025

type: SRA

city: Grand Rapids

first: Jose

middle: M

last: Teixeira

state: MI

address: 400 Monroe Ave NW

department: Ob/Gyn

country: USA

institute: Michigan State University

description: Library name: MP345N

library_source: transcriptomic

data_processing:
Reads were trimmed for quality and adapters using TrimGalore (version 0.6.5)
Trimmed reads were mapped to Homo sapiens (human) using STAR (version 2.7.9a)
Overlapping Ensembl annotations (version 99)
Analysis was performed using edgeR-robust
Assembly: GRCh38 (hg38)
Supplementary files format and content: txt file with the raw cout per gene

molecule: total RNA

organism: Homo sapiens

source_name: myometrium

extract_protocol:
RNA was isolated using trizol or colums from the Qiagen RNAeasy kit
paired-end (2 × 100 bp) RNA-sequencing on an Illumina NextSeq 6000 or paired-end (2 × 75 bp) RNA-sequencing on an Illumina NextSeq 500

tag: tissue

value: myometrium

tag: race

value: C

tag: age

tag: treatment

value: Myometrium from fibroid patient

tag: batch


title: [DDB_PD_087]_[SDT288_WT]_[Fed-batch]_[3h]_[R2]

city: Kgs. Lyngby

first: Felix

last: Beulig

address: Kemitorvet 220

country: Denmark

institute: Novo Nordisk Center for Biosustainability

data_processing:
First, raw read trimming was performed using Trim Galore with default options, followed by FastQC on the trimmed reads. Next, reads were aligned to the E. coli K-12 MG1655 reference genome (NC_000913.3) using Bowtie. The read direction was inferred using RSeQC. Read counts were generated using featureCounts. All quality control metrics were compiled using MultiQC. Finally, the expression dataset was reported in units of log-transformed transcripts per million (log(TPM).
Assembly: Reference genome E. coli MG1655 (NC_000913.3)
Supplementary files format and content: Raw data files and comma-delimited text file reporting logtpm values for each sample

organism: Escherichia coli

source_name: Escherichia coli cells

growth_protocol: Batch-to-fed-batch fermentation experiments were performed in 0.25 L Ambr® fermenters (Sartorius) with 2 different media compositions (“High Metal” and “Low Metal” medium)

extract_protocol:
All transcriptome samples were collected and prepared in biological duplicates, whereby either 2 ml of culture (low cell density culture, batch phase) or 0.5 ml of culture (high cell density culture, fed batch phase) was added to 6 ml of Qiagen RNA-protect Bacteria Reagent immediately after sample collection. This solution was then vortexed for 30 seconds, incubated at room temperature for 5 minutes, and then centrifuged. The supernatant was then removed and the cell pellet was stored at -80° C. The RNeasy Mini Kit (Qiagen) was used to extract and purify RNA from the cell pellets per vendor protocol, including on-columns DNase treatment for 30 minutes at room temperature. RNA was quantified using qubit fluorometer (Thermofisher) and integrity was assessed using fragment analyzer (Agilent Technologies).
Ribosomal RNA was removed using QIAseq FastSelect –5S/16S/23S kit (Qiagen). Sequencing libraries were prepared with the KAPA Stranded RNA-Seq Library Preparation Kit (Kapa Biosystems) and assessed using fragment analyzer (Agilent Technologies). The libraries were then subjected to paired end sequencing on Illumina Nextseq using Nextseq Mid Output kit (Illumina) with a read length of 150 bp.

treatment_protocol: The “Low Metal” batch media contained base medium (22 g L-1 D-(+)-glucose monohydrate, 7.6 g L-1 (NH4)2SO4, 15.7 g L-1 KH2PO4, 0.241 g L-1 MgSO4, 100 mg L-1 thiamine hydrochloride, 0.5 mL L-1 Antifoam 204), and 1 mL L-1 of trace metal solution (0.48 g L-1 CuSO4·5H2O, 0.54 mg L-1 CoCl·7H2O, 0.54 g L-1 ZnSO4·7H2O, 2 g L-1 CaCl2·2H2O, 41.8 g L-1 FeCl3·6H2O, 0.3 g L-1 MnSO4·H2O, 33.4 g L-1 Na2EDTA, 0.5 g L-1 Na2MoO4·2H2O). The “High Metal” batch media contained the same base medium, 3.5 mL L-1 trace metal solution and was additionally supplemented with 1.86 g L-1 citric acid monohydrate and 41.8 mg L-1 FeCl3·6H2O, 21.6 mg L-1 ZnSO4·5H2O). Initial batch fermentations were performed with base medium until complete glucose consumption, marked by a 50% decline in the rate of CO2 formation, triggering an automatic switch to fed-batch operation with continuous supply of the feed medium (550 g L-1 D-(+)-glucose monohydrate, 13.7 g L-1 MgSO4·7H2O)

tag: cell type

value: Escherichia coli cells

tag: strain


title: 24c_B6ME_NI

city: Philadelphia

first: Joseph

middle: W

last: Guarnieri

state: PA

address: 3501 Civic Center Blvd

department: Center for Mitochondrial and Epigenomic Medicine

institute: Children's Hosptial of Philadelphia

description:
IonCode_0119
IonCode_117-124.txt

data_processing:
Sequencing data was aligned using the Ion Torrent S5 ampliSeqRNA and coverageAnalysis plugins.
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

organism: Mus musculus

source_name: Heart

extract_protocol:
RNA was collected using TRIzol™ Reagent (Invitrogen, 15596026) from heart samples.
The RNA was assessed by NanoDrop spectrophotometer (ThermoFisher Scientific) and quantified by Qubit Flex (Thermofisher Scientific) using the Qubit RNA HS Assay Kit (Thermofisher Scientific, Q32855).
The RNA was diluted to 1.43 ng/ul and reverse transcribed into cDNA using the Ion Torrent™ NGS Reverse Transcription Kit (Cat. No. A45003). The RNA library was prepared using the Ion Torrent S5 Chef and Ion AmpliSeq Kit for Chef DL8 (Thermofisher Scientific, A29024) and sequenced using the Ion Torrent S5 Sequencer and Ion 540 Kit (Thermofisher Scientific, A30011).
For snRNA-seq, isolated nuclei were processed using the Chromium Single Cell 3ʹ Reagent V3.1 kit from 10X Genomics. A total of 8,000 nuclei per sample were loaded into a Chip G. Barcoding, cDNA amplification, and library construction were performed according to the Chromium 3ʹ V3.1 protocol. Sequencing was performed on a DNBSEQ-T7 platform targeting 20,000 reads per nucleus.

treatment_protocol: Bulk RNA sequencing and single nucleus RNA Sequencing (snRNA-seq) analysis on C57BL/6JEiJ, C57BL/6JEiJ Ant1-/-, and C57BL/6JEiJ Ant1-/- ND6P25L mice (WT, ANT1, ANT1 ND6), pericardially injected with 2.5x10^11 vg AAV2/9Des-Gfp-mAnt1 or 2.5x10^11 vg AAV2/9Des-Gfp .

value: Heart

tag: genotype

value: 2.5x10^11 vg AAV2/9Des-Gfp


title: 15286X186_blastomere_548B_type_IVF_cell_number_4

city: dallas

first: Edward

last: Grow

state: TEXAS

address: 7053 beltau lane

institute: UTSW

description: cellnumber 4

library_source: genomic single cell

data_processing:
RNA-seq reads were trimmed and filtered for quality using BBDuk and FastQC (version 0.10.1).
Processed reads were aligned to bostau7 with Bowtie2 (v2.2.6) with the following parameters: (--t --q --N1 --L 25 --X 2000 --no-mixed --no-discordant).
PCR duplicates were removed using bedtools
mitochondrial reads were removed using sed '/chrM/d'
counts for each ATACseq union region were generated using ‘Get datasets’ (https://metacpan.org/pod/distribution/Bio-ToolBox/scripts/get_datasets.pl).
Assembly: bostau7
Supplementary files format and content: 20230629-scATAC-seq-cell-ID-conversion.xls excel file containing sample ID and information
Supplementary files format and content: 20180822-scATAC-819-cells-vs-302830-regions.tabular count file for n=819 retained high quality scATACseq libraries in ATAC-seq peaks regions created as a union dataset, tabular format

molecule: genomic DNA

organism: Bos indicus x Bos taurus

source_name: IVF

growth_protocol: Oocyte collection and in vitro maturation: Bovine ovaries were collected from a local abattoir (JBS, Hyrum, Utah) and transported in a cooler containing 0.9% saline solution to the laboratory. Because this research used discarded tissues to generate embryos that were then disposed of without implantation, approval of this work via the Institutional Animal Care and Use Committee was not required. The cumulus-oocyte complexes (COCs) were aspirated from 3-8 mm follicles using an 18-gauge needle and vacuum system. Only compact COCs with homogenous ooplasm and intact layers of cumulus cells were used for somatic cell nuclear transfer (SCNT) or in vitro fertilization (IVF). Following aspiration, COCs were cultured at 38.5°C with 5% CO2 for 22–24 h. The oocytes were cultured in TCM199 maturation medium containing Earles salts, L-glutamine, and sodium bicarbonate (Sigma M4530) supplemented with 10% (v/v) fetal bovine serum (FBS) (Hyclone, SH30070.03), 0.05 mg/ml of bovine follicle stimulating hormone (Sioux Biochemicals, Sioux city, IA), 5 mg/ml of bovine luteinizing hormone (Sioux Biochemicals, Sioux Center, Iowa), 100 U/ml of penicillin, and 100 mg/ml of streptomycin (Gibco 15070-063).  In vitro fertilization: Following 22–24 h of maturation, MII oocytes were fertilized by using the laboratory’s standard in vitro fertilization protocol [Reproduction, 2006, 131:45-51]. Briefly, one straw of cryopreserved bovine semen (Hoffman AI, Logan, Utah) was removed from the liquid nitrogen tank and placed into a 35°C water bath to thaw. Live sperm were isolated by centrifugation through a 45%/90% percoll gradient (MP Biomedical, Irvine, California), suspended (final concentration 1x106/ml) in Tyrodes albumin lactate pyruvate containing 10 μg/ml porcine heparin and used to fertilize the oocytes. Twenty to 22 h post-IVF, cumulus cells were removed by vortexing, and fertilized zygotes were washed in phosphate buffered saline with 0.32 mM sodium pyruvate, 5.55 mM glucose, and 3 mg/ml bovine serum albumin (PB1+). After washing, zygotes were cultured in 40 μl of synthetic oviductal fluid (SOFaa) [Human Reproduction 2000; 15:395-401] with 3% FBS (Hyclone, SH30070.03, Logan, Utah) overlaid with mineral oil. The embryos were cultured at 38.5°C in a humidified atmosphere with 5% CO2. Half of the SOFaa medium was removed and replaced with fresh, equilibrated medium every other day starting the day after in vitro culture. Historically, production of IVF embryos via these methods followed by blastocyst embryo transfers to cattle recipients has generated successful pregnancies at an approximate rate of 50% (number live births/number of embryo transfer procedures) by our research group (unpublished observations). The timing of embryo collection post-fertilization was approximately 24–36 h for 2-cell stage, 48–60 h for 8-cell stage, 156–168 h for morula stage, and 192–204 h for blastocyst stage. Embryos that were obviously dead or arrested by microscopic examination were removed from culture.  Somatic cell nuclear transfer (SCNT): Primary bovine fibroblast cultures were established from ear biopsy tissues from multiple donor Brahma Spanish bull crosses by using well-established procedures [PNAS USA; 2000; 97:990-995]. These cell lines have been previously employed on multiple projects to evaluate their efficiency to generate live calves via SCNT (unpublished observations). Frozen/thawed cells were grown to 80-100% confluence then passaged, with cells from passages 4-5 used as nuclear donors. Three days prior to a cloning session, donor fibroblast cells were thawed and propagated, and incubated in DMEM medium (Hyclone, Logan, Utah) supplemented with 15% (v/v) FBS at 39°C with 5% CO2. Bovine fibroblasts at 80-90% confluence were serum-starved by replacing culture medium with DMEM containing 0.5% (v/v) FBS 24 h prior to SCNT. Oocytes were matured for 18–20 h, then denuded by using 100 μl of 1% (v/v) hyaluronidase (Sigma H3506), incubated for 5 min at 38.5°C with 5% CO2, followed by gentle pipetting. The denuded oocytes were then rinsed with PB1+, and oocytes with polar bodies were selected and separated. SCNT was performed according to established protocols [Reproduction 2006; 131:45-51; Anim Reprod Sci 2006; 95:234-243; Mol Reprod Dev 2004; 68189-197]. Briefly, oocytes with polar bodies were incubated in 0.6 μg/ml demecolcine for 30–40 min and a metaphase plate and a polar body were removed by using a beveled pipette. Fibroblast cells were covered in 0.25% trypsin (Gibco, Carlsbad, CA) for 1 min, and then the trypsin was removed, and fibroblasts were incubated for another 6 min at 39°C with 5% CO2. Once fibroblast cells were detached, they were rinsed in warm medium and centrifuged at 150 × g for 6 min. The supernatant was removed, and the cellular pellet was resuspended in 100 μl of Hepes SOF medium [Hum Reprod 2000; 15:395-401]. One fibroblast cell was injected into the perivitelline space of the recipient oocyte and fused by using one direct pulse of 1.2 kV/cm for 22 μs by an Electro Cell Manipulator 2001 (BTX, San Diego, CA) in 0.28 M sorbitol, 0.05% (w/v) BSA, 0.1 mM CaCl2, 0.5 mM MgCl2, and 0.5 mM Hepes. Following fusion, embryos were washed through Hepes SOF, and incubated in embryo culture medium for 1 h. Activation was then performed, with successfully fused embryos cultured in 5 μM ionomycin for 5 min, followed by 4 h of incubation in activation medium composed of SOFaa medium with 10 μg/ml cyclohexamide and 1 mM 6-dimethylaminopyridine at 38.5°C with 5% CO2. Following activation, embryos were cultured in 40 μl drops of SOFaa with 3% (v/v) FBS overlaid with mineral oil. The embryos were cultured at 38.5°C in a humidified atmosphere with 5% CO2. Half of the SOFaa medium was removed and replaced with fresh, equilibrated medium every other day starting the day after in vitro culture. The timing of embryo collection was the same as for IVF embryos as described above. The rates of development for IVF and SCNT embryos were similar at each developmental stage.

extract_protocol:
ATAC-seq was performed using 2x Tris-DMF-tagmentation buffer (10mM Tris-pH=8.0, 5mM MgCl, 20% DMF). Add (batch-determined actitivty) 2 to 2.5 uL of Nextera Tn5 transposase (Cat# FC-121-1030, Illumina. Samples were incubated at 37C for 30 minutes in a PCR machine. The reactions were stopped with 0.5uL of 10% SDS, pipetted up and down, and placed on ice 5 min. 5x volume of PB buffer was added to the ATAC-seq reaction and purified using a ampure beads and eluted in 10mM Tris-pH=8.0 + 1mM EDTA.
Libraries were PCR amplified in 25uL reaction volumes using custom Nextera PCR primers from Buenrostro, et al. Nature 2015. PCR reaction conditions: ~10uL tagmented DNA, 12.5 uL of 2xphusion PCR mastermix (Phusion High-Fidelity PCR Master Mix with HF Buffer - 100 rxns, NEB, cat #M0531S), 0.625uL of 100uM F primer, 0.625uL of 100uM R primer. QS to 50uL total with H20. Do 5 cycles of “pre-amp” PCR. PCR cycling conditions: 72C incubation for 5 min. 5 cycles of the following: 95C for 30 sec, 72C for 90 sec. Remove 5uL of the “pre-PCR” reaction for qPCR. qPCR reaction conditions: 20uL qPCR reaction: 5uL of pre-amp PCR product, 10 ul of 2x syber (SsoAdvanced SYBR Green Supermix, Biorad catalog #1725275), 0.25uL of 100uM F primer, 0.25uL of 100uM R primer. Run 30-40 cycles of qPCR with the same cycling conditions as above. Select the additional number of PCR cycles to perform as per Buenrostro, et al. Nature Methods 2013. Ampure bead purification (Beckman Coulter, catalog # A63881) as per manufacturer’s instructions.
Nextera tagmentation

treatment_protocol: Each embryo was dissociated into single blastomeres in a single drop of Ca+2/Mg+2 free PBS+0.1% PVP-40 with gentle pipetting. Each individual blastomere of the embryo was pipetted into a PCR strip tube for lysis and ATAC-seq, retaining the embryo identity of each single-cell ATACseq library.

value: IVF


title: Myometrium from fibroid patient (MyoF), patient MP344

description: Library name: MP344N

value: AA


title: Myometrium from fibroid patient (MyoF), patient MP332

description: Library name: MP332N


title: [DDB_PD_087]_[SDT212_GenRed]_[Fed-batch]_[13h]_[R1]


title: 23d_B6ME_NI

description:
IonCode_0118
IonCode_117-124.txt


title: 15286X185_blastomere_548A_type_IVF_cell_number_4

description: cellnumber 4


title: Myometrium from fibroid patient (MyoF), patient MP342

description: Library name: MP342N


title: [DDB_PD_087]_[SDT212_GenRed]_[Fed-batch]_[3h]_[R1]


title: 23c_B6ME_NI

description:
IonCode_0117
IonCode_117-124.txt


title: 15286X183_blastomere_531C_type_IVF_cell_number_4

description: cellnumber 4


title: [DDB_PD_087]_[SDT212_GenRed]_[Fed-batch]_[13h]_[R2]


title: 15286X184_blastomere_531D_type_IVF_cell_number_4

description: cellnumber 4


title: 15287X008_blastomere_589D_type_IVF_cell_number_4

description: cellnumber 4


title: 21b_ANT1_ND6_NI

description:
IonCode_0116
IonCode_109-116.txt

value: C57BL/6JEiJ ANT1 -/- ND6 P25L


title: Myometrium from fibroid patient (MyoF), patient MP330

description: Library name: MP330N


title: [DDB_PD_087]_[SDT212_GenRed]_[Batch]_[0h]_[R1]


title: Myometrium from fibroid patient (MyoF), patient MP323

description: Library name: MP323N


title: 21a_ANT1_ND6_NI

description:
IonCode_0115
IonCode_109-116.txt


title: Myometrium from fibroid patient (MyoF), patient MP322

description: Library name: MP322N

value: A


title: 15286X182_blastomere_531B_type_IVF_cell_number_4

description: cellnumber 4


title: [DDB_PD_087]_[SDT237_GenRed]_[Fed-batch]_[13h]_[R2]


title: 15286X181_blastomere_531A_type_IVF_cell_number_4

description: cellnumber 4


title: 20b_ANT1_ND6_NI

description:
IonCode_0114
IonCode_109-116.txt


title: [DDB_PD_087]_[SDT237_GenRed]_[Fed-batch]_[13h]_[R1]


title: Myometrium from fibroid patient (MyoF), patient MP321

description: Library name: MP321N


title: 15286X179_blastomere_530C_type_IVF_cell_number_4

description: cellnumber 4


title: Myometrium from fibroid patient (MyoF), patient MP319

description: Library name: MP319N


title: Myometrium from fibroid patient (MyoF), patient MP317

description: Library name: MP317N


title: [DDB_PD_087]_[SDT237_GenRed]_[Batch]_[0h]_[R1]


title: Myometrium from fibroid patient (MyoF), patient MP315

description: Library name: MP315N


title: 20a_ANT1_ND6_NI

description:
IonCode_0113
IonCode_109-116.txt


title: 15286X178_blastomere_530B_type_IVF_cell_number_4

description: cellnumber 4


title: 15286X177_blastomere_530A_type_IVF_cell_number_4

description: cellnumber 4


title: 15286X180_blastomere_530D_type_IVF_cell_number_4

description: cellnumber 4


title: 36b_ANT1_NI

description:
IonCode_0110
IonCode_109-116.txt

value: C57BL/6JEiJ ANT1 -/-


title: Myometrium from fibroid patient (MyoF), patient MP313

description: Library name: MP313N


title: [DDB_PD_087]_[SDT211_GenRed]_[Fed-batch]_[13h]_[R1]


title: Myometrium from fibroid patient (MyoF), patient MP308

description: Library name: MP308N


title: [DDB_PD_087]_[SDT211_GenRed]_[Fed-batch]_[3h]_[R2]


title: 38a_ANT1_NI

description:
IonCode_0111
IonCode_109-116.txt


title: 36a_ANT1_NI

description:
IonCode_0109
IonCode_109-116.txt


title: 35b_ANT1_NI

description:
IonCode_0108
IonCode_101-108.txt


title: 15286X176_blastomere_518D_type_IVF_cell_number_4

description: cellnumber 4


title: 15286X175_blastomere_518C_type_IVF_cell_number_4

description: cellnumber 4


title: [DDB_PD_087]_[SDT211_GenRed]_[Batch]_[0h]_[R1]


title: 15286X174_blastomere_518B_type_IVF_cell_number_4

description: cellnumber 4


title: [DDB_PD_087]_[SDT237_GenRed]_[Batch]_[0h]_[R2]


title: Myometrium from fibroid patient (MyoF), patient MP305

description: Library name: MP305N


title: 35a_ANT1_NI

description:
IonCode_0107
IonCode_101-108.txt


title: [DDB_PD_074]_[HMP3427_ZnFeLow]_[Fed-batch]_[24h]_[R1]


title: 25b_B6ME_NI

description:
IonCode_0106
IonCode_101-108.txt


title: Myometrium from fibroid patient (MyoF), patient MP111

description: Library name: MP111N


title: [DDB_PD_087]_[SDT211_GenRed]_[Fed-batch]_[13h]_[R2]


title: [DDB_PD_074]_[HMP3427_ZnFeLow]_[Batch]_[0h]_[R1]


title: 15286X171_blastomere_517C_type_IVF_cell_number_4

description: cellnumber 4


title: Myometrium from fibroid patient (MyoF), patient MP100

description: Library name: MP100N


title: 24b_B6ME_NI

description:
IonCode_0104
IonCode_101-108.txt


title: 15286X172_blastomere_517D_type_IVF_cell_number_4

description: cellnumber 4


title: 25a_B6ME_NI

description:
IonCode_0105
IonCode_101-108.txt


title: [DDB_PD_074]_[HMP3427_ZnFeLow]_[Fed-batch]_[8h]_[R1]


title: Myometrium from fibroid patient (MyoF), patient GO537

description: Library name: GO537N


title: [DDB_PD_072]_[HMP3427_ZnFeHigh]_[Fed-batch]_[23h]_[R1]


title: 15286X170_blastomere_517B_type_IVF_cell_number_4

description: cellnumber 4


title: ChromatinRNA replicate 2

city: Berlin

first: Dubravka

last: Vucicevic

address: Hannoversche Straße 28

department: Berliner Institut for Medical Systems Biology

country: Germany

institute: Max Delbrück Center for Molecular Medicine in the Helmholtz Association

data_processing:
Unique molecular identifiers (UMIs) were extracted from .fastq files using UMI-tools (Smith, Heger and Sudbery, 2017), and reads were trimmed using fastx_trimmer from the FASTX-toolkit (http://hannonlab.cshl.edu/fastx_toolkit/). Reads were then filtered for ERCC spike-in reads and rRNA by mapping to a custom index with Bowtie 1 (Langmead et al., 2009). Trimmed and filtered reads were then mapped using STAR (Dobin et al., 2013). Mapped .bam files were subjected to PCR deduplication using UMI-tools (Smith, Heger and Sudbery, 2017), followed by conversion to .fastq and remapping with STAR to generate final mapped files and normalized coverage tracks.
Assembly: hg38
Supplementary files format and content: Tab deliminated files of reads per gene.
Library strategy: Chromatin RNA-seq

molecule: nuclear RNA

extract_protocol: Described in the manuscript.

tag: cell line

tag: genetic modification


title: 15286X168_blastomere_516D_type_IVF_cell_number_4

description: cellnumber 4


title: 15286X173_blastomere_518A_type_IVF_cell_number_4

description: cellnumber 4


title: 15286X169_blastomere_517A_type_IVF_cell_number_4

description: cellnumber 4


title: [DDB_PD_074]_[HMP3427_ZnFeLow]_[Fed-batch]_[16h]_[R1]


title: nuCaptureC

library_source: genomic

data_processing:
Nuclear Capture C reads were initially processed using the HiCUP pipeline (Wingett et al., 2015) with Bowtie2 mapping to hg38. Mapped reads were then converted to .chinput format using chicagoTools and used as input to chicagoPipeline (Cairns et al., 2016) along with DpnII genomic fragment regions targeted for capture during library preparation.
Assembly: hg38
Supplementary files format and content: bedpe
Library strategy: Nuclear Capture C


title: 23a_B6ME_NI

description:
IonCode_0101
IonCode_101-108.txt


title: [DDB_PD_072]_[HMP3427_ZnFeHigh]_[Fed-batch]_[16h]_[R1]


title: TESLA-seq replicate 2

data_processing:
The raw sequencing output files were preprocessed using BD’s Rhapsody™ Targeted Analysis pipeline (https://scomix.bd.com/hc/en-us/articles/360019763251-Bioinformatics-Guides) on the Seven Bridges Platform (https://www.sevenbridges.com/bdgenomics/), which generated a cell-by-gene count matrix corrected for base-calling errors in cell barcodes, followed by quality-filtering on cells. Processed count matrices of two sample runs contain 12,597 (run1) and 19,406 (run2) cells, respectively, with features consisting of 1,046 guide RNAs (gRNA) targeting the 2Mb region around the PHOX2B gene, 52 control gRNAs, and 78 genes within the 6Mb region around the PHOX2B gene. The count matrices were loaded into the R environment for further preprocessing with Seurat v4 (Stuart et al., 2019). Logarithm base 10 was applied to both the gene count matrices and gRNA count matrices. The gRNA count values display a clear bimodal pattern, suggesting that the peak of lower values could be noise. After setting the lower values in gRNA matrices to zero, gRNAs with no count values across cells and genes with no expression were removed. Cells with either low gRNA values or low gene expression were filtered. After filtering, run1 has 6,196 cells with 1,090 gRNAs and 62 genes, while run2 has 10,363 cells with 1,097 gRNAs and 64 genes. The quality-filtered matrices of two runs were normalized using SCTransform (Hafemeister and Satija, 2019) and integrated with batch correction done by linear regression between runs (SCTransform argument ‘var.to.regress’). Cells  that had less  than two normalized and batch-corrected guide counts were removed and genes that have no expression following the cell removal were filtered. gRNA capture efficiency was computed using a generative model that takes into account the multiplicity of infection (Dixit et al., 2016; Hill et al., 2018). To test the effect of each gRNA and avoid potential confounding caused by nearby gRNAs, differential expression analysis of each targeted gene was performed between cells that contain the considered gRNA and all other cells that contain other gRNAs targeting at least 400 kb away from the considered gRNA. MAST.cov test was chosen to perform differential expression analysis as recommended for targeted single-cell data (Schraivogel et al., 2020).
TESLA-seq_gRNA_results.txt summarises the results at the gRNA level.
TESLA-seq_CaREs_results.txt summarises the results at the CaRE level.
TESLA-seq_raw_output_run1.csv and TESLA-seq_raw_output_run2.csv are outputs from the above described SevenBirdgesPlatform with molecules per cell.
Assembly: hg38
Supplementary files format and content: Tab deliminated text files.
Library strategy: TESLA-seq

value: CRISPR activation


title: 15286X167_blastomere_516C_type_IVF_cell_number_4

description: cellnumber 4


title: 15286X166_blastomere_516B_type_IVF_cell_number_4

description: cellnumber 4


title: [DDB_PD_072]_[HMP3427_ZnFeHigh]_[Fed-batch]_[16h]_[R2]


title: 24a_B6ME_NI

description:
IonCode_0103
IonCode_101-108.txt


title: 23b_B6ME_NI

description:
IonCode_0102
IonCode_101-108.txt


title: CRISPRi bulk screen day 33 replicate 2

data_processing:
Described in the manuscript.Sequencing reads were assigned to sgRNA using a modified version of a script in (Sanjana, 2016). Mean guide-counts were obtained at each time-point and all time-points were combined in a single table. Normalization was performed using the following equation: counts = qi/Σ(q)jx106qi (where qi is reads mapped to a specific guide and Σ(q)j is total number of reads mapped to all guides). We employed a sliding window strategy to score each bin based on the information from the sgRNAs targeting it and the adjacent bins upstream and downstream. Each bin was analyzed using guides targeting a 300bp window centered on it. To assess guide enrichment or depletion within these windows, we utilized a mixed linear model (MLM) with random intercepts: The model was fitted using the ‘lme4’(v. 1.1.28) R package (REML = FALSE) (Bates et al., 2015). Hypothesis testing was done by comparing our full model to a reduced version that does not account for time using a maximum likelihood ratio via ANOVA (Kaufmann and Schering, 2014). Adjustment of the p-value for correction of multiple tests was performed using the Benjamini-Hochberg method (Benjamini and Hochberg, 1995). After identifying significant windows, bedtools (v 2.30.0) (Quinlan and Hall, 2010) was used to merge significant bins within 500bp of each other into CaREs. If a significant bin was not within 500 bp of another significant bin, it was classified as a distinct CaRE. CaREs were scored by MLM using information from all guides targeting the genomic area defined by the merged CaRE. Scores were calculated as: -log10 (adjusted p-value).
CRISPRa_bulk_screen_CaREs_gRNAs_results.txt are the results of the CRISPRa at gRNA and CaRE level.
CRISPRi_gRNA_bulk_screen_results.txt are the results of the CRISPRi screen at the gRNA level.
Assembly: hg38
Supplementary files format and content: Tab deliminated files summarising the results.
Library strategy: bulkCRISPR-screen

tag: time

value: day 33

value: CRISPR inhibition


title: [DDB_PD_072]_[HMP3427_ZnFeHigh]_[Fed-batch]_[23h]_[R2]


title: CRISPRi bulk screen day 33 replicate 1


title: TESLA-seq replicate 1


title: ChromatinRNA replicate 1


title: 15286X163_blastomere_514C_type_IVF_cell_number_4

description: cellnumber 4


title: [DDB_PD_065]_[DDB7_WT]_[Fed-batch]_[15h]_[R1]


title: [DDB_PD_072]_[HMP3427_ZnFeHigh]_[Fed-batch]_[8h]_[R2]


title: CRISPRi bulk screen day 29 replicate 2

value: day 29


title: S. mutans0.025uM HP-29, 0.5mM ZnSO4, rep 3

city: Gainesville

first: Jessica

middle: K

last: Kajfasz

state: FL

address: 1395 Center Drive

department: Oral Biology

institute: University of Florida

description: Library name: HP29_Zn-3

data_processing:
Sequencing was performed on the Illumina NovaSeq platform
Read quantification was performed using Subread’s featureCounts2 functionality.
Quality control and adapter trimmer was performed with bcl-convert.
Read counts loaded into R were normalized using edgeR’s Trimmed Mean of M values (TMM) algorithm.
Subsequent values were then converted to counts per million (CPM).  Differential expression analysis was performed using edgeR’s glmQLFTest.
Assembly: Read mapping was performed with HISAT2 using the S. mutans UA159 genome (GenBank accession number NC_004350.2).
Supplementary files format and content: The processed .csv data files indicate the number of reads obtained for each open reading frame (SMU_RSxxxxx) for each sample after each of two original raw data files (.fastq) were compiled and mapped against the S. mutans UA159 genome NC_004350.2) as described above.

organism: Streptococcus mutans UA159

source_name: Streptococcus mutans

growth_protocol: Overnight cultures of S.mutans UA159 were diluted 1:20 into BHI medium.  Cultures were grown to DO600 = 0.4

extract_protocol:
Harvested cells were resuspended in 1mL of RNA Protect Bacteria Reagent (Qiagen). Total RNA was isolated from homogenized S. mutans cell lysates by acid-phenol:chloroform extractions.  The nucleic acid was subjected to DNase I digestion (Ambion).   The RNA was then purified using the Qiagen RNeasy colum purification kit, including an additional on-column DNase digest.  Total RNA was subjected to two rounds of mRNA enrichment using the MICROBExpress Bacterial mRNA Purification kit (ThermoFisher).
rRNA depletion was performed with the Ribo-Zero Plus Microbiome kit (Illumina) to generate RNA libraries. cDNA librariers were geneated by SeqCenter using an Illumina TrueSeq library prep kit. All sequencing and subsequent steps were performed by SeqCenter.

treatment_protocol: Each tube was then split into three tubes: 1) BHI control, 2) 0.025uM HP-29, 3) 0.5mM ZnSO4 + 0.025uM HP-29.  These samples were incubated for an additional 30 minutes, then harvested by centrifugation.

value: Streptococcus mutans

value: 0.025uM HP-29 and 0.05mM ZnSO4 for 30 minutes


title: 15286X162_blastomere_514B_type_IVF_cell_number_4

description: cellnumber 4


title: [DDB_PD_065]_[DDB7_WT]_[Fed-batch]_[9h]_[R1]


title: S. mutans 0.025uM HP-29, 0.5mM ZnSO4, rep 2

description: Library name: HP29_Zn-2


title: [DDB_PD_065]_[DDB7_WT]_[Fed-batch]_[3h]_[R1]


title: 15286X161_blastomere_514A_type_IVF_cell_number_4

description: cellnumber 4


title: [DDB_PD_065]_[DDB7_WT]_[Batch]_[0h]_[R1]


title: S. mutans 0.025uM HP-29, 0.5mM ZnSO4, rep 1

description: Library name: HP29_Zn-1


title: 15286X164_blastomere_514D_type_IVF_cell_number_4

description: cellnumber 4


title: 15286X160_blastomere_513D_type_IVF_cell_number_4

description: cellnumber 4


title: BJ shp53-1

type: RNA

city: Jerusalem

first: Batsheva

last: Kerem

address: Edmond J Safra Campus

department: Genetics

country: Israel

institute: The Hebrew University

description: Gene expression data from iPS cell line 11 derived from patient A

hyb_protocol: Affymetrix protocol, 11ug cRNA

scan_protocol: GeneChip scanner 3000 7G, GeneChip Operating Software v1.4

data_processing: Affymetrix Expression Console RMA

label: biotin

source_name: BJ-hTERT cells expressing shp53

label_protocol: 200ng total RNA, Affymetrix protocol

growth_protocol: BJ hTERT cells grown in DMEM supplemented with 10% FBS, 100,000 U/L penicillin, 100 µg/L streptomycin

extract_protocol: RNA  was isolated using Qiagen Rneasy mini kit

treatment_protocol: Total RNA was isolated from cells infected with empty shRNA vector or shRNA against p53

tag: gender

value: Male

value: fibroblast


title: 15286X159_blastomere_513C_type_IVF_cell_number_4

description: cellnumber 4


title: S. mutans 0.025uM HP-29, rep 2

description: Library name: HP29-2

value: 0.025uM HP-29 for 30 minutes


title: BJ shp53-2

description: Gene expression data from fibroblast - B


title: CRISPRi bulk screen day 5 replicate 1

value: day 5


title: CRISPRi bulk screen day 20 replicate 1

value: day 20


title: [DDB_PD_065]_[SDT172_del_purR]_[Fed-batch]_[15h]_[R2]

value: Escherichia coli cells


title: CRISPRi bulk screen day 5 replicate 2


title: BJ control shRNA-2

description: Gene expression data from iPS cell line 26 derived from patient A

source_name: BJ-hTERT cells expressing empty shRNA vector


title: S. mutans 0.025uM HP-29, rep 3

description: Library name: HP29-3


title: S. mutans 0.025uM HP-29, rep 1

description: Library name: HP29-1


title: CRISPRa bulk screen day 33 replicate 2


title: [DDB_PD_065]_[SDT172_del_purR]_[Fed-batch]_[15h]_[R1]


title: CRISPRi bulk screen day 29 replicate 1


title: 15286X157_blastomere_513A_type_IVF_cell_number_4

description: cellnumber 4

value: IVF


title: 15286X156_blastomere_512D_type_IVF_cell_number_4

description: cellnumber 4


title: CRISPRa bulk screen day 33 replicate 1


title: [DDB_PD_065]_[SDT172_del_purR]_[Batch]_[0h]_[R2]


title: S. mutans BHI control, rep 3

description: Library name: Control3

value: BHI control


title: [DDB_PD_065]_[SDT172_del_purR]_[Batch]_[0h]_[R1]


title: Myometrium from fibroid patient (MyoF), patient MP306

description: Library name: MP306N

value: myometrium

value: H

value: Myometrium from fibroid patient


title: 15286X158_blastomere_513B_type_IVF_cell_number_4

description: cellnumber 4


title: [DDB_PD_065]_[SDT173_del_prpR]_[Fed-batch]_[15h]_[R2]


title: CRISPRa bulk screen day 20 replicate 1

value: CRISPR activation


title: S. mutans BHI control, rep 2

description: Library name: Control2


title: [DDB_PD_065]_[SDT173_del_prpR]_[Fed-batch]_[15h]_[R1]


title: 15286X155_blastomere_512C_type_IVF_cell_number_4

description: cellnumber 4


title: CRISPRa bulk screen day 5 replicate 2


title: [DDB_PD_065]_[SDT173_del_prpR]_[Batch]_[0h]_[R1]


title: CRISPRa bulk screen day 29 replicate 2


title: S. mutans BHI control, rep 1

description: Library name: Control1


title: CRISPRa bulk screen day 29 replicate 1


title: BJ control shRNA-1

description: Gene expression data from iPS cell line 20 derived from patient A


title: 15286X154_blastomere_512B_type_IVF_cell_number_4

description: cellnumber 4


title: [DDB_PD_065]_[SDT173_del_prpR]_[Batch]_[0h]_[R2]


title: Wildtype, PCB126, replicate 4

city: Woods Hole

first: Sibel

middle: I

last: Karchner

state: MA

address: 45 Water St

department: Biology

institute: Woods Hole Oceanographic Institution

description: Library name: AIPex2_WP4

data_processing:
Sequences were mapped to genome using STAR v2.7.10b.
Reads were counted using HTseq-count.
Assembly: Danio rerio genome Ensembl GRCz11.113.
Supplementary files format and content: HTseq read counts.

organism: Danio rerio

source_name: whole embryo

extract_protocol:
RNA was isolated using the Aurum total RNA mini kit (BioRad). 500 ng of RNA was used for each RNAseq library.
Illumina Stranded mRNA kit was used for library synthesis.

value: whole embryo

value: Wildtype


title: 15286X153_blastomere_512A_type_IVF_cell_number_4

description: cellnumber 4


title: [DDB_PD_065]_[SDT169_del_nac]_[Fed-batch]_[15h]_[R2]


title: 15286X152_blastomere_551D_type_IVF_cell_number_4

description: cellnumber 4


title: [DDB_PD_065]_[SDT169_del_nac]_[Fed-batch]_[15h]_[R1]


title: Wildtype, DMSO, replicate 4

description: Library name: AIPex2_WD4

value: DMSO


title: CRISPRa bulk screen day 5 replicate 1


title: 15286X151_blastomere_511C_type_IVF_cell_number_4

description: cellnumber 4


title: Wildtype, PCB126, replicate 2

description: Library name: AIPex2_WP2


title: Wildtype, PCB126, replicate 1

description: Library name: AIPex2_WP1


title: ATAC-seq in SK-N-SH cell line

data_processing:
ATAC-seq reads were trimmed for adapter content using flexbar (-f i1.8 -u 10 -ae RIGHT -at 1.0; (Dodt et al., 2012)), mapped to hg19 using bowtie2 (-X 1500 --no-discordant; reads eventually lifted over to hg38; see below; (Langmead and Salzberg, 2012), filtered for unique mapping reads (grep -v "XS:i:"), and collapsed for PCR duplicates using Picard Tools MarkDuplicates (http://broadinstitute.github.io/picard). Finally, the 5’ends of reads were selected and extended to account for the estimated footprint size of Tn5 on the DNA using bedtools slop (-l 15 -r 22 -s; (Adey et al., 2010; Quinlan and Hall, 2010); 11(12): R119). Peaks were called using JAMM (-e auto -b 100; (Ibrahim, Lacadie and Ohler, 2015)) on fragment extended reads.
Assembly: hg19
Supplementary files format and content: BigWig files

source_name: SK-N-SH

value: SK-N-SH


title: 15286X150_blastomere_511B_type_IVF_cell_number_4

description: cellnumber 4


title: ATAC-seq in NGP cell line

source_name: NGP

value: NGP


title: Wildtype, PCB126, replicate 3

description: Library name: AIPex2_WP3


title: ATAC-seq in SHSY-5Y cell line


title: [DDB_PD_065]_[SDT169_del_nac]_[Batch]_[0h]_[R2]


title: 15286X147_blastomere_582B_type_IVF_cell_number_3

description: cellnumber 3


title: 15286X146_blastomere_582A_type_IVF_cell_number_3

description: cellnumber 3


title: Wildtype, DMSO, replicate 3

description: Library name: AIPex2_WD3


title: [DDB_PD_065]_[SDT175_del_fur]_[Fed-batch]_[15h]_[R2]


title: [DDB_PD_065]_[SDT169_del_nac]_[Batch]_[0h]_[R1]


title: 15286X148_blastomere_582C_type_IVF_cell_number_3

description: cellnumber 3


title: [DDB_PD_065]_[SDT175_del_fur]_[Fed-batch]_[15h]_[R1]


title: [DDB_PD_065]_[SDT175_del_fur]_[Batch]_[0h]_[R1]


title: Wildtype, DMSO, replicate 2

description: Library name: AIPex2_WD2


title: ATAC-seq in CLB-Ga cell line

source_name: CLB-Ga

value: CLB-Ga


title: 15286X145_blastomere_581C_type_IVF_cell_number_3

description: cellnumber 3


title: 15286X149_blastomere_511A_type_IVF_cell_number_4

description: cellnumber 4


title: 38b_ANT1_NI

description:
IonCode_0112
IonCode_109-116.txt

value: Heart

value: C57BL/6JEiJ ANT1 -/-

value: 2.5x10^11 vg AAV2/9Des-Gfp


title: Homozygous, PCB126, replicate 2

description: Library name: AIPex2_HOP2

value: Homozygous mutant


title: 15286X144_blastomere_581B_type_IVF_cell_number_3

description: cellnumber 3


title: [DDB_PD_072]_[HMP3427_ZnFeHigh]_[Fed-batch]_[8h]_[R1]

value: Escherichia coli cells


title: SU 86.86  Cells pGIPZ-#2 (Replicate_3)

city: Birmingham

first: Narendra

last: Wajapeyee

state: AL

address: 720 20th Street South, Kaul 540A

department: Department of Biochemistry and Molecular Genetics

institute: University of Alabama at Birmingham

data_processing:
The reads were first mapped to the latest UCSC transcript set using Bowtie2 version 2.1.0 and the gene expression level was estimated using RSEM v1.2.15.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw count values for each Sample

source_name: SU 86.86  Cells

growth_protocol: SU.86.86 Cells  were grown in RPMI-1640  with 10% Fetal bovine serum and Penicilline and Streptomycin at  37 C under 5% CO2 condition.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen) as per the instruction from the manufacture and then purified using RNAeasy mini columns (Qiagen) as per the manufactures instructions.
mRNA is purified from approximately 500ng of total RNA with oligo-dT beads and sheared by incubation at 94C.  Following first-strand synthesis with random primers, second strand synthesis is performed with dUTP for generating strand-specific sequencing libraries.  The cDNA library is then end-repaired, and A-tailed, adapters are ligated and second-strand digestion is performed by Uricil-DNA-Glycosylase. Indexed libraries that meet appropriate cut-offs for both are quantified by qRT-PCR using a commercially available kit (KAPA Biosystems) and insert size distribution determined with the LabChip GX or Agilent Bioanalyzer. Samples with a yield of ≥0.5 ng/ul are used for sequencing.

treatment_protocol: SU.86.86 Cells used for preparing the total RNA and to perfrom gene expression array.

value: p53 shRNA#2 Expressing cells


title: Homozygous, PCB126, replicate 3

description: Library name: AIPex2_HOP3


title: [DDB_PD_065]_[SDT176_del_csgD]_[Fed-batch]_[15h]_[R2]


title: ATAC-seq in Kelly cell line

source_name: Kelly

value: Kelly


title: SU 86.86  Cells pGIPZ-#2 (Replicate_2)


title: SU 86.86  Cells pGIPZ-#2 (Replicate_1)


title: ATAC-seq in IMR-5 cell line


title: Homozygous, PCB126, replicate 1

description: Library name: AIPex2_HOP1


title: Wildtype, DMSO, replicate 1

description: Library name: AIPex2_WD1


title: Homozygous, PCB126, replicate 4

description: Library name: AIPex2_HOP4


title: [DDB_PD_065]_[SDT176_del_csgD]_[Batch]_[0h]_[R1]


title: Homozygous, DMSO, replicate 4

description: Library name: AIPex2_HOD4


title: 15286X142_blastomere_551C_type_IVF_cell_number_3

description: cellnumber 3

value: IVF


title: 15286X141_blastomere_551B_type_IVF_cell_number_3

description: cellnumber 3


title: [DDB_PD_065]_[SDT176_del_csgD]_[Batch]_[0h]_[R2]


title: SU 86.86  Cells pGIPZ-#1 (Replicate_2)

value: p53 shRNA#1 Expressing cells


title: Homozygous, DMSO, replicate 3

description: Library name: AIPex2_HOD3


title: 15286X140_blastomere_551A_type_IVF_cell_number_3

description: cellnumber 3


title: 15286X143_blastomere_581A_type_IVF_cell_number_3

description: cellnumber 3


title: SU 86.86  Cells pGIPZ-#1 (Replicate_1)


title: [DDB_PD_063]_[BL21(DE3)_NEB]_[Fed-batch]_[6h]_[R1]


title: 15286X139_blastomere_549C_type_IVF_cell_number_3

description: cellnumber 3


title: Homozygous, DMSO, replicate 2

description: Library name: AIPex2_HOD2


title: Homozygous, DMSO, replicate 1

description: Library name: AIPex2_HOD1


title: [DDB_PD_063]_[BL21(DE3)_NEB]_[Batch]_[0h]_[R1]


title: 15286X138_blastomere_549B_type_IVF_cell_number_3

description: cellnumber 3


title: Heterozygous, PCB126, replicate4

description: Library name: AIPex2_HEP4

value: Heterozygous mutant


title: [DDB_PD_063]_[DDB35_WT]_[Fed-batch]_[15h]_[R2]


title: SU 86.86  Cells pGIPZ-#1 (Replicate_3)


title: SU 86.86  Cells pGIPZ-NS (Replicate_1)

value: Non-silencing shRNA Expressing cells


title: Heterozygous, PCB126, replicate3

description: Library name: AIPex2_HEP3

value: whole embryo


title: [DDB_PD_063]_[DDB35_WT]_[Fed-batch]_[15h]_[R1]


title: [DDB_PD_063]_[BL21(DE3)_NEB]_[Fed-batch]_[15h]_[R1]


title: 15286X136_blastomere_515C_type_IVF_cell_number_3

description: cellnumber 3


title: [DDB_PD_063]_[DDB35_WT]_[Fed-batch]_[5h]_[R2]


title: SU 86.86  Cells pGIPZ-NS (Replicate_3)


title: Heterozygous, DMSO, replicate4

description: Library name: AIPex2_HED4


title: Heterozygous, PCB126, replicate1

description: Library name: AIPex2_HEP1


title: 15286X165_blastomere_516A_type_IVF_cell_number_4

description: cellnumber 4


title: 15286X134_blastomere_515A_type_IVF_cell_number_3

description: cellnumber 3


title: [DDB_PD_063]_[DDB35_WT]_[Fed-batch]_[5h]_[R1]


title: 15286X133_blastomere_510C_type_IVF_cell_number_3

description: cellnumber 3


title: risk2-5

city: West Hollywood

first: AGCT

last: Core

state: CA

address: 8687 Melrose Ave, PDC B230

department: BMS

institute: Cedars Sinai Medical Center

description:
stimulated CD4+ TE/M cells carrying rs6911490
risk2-5

data_processing:
Raw reads obtained from RNAseq were aligned to the transcriptome by using STAR (version 2.2.1) and expression for each gene was quantified by using RSEM (version 1.2.20) with default parameters. Reference genome is custom human GRCh38 transcriptome reference (from http://www.gencodegenes.org ), containing all protein coding and long non-coding RNA genes based on GENCODE version 23 annotation. Expression counts for each gene in all samples were normalized by a modified trimmed mean of the M-values normalization method and the unsupervised principal component analysis (PCA) was performed with DESeq2 Bioconductor package version 1.10.1 in R version 3.2.2. Each gene was fitted intoa negative binomial generalized linear model and Wald test was applied to assess thedifferential expressions between two sample groups by DESeq2. Benjamini and Hochbergprocedure was applied to adjust for multiple hypothesis testing and differential expressed genecandidates were selected with a false discovery rate less than 0.05. For visualization ofcoordinated gene expression in samples, a two-way hierarchical clustering with Pearsoncorrelation distance matrix was performed with samples and differential expressed genecandidates (1.5 fold) using the Bioconductor g-plots package (version 2.14.2) in R. The pathwayenrichment analysis was performed on these candidates with DAVID(https://david.ncifcrf.gov/summary.jsp) and Ingenuity Pathway Analysis (Qiagen). Expression foreach PRDM1 isoform was quantified as transcript per million (TPM) by using RSEM (version1.2.20). A two-tailed t-test was applied to assess the differential expressions of each isoform ofPRDM1 between two sample groups
Genome_build: custom human GRCh38 transcriptome reference (from http://www.gencodegenes.org ), containing all protein coding and long non-coding RNA genes based on GENCODE version 23 annotation
Supplementary_files_format_and_content: text files include raw counts for each Sample calculated by RSEM

source_name: stimulated CD4+ TE/M cells

growth_protocol: Peripheral blood was obtained from healthy volunteers or IBD patients after informed consent through the Cedars-Sinai MIRIAD IBD Biobank. Peripheral blood mononuclear cells (PBMC) were isolated by separation with lymphocyte separation media (Corning). Intestinal specimens were obtained (after informed consent) from the lamina propria of patients undergoing surgical resection of the colon at Cedars-Sinai Medical Center, Los Angeles. Approval for the use of human tissues was granted by the Institutional Review Board at Cedars-Sinai Medical Center. In this study, all tissue specimens were taken from involved or uninvolved areas from patients with UC and CD. Lamina propria mononuclear cells (LPMC) were isolated from the resection samples as previously described18. Genotyping (and associated quality control) of healthy control and patient donors samples are as described in supplemental methods.

extract_protocol:
RNA extraction with on-column DNase1 digestion was performed using the RNeasy kit (Qiagen) according to manufacturer’s instructions
Total RNA (extracted as described above in qRTPCR) was quantified using both, NanoDrop to assess sample contamination by proteins or carryover reagents from RNA isolation, and Qubit fluorometer (Invitrogen). Samples were then qualified using the Fragment Analyzer (Advanced Analytical Technologies, Ankeny, IA) to determine integrity of the total RNA by measuring the ratio between the 18S and 28S ribosomal peaks. RNAseq libraries maintaining strand-specificity were made using 10ng of material per sample with the SMARTer Ultra Low Input RNA v4 kit (Clontech), and indexed using Nextera indices (Illumina), according to the manufacturer’s instructions. Final libraries were again quantitated with the Qubit fluorometer and checked for size via the Fragment Analyzer. Libraries were diluted to 4nM and pooled in equal volumes for denaturation, hybridization, and sequencing on the Illumina NextSeq 500 (Illumina) with paired end 150bp sequencing chemistry .

treatment_protocol: CD4+T cells: healthy controls and IBD patients PBMC were enriched for CD4+ T cells using the human CD4+ T cell negative selection isolation kit (Stem Cell Technologies Inc) according to the manufacturer’s instructions and CD4+ TE/M (CD3+CD4+HLADR+CD45RO+CD25-/Low), regulatory (CD3+CD4+CD45RO+CD25high), or naïve (CD3+CD4+CD45RA+HLADR-) T cells were isolated by FACS sorting. In vitro stimulation of CD4+ T cells was performed by culture with plate-bound anti-CD3 (clone OKT3, purified over a protein G column and quantified by ELISA) and anti CD28 (clone 9.3, Bristol-Meyers Squibb Pharmaceutical Research Institute, Princeton, NJ) and recombinant human IL-2 (100ng/ml) (Proleukin®, Novartis) for 24 hours. Intestinal LPMC isolated from human intestinal resection were enriched for CD3+ or CD4+ T cells using cell enrichment kits (Stem Cell Technologies Inc) according to the manufacturer’s instructions and were used for DNA methylation analysis or Immunofluorescence, respectively.

value: stimulated CD4+ TE/M cells

value: peripheral blood

tag: rs6911490 snp risk allele carrier

value: yes

tag: diagnosis

value: ulcerative colitis


title: [DDB_PD_065]_[SDT176_del_csgD]_[Fed-batch]_[15h]_[R1]


title: risk2-9

description:
stimulated CD4+ TE/M cells carrying rs6911490
risk2-9


title: risk2-7

description:
stimulated CD4+ TE/M cells carrying rs6911490
risk2-7


title: Heterozygous, DMSO, replicate3

description: Library name: AIPex2_HED3

value: DMSO


title: Heterozygous, DMSO, replicate2

description: Library name: AIPex2_HED2


title: 15286X137_blastomere_549A_type_IVF_cell_number_3

description: cellnumber 3


title: 15286X132_blastomere_510B_type_IVF_cell_number_3

description: cellnumber 3


title: risk2-3

description:
stimulated CD4+ TE/M cells carrying rs6911490
risk2-3


title: 15286X131_blastomere_510A_type_IVF_cell_number_3

description: cellnumber 3


title: [DDB_PD_056]_[DDB35_parent_reactor]_[Fed-batch]_[20h]_[R2]


title: protective2-6

description:
stimulated CD4+ TE/M cells lacking rs6911490
protective2-6

value: no


title: Heterozygous, PCB126, replicate2

description: Library name: AIPex2_HEP2


title: Heterozygous, DMSO, replicate1

description: Library name: AIPex2_HED1


title: protective2-8

description:
stimulated CD4+ TE/M cells lacking rs6911490
protective2-8


title: 15286X130_blastomere_609B_type_IVF_cell_number_2

description: cellnumber 2


title: [DDB_PD_056]_[DDB35_parent_reactor]_[Fed-batch]_[20h]_[R1]


title: cv_mutant_9

city: Durham

first: John

middle: F

last: Rawls

state: North Carolina

address: 213 Research Drive

institute: Duke University School of Medicine

description: Library name: sample 16

data_processing:
sequence reads were trimmed using Trim Galore! (0.6.7+galaxy0) hosted on Galaxy server to remove adapter sequence and low quality sequence
trimmed sequence reads were mapped to GRCz11 (danRer11) with Lawson Lab Annotation gene model (v4.3.2.gtf) using RNA STAR (2.7.11a+galaxy1) hosted on the Galaxy server
read count extraction was performed using FeatureCounts program (2.0.3+galaxy2)
raw read counts were used as input for differential gene expression analysis using Deseq2
Assembly: GRCz11 (danRer11) with Lawson Lab Annotation gene model (v4.3.2.gtf)
Supplementary files format and content: tab-deliminted text file includes raw counts for each sample
Supplementary files format and content: tab deliminted Lawson Lab Annotation v4.3.2 gtf file (v4.3.2.gtf)

source_name: 6 dpf whole larvae

growth_protocol: larval zebrafish of both genotypes (elf3 mutant and wildtype) were derived germ-free and remained germ-free until 3 days post-fertilization. At 3 days post-fertilization, half of the larvae of each genotype were exposed to a conventional microbiota

extract_protocol:
total RNA was extracted from whole larval zebrafish using TRIzol-chloroform extraction followed by the PureLink RNA Mini Kit (Invitrogen)
mRNA libraries were constructed with KAPA HyperPrep kit

value: 6 dpf whole larvae

value: mutant

value: conventionalized


title: 15286X135_blastomere_515B_type_IVF_cell_number_3

description: cellnumber 3


title: [DDB_PD_063]_[DDB35_WT]_[Batch]_[0h]_[R2]

value: Escherichia coli cells


title: [DDB_PD_063]_[DDB35_WT]_[Batch]_[0h]_[R1]


title: protective2-4

description:
stimulated CD4+ TE/M cells lacking rs6911490
protective2-4


title: [DDB_PD_056]_[DDB35_child_reactor]_[Batch]_[0h]_[R2]


title: protective2-2

description:
stimulated CD4+ TE/M cells lacking rs6911490
protective2-2


title: [DDB_PD_056]_[DDB35_parent_reactor]_[Batch]_[0h]_[R2]


title: cv_mutant_8

description: Library name: sample 15


title: 15286X128_blastomere_608B_type_IVF_cell_number_2

description: cellnumber 2


title: [DDB_PD_056]_[DDB35_child_reactor]_[Batch]_[0h]_[R1]


title: cv_mutant_6

description: Library name: sample 14


title: HFD+STZ+ExT_KO2

city: Boston

first: Haobo

last: Li

address: MEDR410 / Lunder Bldg Dock, 255 Charles St

department: Department of Anesthesia, Critical Care, and Pain Medicine

institute: Massachusetts General Hospital and Harvard Medical School

description:
Library name: ExT_KO2
Whole heart tissue

data_processing:
Illumina Casava1.8 software used for basecalling.
Raw sequeence image files from the sequencer were converted to the fastq format and checked for quality: per base sequence quality, the per base sequence content, per base N content, sequence length distribution, adapter and k-mer content and sequence duplication levels are collected for each sequencing run using fastqc.
fastqs are then aligned to the mouse reference genome (mm10) using STAR46 aligner.
Alignment statistics such as average red length, percentage of uniquely mapped reads, percentage of multi-mapped reads and number of splice junctions are collated. Only reads that are uniquely mapped will be considered for read annotation to gene features. Reads are annotated with the ENSEMBL 75 gene transfer format (gtf) file using Salmon.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
Hearts were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. 1 ug of total RNA for the construction of sequencing libraries. Libraries were made with the RiboZero kit followed by the NEB RNA lib kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Heart

value: NAT10 knockout

value: HFD+STZ+Exercise


title: cv_mutant_7

description: Library name: sample 13


title: 15286X127_blastomere_608A_type_IVF_cell_number_2

description: cellnumber 2

value: IVF


title: [DDB_PD_045]_[SDT189_del_yieP]_[Batch]_[0h]_[R2]


title: 15286X126_blastomere_607B_type_IVF_cell_number_2

description: cellnumber 2


title: HFD+STZ+ExT_Con2

description:
Library name: ExT_CON2
Whole heart tissue

value: control


title: cv_mutant_10

description: Library name: sample 12


title: 15286X125_blastomere_607A_type_IVF_cell_number_2

description: cellnumber 2


title: [DDB_PD_045]_[SDT189_del_yieP]_[Batch]_[0h]_[R1]


title: HFD+STZ+ExT_Con1

description:
Library name: ExT_CON1
Whole heart tissue


title: cv_wildtype_6

description: Library name: sample 11

value: wildtype


title: cv_wildtype_5

description: Library name: sample 10


title: 15286X129_blastomere_609A_type_IVF_cell_number_2

description: cellnumber 2


title: [DDB_PD_045]_[SDT172_del_purR]_[Batch]_[0h]_[R2]


title: [DDB_PD_045]_[SDT172_del_purR]_[Batch]_[0h]_[R1]


title: 15286X123_blastomere_606A_type_IVF_cell_number_2

description: cellnumber 2


title: HFD+STZ+ExT_KO1

description:
Library name: ExT_KO1
Whole heart tissue


title: cv_wildtype_1

description: Library name: sample 9


title: 15286X124_blastomere_606B_type_IVF_cell_number_2

description: cellnumber 2


title: 220Math1Cre*PR mAchR4 fl/fl small intestine

city: St. Louis

first: Rodney

middle: D

last: Newberry

address: 660 S. Euclid Ave

department: Medicine

institute: Washington University School of Medicine

data_processing:
Partek Flow
Assembly: mus musculus mm10
Supplementary files format and content: .txt file with counts for each sample

source_name: small intestine

extract_protocol:
QIAGEN total RNA
rRNA depletion
Libraries prepared by Azenta per protocol

treatment_protocol: gavage 10mg/Kg RU486 daily for four days

value: small intestine

value: Cre+


title: 15286X122_blastomere_605B_type_IVF_cell_number_2

description: cellnumber 2


title: [DDB_PD_045]_[SDT173_del_prpR]_[Batch]_[0h]_[R2]


title: 218mAchR4 fl/fl small intestine

value: Cre-


title: SU 86.86  Cells pGIPZ-NS (Replicate_2)

value: Non-silencing shRNA Expressing cells


title: [DDB_PD_045]_[SDT177_del_proV]_[Batch]_[0h]_[R2]


title: gf_mutant 5

description: Library name: sample 7

value: germ-free


title: 15286X121_blastomere_605A_type_IVF_cell_number_2

description: cellnumber 2


title: [DDB_PD_045]_[SDT173_del_prpR]_[Batch]_[0h]_[R1]


title: 219Math1Cre*PR mAchR4 fl/fl small intestine


title: gf_mutant_4

description: Library name: sample 6


title: 217mAchR4 fl/fl small intestine


title: 216mAchR4 fl/fl small intestine


title: [DDB_PD_045]_[SDT177_del_proV]_[Batch]_[0h]_[R1]


title: 15286X119_blastomere_604A_type_IVF_cell_number_2

description: cellnumber 2


title: ccl4, scRNA-seq

city: Nanjing

first: xue

last: fan

address: 24 Tong Jia Xiang

country: China

institute: China Pharmaceutical University

description: 10× Genomics

library_source: transcriptomic single cell

data_processing:
The 10× Genomics analysis software CellRanger (http://support.10xgenomics.com/single-cell/software/overview/welcome)  was used to analyze the quality statistics of the raw data.
Assembly: mm10
Supplementary files format and content: matrix files
Supplementary files format and content: barcodes files

source_name: liver

extract_protocol:
The fresh samples were cut into small pieces after washing with Hanks balanced salt solution (HBSS). A mixture of hyaluronidase, collagenase I, and DNase I was used to digest the tissues at a constant low rate, and gradient centrifugation followed by using a 40 μm filter to remove tissue debris. Then, the cell suspensions were cleaned with DPBS solution excluding calcium and magnesium ions.
The 10× genomics technology platform was used for library construction. For specific experimental procedures, please refer to the descriptions of manufacter. The general procedures are as follows: single-cell suspensions are injected and combined with gel beads containing barcode information  with a mixture of cells and enzymes. Then, it enters the reservoir separated by oil to form GEMs, ensuring that the mRNA in cells is only bound to the captured sequences of one gel bead. Subsequently, the gel beads within the GEMs were dissolved, and the cells were lysed to release mRNA, which was reverse-transcribed to produce the barcoded cDNA for sequencing. After the liquid oil reservoir was disrupted, PCR amplification was performed using cDNA as a template.

value: liver


title: [DDB_PD_045]_[SDT169_del_nac]_[Batch]_[0h]_[R2]

data_processing:
First, raw read trimming was performed using Trim Galore with default options, followed by FastQC on the trimmed reads. Next, reads were aligned to the E. coli K-12 MG1655 reference genome (NC_000913.3) using Bowtie. The read direction was inferred using RSeQC. Read counts were generated using featureCounts. All quality control metrics were compiled using MultiQC. Finally, the expression dataset was reported in units of log-transformed transcripts per million (log(TPM).
Assembly: Reference genome E. coli MG1655 (NC_000913.3)
Supplementary files format and content: Raw data files and comma-delimited text file reporting logtpm values for each sample


title: control, scRNA-seq

description: 10× Genomics


title: gf_mutant_2

description: Library name: sample 4


title: 15286X117_blastomere_603A_type_IVF_cell_number_2

description: cellnumber 2


title: cv_wildtype_10

description: Library name: sample 8


title: 15286X120_blastomere_604B_type_IVF_cell_number_2

description: cellnumber 2


title: gf_wildtype_7

description: Library name: sample 3


title: 15286X116_blastomere_602B_type_IVF_cell_number_2

description: cellnumber 2


title: gf_wildtype_4

description: Library name: sample 2


title: Cre_PMA_3

city: Yangzhou

first: Guotao

last: Lu

address: 368 Hanjiang Middle Road, Yangzhou

institute: The Affiliated Hospital of Yangzhou University, Yangzhou University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were timmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit 0.05)
Timmed sequence reads were mapped to GrCM38m10 using CLC geromic benchwok (parameters- mismath cost 2 insertion cost 3 deleton cost 3 length fracion: 0.8 similarity ftaction- 0.8
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10

source_name: primary neutrophils

growth_protocol: Primary neutrophils were aintained in RPMI 1640 suplemented with 10% fetal bovne serum (FBS)  in humidfed atmosphere with 5% CO2 at 37°C

extract_protocol:
RNA was havested using Rneasy mini plus kit (Qiagen). 2 ug of total RNA was used for the construction of sequencing libraries
RNA libraries for RNA-seg were prepared using SMARTER mRNA-Seg Library Prep Kit following manufacturer's protocols.

treatment_protocol: NETs formation was induced by adding 100 nM Phorbol 12-myristate 13-acetate (PMA) for 4 h.

value: primary neutrophils

value: Src fl/fl S100a8 Cre


title: 15286X115_blastomere_602A_type_IVF_cell_number_2

description: cellnumber 2

data_processing:
RNA-seq reads were trimmed and filtered for quality using BBDuk and FastQC (version 0.10.1).
Processed reads were aligned to bostau7 with Bowtie2 (v2.2.6) with the following parameters: (--t --q --N1 --L 25 --X 2000 --no-mixed --no-discordant).
PCR duplicates were removed using bedtools
mitochondrial reads were removed using sed '/chrM/d'
counts for each ATACseq union region were generated using ‘Get datasets’ (https://metacpan.org/pod/distribution/Bio-ToolBox/scripts/get_datasets.pl).
Assembly: bostau7
Supplementary files format and content: 20230629-scATAC-seq-cell-ID-conversion.xls excel file containing sample ID and information
Supplementary files format and content: 20180822-scATAC-819-cells-vs-302830-regions.tabular count file for n=819 retained high quality scATACseq libraries in ATAC-seq peaks regions created as a union dataset, tabular format


title: [DDB_PD_045]_[SDT175_del_fur]_[Batch]_[0h]_[R2]

source_name: Escherichia coli cells


title: Cre_PMA_2


title: gf_wildtype_3

description: Library name: sample 1

value: 6 dpf whole larvae


title: Cre_PMA_1


title: Wildtype, PCB126, replicate 4

description: Library name: AIPex5_WP4

data_processing:
Sequences were mapped to genome using STAR v2.7.10b.
Reads were counted using HTseq-count.
Assembly: Danio rerio genome Ensembl GRCz11, v84.
Supplementary files format and content: HTseq read counts.

value: whole embryo

value: Wildtype


title: [DDB_PD_045]_[SDT179_del_fnr]_[Batch]_[0h]_[R1]

value: Escherichia coli cells


title: Flox_PMA_3

value: Src fl/fl


title: [DDB_PD_045]_[SDT175_del_fur]_[Batch]_[0h]_[R1]


title: [DDB_PD_045]_[SDT179_del_fnr]_[Batch]_[0h]_[R2]


title: 15286X114_blastomere_601B_type_IVF_cell_number_2

description: cellnumber 2


title: Flox_PMA_2


title: [DDB_PD_045]_[SDT176_del_csgD]_[Batch]_[0h]_[R2]


title: Wildtype, PCB126, replicate 3

description: Library name: AIPex5_WP3


title: 15286X113_blastomere_601A_type_IVF_cell_number_2

description: cellnumber 2


title: 15286X112_blastomere_600B_type_IVF_cell_number_2

description: cellnumber 2


title: Flox_PMA_1


title: 15286X111_blastomere_600A_type_IVF_cell_number_2

description: cellnumber 2


title: ParBF-R156A, E. coli, F, IP2

city: Toulouse

first: Jean-Yves

last: Bouet

address: 169 avenue Marianne Grunberg-Manago

country: France

institute: CNRS

description:
Library name: ParBF-R156A_E.coli_F1-10B17_IP009
Mapped reads: 17206334; average fragment size: 159

data_processing:
Basecalls and alignment performed using Torrent_Suite 5.12.1
ChIP-seq reads were aligned to the corresponding genomes of reference, including the plasmids content.
The F plasmid reads were counted in the centre of DNA fragment according to each average librairy size.
The F plasmid reads, substracted from background, were binned with a window and a step of 40 and 20, respectively.
The counting of reads over the genomic sequences was performed using bedtools 2.26.0 with the tool genomecov and the options -d, -s, -strand and -ibam
Assembly: Escherichia coli str. K-12 substr. MG1655 ASM584v2
Supplementary files format and content: The counting of reads over the genomic sequences

source_name: bacterial cell

growth_protocol: Samples were prepared from exponential  phase cultures of E. coli  in LB media (OD600 ~0.5) at 37°C

extract_protocol:
Lysates were clarified from sonicated cell and protein-DNA complexes were isolated with anti ParBF antibody
A maximum of 2 ng of ChIP DNA was used to synthetize the library as described in manufacturer’s instructions (Ion ChIP-Seq Library Preparation on the Ion Proton™ System - revision B - Step10). The last size selection was modified by a double size selection (0.55X/0.25X) of binding to AMPure® XP beads followed by a step of wash and elution. Then, qualification and quantification were made with the Bioanalyzer - Agilent, Santa Clara, CA

treatment_protocol: Cells were treated with formalhedyde (1 %)

value: bacterial cell

value: thi leu thyA deoB supE rpsL, D(ara-leu), zac3051::Tn10 / F1-10B17 (ParBF-R156A)

tag: plasmid

tag: chip antibody

value: anti ParBF


title: Wildtype, PCB126, replicate 2

description: Library name: AIPex5_WP2


title: [DDB_PD_045]_[SDT178_del_cra]_[Batch]_[0h]_[R2]


title: [DDB_PD_045]_[SDT176_del_csgD]_[Batch]_[0h]_[R1]


title: Wildtype, PCB126, replicate 1

description: Library name: AIPex5_WP1


title: 15286X110_blastomere_599B_type_IVF_cell_number_2

description: cellnumber 2

source_name: IVF

value: IVF


title: 15286X109_blastomere_599A_type_IVF_cell_number_2

description: cellnumber 2


title: ParBF-R156A, E. coli, F, input2

description:
Library name: ParBF-R156A_E.coli_F1-10B17_input010
Mapped reads: 6325043; average fragment size: 164


title: Wildtype, DMSO, replicate 4

description: Library name: AIPex5_WD4

value: DMSO


title: ParBF-R156A, E. coli, F, IP1

description:
Library name: ParBF-NR156_E.coli_F1-10B17_IP011
Mapped reads: 22452962; average fragment size: 197


title: Wildtype, DMSO, replicate 3

description: Library name: AIPex5_WD3


title: [DDB_PD_038]_[SDT64]_[Fed-batch]_[13h]_[R2]


title: 15286X108_blastomere_598B_type_IVF_cell_number_2

description: cellnumber 2


title: Wildtype, DMSO, replicate 2

description: Library name: AIPex5_WD2


title: 15286X107_blastomere_598A_type_IVF_cell_number_2

description: cellnumber 2


title: ParBF-R156A, E. coli, F, input1

description:
Library name: ParBF-R156A_E.coli_F1-10B17_input008
Mapped reads: 6003273; average fragment size: 179


title: ParBF-N153A, E. coli, F, IP2

description:
Library name: ParBF-N153A_E.coli_F1-10B16_IP007
Mapped reads: 30177537; average fragment size: 158

value: thi leu thyA deoB supE rpsL, D(ara-leu), zac3051::Tn10 / F1-10B16 (ParBF-N153A)


title: [DDB_PD_038]_[SDT64]_[Fed-batch]_[3h]_[R2]


title: [DDB_PD_045]_[SDT178_del_cra]_[Batch]_[0h]_[R1]


title: 15286X106_blastomere_597B_type_IVF_cell_number_2

description: cellnumber 2


title: Homozygous, PCB126, replicate 4

description: Library name: AIPex5_HOP4

value: Homozygous mutant


title: [DDB_PD_045]_[SDT169_del_nac]_[Batch]_[0h]_[R1]


title: Wildtype, DMSO, replicate 1

description: Library name: AIPex5_WD1


title: 15286X118_blastomere_603B_type_IVF_cell_number_2

description: cellnumber 2


title: 15286X105_blastomere_597A_type_IVF_cell_number_2

description: cellnumber 2


title: [DDB_PD_038]_[SDT64]_[Fed-batch]_[3h]_[R1]


title: [DDB_PD_038]_[SDT64]_[Fed-batch]_[13h]_[R1]


title: [DDB_PD_038]_[SDT64]_[Batch]_[0h]_[R2]


title: 15286X104_blastomere_596B_type_IVF_cell_number_2

description: cellnumber 2


title: Homozygous, PCB126, replicate 3

description: Library name: AIPex5_HOP3


title: ParBF-N153A, E. coli, F, IP1

description:
Library name: ParBF-N153A_E.coli_F1-10B16_IP010
Mapped reads: 20363476; average fragment size: 195


title: Homozygous, PCB126, replicate 2

description: Library name: AIPex5_HOP2


title: ParBF-N153A, E. coli, F, input1

description:
Library name: ParBF-N153A_E.coli_F1-10B16_input007
Mapped reads: 4754056; average fragment size: 189

value: thi leu thyA deoB supE rpsL, D(ara-leu), zac3051::Tn10 /F1-10B16 (ParBF-N153A)


title: 15286X103_blastomere_596A_type_IVF_cell_number_2

description: cellnumber 2


title: [DDB_PD_038]_[SDT162_GenRed]_[Fed-batch]_[13h]_[R1]


title: 15286X102_blastomere_595B_type_IVF_cell_number_2

description: cellnumber 2


title: [DDB_PD_038]_[SDT162_GenRed]_[Fed-batch]_[13h]_[R2]


title: Homozygous, DMSO, replicate 4

description: Library name: AIPex5_HOD4


title: Glut1 deltaRCM#1 GFP- 4

city: Freiburg

first: Valérie

last: Hilgers

address: Stübeweg 51

institute: MPI of Immunobiology and Epigenetics

description: Library name: Glut1deltaRCM#1_GFP-_4

data_processing:
Bases were called on an Illumina NovaSeq 6000 platform
Assembly: D. melanogaster Assembly: dm6_ensembl ; D. melanogaster Annotation: ensembl release 96
Supplementary files format and content: tsv file format, with the gene counts for all the included samples of the  dataset

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: whole 18-20 hour old embryos

growth_protocol: Flies were grown in 25C on standard apple juice based food

extract_protocol:
RNA was purified with TRIzol LS Reagent (Ambion 10296028) according to the manufacturer’s instructions.
Illumina Stranded mRNA Prep -- Ligation, 2x150 bp reads

value: whole 18-20 hour old embryos

value: whole embryos


title: [DDB_PD_038]_[SDT162_GenRed]_[Fed-batch]_[3h]_[R1]


title: Homozygous, DMSO, replicate 2

description: Library name: AIPex5_HOD2


title: 15286X101_blastomere_595A_type_IVF_cell_number_2

description: cellnumber 2


title: Glut1 deltaRCM#1 GFP- 2

description: Library name: Glut1deltaRCM#1_GFP-_2


title: Homozygous, DMSO, replicate 3

description: Library name: AIPex5_HOD3


title: Glut1 deltaRCM#1 GFP- 1

description: Library name: Glut1deltaRCM#1_GFP-_1


title: 15286X100_blastomere_594B_type_IVF_cell_number_2

description: cellnumber 2


title: 15286X099_blastomere_594A_type_IVF_cell_number_2

description: cellnumber 2


title: [DDB_PD_038]_[SDT162_GenRed]_[Fed-batch]_[3h]_[R2]


title: Glut1 deltaRCM#1 GFP+ 4

description: Library name: Glut1deltaRCM#1_GFP+_4


title: Homozygous, DMSO, replicate 1

description: Library name: AIPex5_HOD1


title: 15286X098_blastomere_593B_type_IVF_cell_number_2

description: cellnumber 2


title: Glut1 deltaRCM#1 GFP- 3

description: Library name: Glut1deltaRCM#1_GFP-_3


title: Heterozygous, PCB126, replicate4

description: Library name: AIPex5_HEP4

value: Heterozygous mutant


title: Glut1 deltaRCM#1 GFP+ 3

description: Library name: Glut1deltaRCM#1_GFP+_3


title: [DDB_PD_038]_[SDT64]_[Batch]_[0h]_[R1]


title: [DDB_PD_038]_[SDT162_GenRed]_[Batch]_[0h]_[R1]


title: Glut1 deltaRCM#1 GFP+ 2

description: Library name: Glut1deltaRCM#1_GFP+_2


title: Heterozygous, PCB126, replicate3

description: Library name: AIPex5_HEP3


title: 15286X095_blastomere_578A_type_IVF_cell_number_2

description: cellnumber 2


title: Heterozygous, PCB126, replicate2

description: Library name: AIPex5_HEP2


title: Homozygous, PCB126, replicate 1

description: Library name: AIPex5_HOP1


title: Heterozygous, PCB126, replicate1

description: Library name: AIPex5_HEP1


title: Glut1 deltaRCM#2 GFP- 3

description: Library name: Glut1deltaRCM#2_GFP-_3


title: Glut1 deltaRCM#2 GFP- 4

description: Library name: Glut1deltaRCM#2_GFP-_4


title: [DDB_PD_038]_[SDT158_GenRed]_[Batch]_[0h]_[R1]


title: [DDB_PD_038]_[SDT162_GenRed]_[Batch]_[0h]_[R2]


title: 15286X093_blastomere_577A_type_IVF_cell_number_2

description: cellnumber 2


title: 15286X096_blastomere_578B_type_IVF_cell_number_2

description: cellnumber 2


title: [DDB_PD_038]_[SDT122_WT]_[Fed-batch]_[13h]_[R2]


title: ParBF-N153A, E. coli, F, input2

description:
Library name: ParBF-N153A_E.coli_F1-10B16_input008
Mapped reads: 6155443; average fragment size: 164


title: Heterozygous, DMSO, replicate3

description: Library name: AIPex5_HED3


title: Heterozygous, DMSO, replicate2

description: Library name: AIPex5_HED2


title: Glut1 deltaRCM#2 GFP- 1

description: Library name: Glut1deltaRCM#2_GFP-_1


title: [DDB_PD_038]_[SDT122_WT]_[Fed-batch]_[13h]_[R1]


title: 15286X091_blastomere_576A_type_IVF_cell_number_2

description: cellnumber 2


title: Glut1 deltaRCM#1 GFP+ 1

description: Library name: Glut1deltaRCM#1_GFP+_1


title: [DDB_PD_038]_[SDT122_WT]_[Fed-batch]_[3h]_[R2]


title: [DDB_PD_038]_[SDT158_GenRed]_[Fed-batch]_[3h]_[R1]


title: Heterozygous, DMSO, replicate1

description: Library name: AIPex5_HED1


title: 15286X090_blastomere_575B_type_IVF_cell_number_2

description: cellnumber 2


title: Dam_3

city: Bronx

first: Matanel

last: Yheskel

state: NY

address: 1300 Morris Park

institute: Albert Einstein College of Medicine

description:
Library name: Dam_3
DamID background

data_processing:
Raw reads quality controlled and trimmed using rfastp (v 1.6.0) and were aligned using Rsubread (2.10.5) to the dm6 Drosophila melanogaster genome assembly
Assembly: dm6
Supplementary files format and content: averaged bigwig files
Library strategy: Targeted DamID

source_name: Brain

extract_protocol:
Samples were homogenized in 75μl UltraPure Distilled Water and 20 μl 500 mM EDTA then digested with Proteinase K for 1.5h. DNA extraction was performed using the Zymo Quick-DNA Miniprep Plus Kit (Zymo, D3024). DpnI digestion, PCR adaptor ligation, DpnII digestion, and PCR amplification were performed as described. DNA was sonicated using a Diagenode Bioruptor Pico for 6 cycles (30s on/90s off at 4°C), and DNA fragments were analyzed using an Agilent Bioanalyzer to confirm ∼300 bp fragment size.
DamID adaptor removal and DNA cleanup were performed as previously described, and samples were submitted to BGI Genomics for library construction and sequencing. Libraries were prepared at BGI Genomics following a ChIP-seq workflow and sequenced on the NovaSeq S4.

value: Brain

value: WT


title: Heterozygous, DMSO, replicate4

description: Library name: AIPex5_HED4

value: whole embryo


title: [DDB_PD_038]_[SDT158_GenRed]_[Batch]_[0h]_[R2]

city: Kgs. Lyngby

first: Felix

last: Beulig

address: Kemitorvet 220

institute: Novo Nordisk Center for Biosustainability

extract_protocol:
All transcriptome samples were collected and prepared in biological duplicates, whereby either 2 ml of culture (low cell density culture, batch phase) or 0.5 ml of culture (high cell density culture, fed batch phase) was added to 6 ml of Qiagen RNA-protect Bacteria Reagent immediately after sample collection. This solution was then vortexed for 30 seconds, incubated at room temperature for 5 minutes, and then centrifuged. The supernatant was then removed and the cell pellet was stored at -80° C. The RNeasy Mini Kit (Qiagen) was used to extract and purify RNA from the cell pellets per vendor protocol, including on-columns DNase treatment for 30 minutes at room temperature. RNA was quantified using qubit fluorometer (Thermofisher) and integrity was assessed using fragment analyzer (Agilent Technologies).
Ribosomal RNA was removed using QIAseq FastSelect –5S/16S/23S kit (Qiagen). Sequencing libraries were prepared with the KAPA Stranded RNA-Seq Library Preparation Kit (Kapa Biosystems) and assessed using fragment analyzer (Agilent Technologies). The libraries were then subjected to paired end sequencing on Illumina Nextseq using Nextseq Mid Output kit (Illumina) with a read length of 150 bp.


title: 15286X094_blastomere_577B_type_IVF_cell_number_2

description: cellnumber 2


title: Glut1 deltaRCM#2 GFP- 2

description: Library name: Glut1deltaRCM#2_GFP-_2


title: Dam_2

description:
Library name: Dam_2
DamID background


title: Glut1 deltaRCM#2 GFP+ 2

description: Library name: Glut1deltaRCM#2_GFP+_2


title: 15286X089_blastomere_575A_type_IVF_cell_number_2

description: cellnumber 2


title: [DDB_PD_038]_[SDT122_WT]_[Batch]_[0h]_[R2]


title: gf_mutant_3

description: Library name: sample 5

value: 6 dpf whole larvae

value: mutant

value: germ-free


title: 15286X092_blastomere_576B_type_IVF_cell_number_2

description: cellnumber 2


title: Glut1 deltaRCM#2 GFP+ 1

description: Library name: Glut1deltaRCM#2_GFP+_1


title: 15286X087_blastomere_574A_type_IVF_cell_number_2

description: cellnumber 2


title: Dam_1

description:
Library name: Dam_1
DamID background


title: [DDB_PD_038]_[SDT122_WT]_[Batch]_[0h]_[R1]

value: Escherichia coli cells


title: w1118_RNAseq_3

city: Madison

first: Melissa

last: Harrison

state: Wisconsin

address: 6204B Biochemical Sciences Building, 440 Henry Mall

department: Biomolecular Chemistry

institute: University of Wisconsin- Madison

data_processing:
The analysis was performed using the nf-core/rnaseq best-practice analysis pipeline (10.5281/zenodo.1400710).
Assembly: dm6
Supplementary files format and content: Aligned reads were annotated to genes using FeatureCounts 2.0 in a stranded mode.

source_name: Embryo 2h15min-3h (nc14)

growth_protocol: Drosophila embryos were collected at 25˚C for 45 min on apple juice agar plates and aged for 2 hours 15 minutes afterwords.

extract_protocol:
After collection, embryos were dechorionated in bleach and added to Trizol. After chloroform extraction, RNA was purified with RNEasy Mini Elute Clean up Kit (Qiegen).
Libraries were prepared with the TrueSeq Stranded mRNA kit and sequenced on a NovaSeq 6000.

value: Embryo 2h15min-3h (nc14)


title: 15286X086_blastomere_573B_type_IVF_cell_number_2

city: dallas

first: Edward

last: Grow

address: 7053 beltau lane

institute: UTSW

description: cellnumber 2

extract_protocol:
ATAC-seq was performed using 2x Tris-DMF-tagmentation buffer (10mM Tris-pH=8.0, 5mM MgCl, 20% DMF). Add (batch-determined actitivty) 2 to 2.5 uL of Nextera Tn5 transposase (Cat# FC-121-1030, Illumina. Samples were incubated at 37C for 30 minutes in a PCR machine. The reactions were stopped with 0.5uL of 10% SDS, pipetted up and down, and placed on ice 5 min. 5x volume of PB buffer was added to the ATAC-seq reaction and purified using a ampure beads and eluted in 10mM Tris-pH=8.0 + 1mM EDTA.
Libraries were PCR amplified in 25uL reaction volumes using custom Nextera PCR primers from Buenrostro, et al. Nature 2015. PCR reaction conditions: ~10uL tagmented DNA, 12.5 uL of 2xphusion PCR mastermix (Phusion High-Fidelity PCR Master Mix with HF Buffer - 100 rxns, NEB, cat #M0531S), 0.625uL of 100uM F primer, 0.625uL of 100uM R primer. QS to 50uL total with H20. Do 5 cycles of “pre-amp” PCR. PCR cycling conditions: 72C incubation for 5 min. 5 cycles of the following: 95C for 30 sec, 72C for 90 sec. Remove 5uL of the “pre-PCR” reaction for qPCR. qPCR reaction conditions: 20uL qPCR reaction: 5uL of pre-amp PCR product, 10 ul of 2x syber (SsoAdvanced SYBR Green Supermix, Biorad catalog #1725275), 0.25uL of 100uM F primer, 0.25uL of 100uM R primer. Run 30-40 cycles of qPCR with the same cycling conditions as above. Select the additional number of PCR cycles to perform as per Buenrostro, et al. Nature Methods 2013. Ampure bead purification (Beckman Coulter, catalog # A63881) as per manufacturer’s instructions.
Nextera tagmentation


title: [DDB_PD_036]_[DDB35_ZnHigh]_[Fed-batch]_[16h]_[R2]


title: TaDa_L854F_2

description:
Library name: TaDa_L854F_2
TaDa for L854F


title: [DDB_PD_036]_[DDB35_ZnHigh]_[Fed-batch]_[16h]_[R1]


title: w1118_RNAseq_2


title: TaDa_L854F_1

description:
Library name: TaDa_L854F_1
TaDa for L854F


title: [DDB_PD_038]_[SDT122_WT]_[Fed-batch]_[3h]_[R1]


title: Glut1 deltaRCM#2 GFP+ 3

description: Library name: Glut1deltaRCM#2_GFP+_3


title: w1118_RNAseq_1


title: Glut1 deltaRCM#2 GFP+ 4

description: Library name: Glut1deltaRCM#2_GFP+_4


title: [DDB_PD_036]_[DDB35_ZnLow]_[Fed-batch]_[6h]_[R1]


title: 15286X088_blastomere_574B_type_IVF_cell_number_2

description: cellnumber 2


title: TaDa_JmjC_2

description:
Library name: TaDa_JmjC_2
TaDa for JmjC

value: JmjC


title: [DDB_PD_036]_[DDB35_ZnLow]_[Fed-batch]_[6h]_[R2]


title: 15286X083_blastomere_572A_type_IVF_cell_number_2

description: cellnumber 2

value: IVF


title: 15286X097_blastomere_593A_type_IVF_cell_number_2

description: cellnumber 2


title: TaDa_JmjC_3

description:
Library name: TaDa_JmjC_3
TaDa for JmjC


title: TaDa_JmjC_1

description:
Library name: TaDa_JmjC_1
TaDa for JmjC


title: 15286X084_blastomere_572B_type_IVF_cell_number_2

description: cellnumber 2


title: CBPHAT_RNAseq_2

value: CBPHAT FRT19A


title: [DDB_PD_036]_[DDB35_ZnLow]_[Batch]_[0h]_[R2]


title: 15286X082_blastomere_571B_type_IVF_cell_number_2

description: cellnumber 2


title: CBPHAT_RNAseq_1


title: TaDa_WT_3

description:
Library name: TaDa_WT_3
TaDa for WT


title: 15286X085_blastomere_573A_type_IVF_cell_number_2

description: cellnumber 2


title: TaDa_WT_2

description:
Library name: TaDa_WT_2
TaDa for WT


title: [DDB_PD_036]_[DDB35_ZnHigh]_[Batch]_[0h]_[R2]


title: TaDa_WT_1

description:
Library name: TaDa_WT_1
TaDa for WT


title: 15286X079_blastomere_570A_type_IVF_cell_number_2

description: cellnumber 2


title: 15286X080_blastomere_570B_type_IVF_cell_number_2

description: cellnumber 2


title: CBPHAT_RNAseq_3


title: [DDB_PD_036]_[SDT107_ZnLow]_[Fed-batch]_[6h]_[R1]


title: [DDB_PD_036]_[DDB35_ZnHigh]_[Batch]_[0h]_[R1]


title: S2-Zld_CuSO4_DMSO_R1

data_processing:
Adapter sequences were trimmed from reads using NGmerge v0.377.
Bowtie2 v2.4.478 was used to align trimmed reads to the dm6 reference genome with a mapping quality threshold of ≥ 30. Reads with a poor mapping quality or aligned to mitochondrial or scaffold DNA were thrown out. For analysis, only fragment sizes smaller than 100bp were used.
Assembly: dm6
Supplementary files format and content: bigwig files were formed from merged replicates and z-score normalized

growth_protocol: Drosophila embryos were maintained at 25˚C on molasses plates for 90mins after egg laying in which they were mounted for live imaging on a fluorescent scope and precisely staged by nuclear density at nuclear cycle 10 for catalytic inactivation experiments or 15min into nuclear cycle 14 for CBP knockdown experiments. S2 cells were cultured in Schneider’s medium with supplemented antibiotic/antimycotic and 10% FBS at 27 ˚C.

extract_protocol:
Embryos were collected and washed prior to mounting in halocarbon oil on a glass bottom dish. Real time staging of embryos was possible through the His2av-RFP marker used to measure nuclear density (nuclei/2500µm2). Live imaging was performed on a Nikon Eclipse Ti2 inverted fluorescent microscope. Embryos were processed for ATACseq exactly 15 min into NC14. For optogenetic experiments, His2Av-RFP and CBPCRY2;His2Av-RFP embryos were treated with a repeating sequence of 60s exposure to 470nm filtered light followed immediately by a 10 ms exposure to 555nm. This sequence was initiated upon entry into NC10 and ended 15 min into nuclear-cycle 14. Staged single embryos were picked and homogenized in 10µL of pre-chilled lysis buffer (10mM Tris pH 7.5, 10mM NaCl, 3mM MgCl2, 0.1%NP-40). Embryo homogenate was resuspended by adding an additional 40µL of lysis buffer and spun down at 500g for 10 min at 4˚C. The supernatant was removed under a dissecting scope to ensure the small pellet was not disturbed. 2.5µL of water, 2.5µL of Tn5 enzyme, and 5µL of TD buffer (Illumina Tagment DNA Enzyme and Buffer Kit) were added to resuspend the pellet, followed by a 37˚C incubation for 30 min. ATAC-seq in S2 cells was carried out similarly, in which 200,000 cells were spun down for 3min at 600g at 4˚C, washed with 1X PBS, and resuspended in 100μL lysis buffer. Lysed cell material was pelleted after centrifuging for 10min at 600g at 4˚C. The supernatant was replaced with 47.5UL TD buffer and 2.5 Tn5 enzyme (Illumina) and incubated at 37˚C for exactly 30min.
Libraries were prepared using IDT for Illumina Nextera DNA Unique Dual indices, and PCR amplified with NEBNext Hi-Fi 2x PCR Master Mix (72˚C for 5min, 98˚C for 30s, followed by 12 cycles of 98˚C for 10s, 63˚C for 30s, and 72˚C for 1min). Libraries were DNA purified using magnetic axygen beads and washed with ethanol (Thermo Fisher Scientific).

treatment_protocol: S2 cells were induced to express Zld using CuSO4, and were treated either with control DMSO drug or a CBP catalytic inhibitor A485.

value: 1000 uM CuSO4

tag: condition

value: DMSO


title: S2-Zld_A-485_R2

value: 0 uM CuSO4


title: 15286X078_blastomere_569B_type_IVF_cell_number_2

description: cellnumber 2


title: S2-Zld_CuSO4_DMSO_R2


title: S2-Zld_CuSO4_A-485_R2

value: 400 uM CuSO4


title: Dreamboy whole genome sequencing

data_processing:
WGS reads were trimmed and filtered for quality using BBDuk and FastQC (version 0.10.1).
Processed reads were aligned to bostau7 with Bowtie2 (v2.2.6) with the following parameters: (--t --q --N1 --L 25 --X 2000 --no-mixed --no-discordant).
PCR duplicates were removed using bedtools
VarScan.v2.4.2 to identify homozygous SNVs using command “--min-coverage 20 --min-var-freq 0.1  --p-value 0.05”.
Homozygous SNVs exclusively found in Dreamboy were identified using VarScan.v2.4.2.jar  compare
Assembly: Bostau7
Supplementary files format and content: VCF= Varscan output of SNVs found with indivated variant detected
Library strategy: whole genome sequencing

organism: Bos indicus

source_name: semen

growth_protocol: Cells were maintained in DMEM-high glucose (Thermo-Fisher 11965118) + 10% FBS, 1X Non-essential amino acids, 1X glutamax, 1X penicillin/streptomycin at 20% oxygen, and passaged using trypsin every 2-5 days.

extract_protocol:
genomic DNA was extracted using phenol:chlorform:isoamyl alcohol and precipitated with sodium acetated and ethanol at -80C for 20 min
gDNA was tagmented using Nextera XT DNA Library Preparation Kit (Illumina catalog #FC-131-1024) and libraries were amplified by PCR

treatment_protocol: Cumulus cells were harvested with trypsinization from expanded COC complexes, semen genomic DNA was harvested directly from cryopreserved samples.

tag: tissue

value: semen

value: male


title: [DDB_PD_036]_[SDT107_ZnLow]_[Batch]_[0h]_[R1]


title: [DDB_PD_036]_[DDB35_ZnLow]_[Batch]_[0h]_[R1]


title: S2-Zld_CuSO4_A-485_R1


title: 15286X081_blastomere_571A_type_IVF_cell_number_2

description: cellnumber 2


title: 15286X077_blastomere_569A_type_IVF_cell_number_2

description: cellnumber 2


title: TNFa and Af 3 Sample 24

first: Jatin

last: Vyas

address: 55 Fruit Street

institute: Massachusetts General Hospital

hyb_protocol: 25 ng of total RNA were used for hybridization reactions at 65C for 22h and loaded onto a Sprint cartridge

scan_protocol: Data was captured using nCounter SPRINT Profiler (NanoString Technologies)

data_processing: Data analyses was performed using nSolver 4.0. To adjust for differences in total RNA per lane, hybridization efficiency, and post-hybridization processing, the counts of 733 target RNAs were normalized based on negative controls (background subtraction) and the geometric mean of 12 positive control RNA counts.

source_name: Primary neutrophils

growth_protocol: Neutrophils were isolated from peripheral blood using EasySep Direct Human Neutrophil Isolation Kit and suspended in RPMI supplemented with 10% fetal calf serum. A. fumigatus (B5233 strain) was grown in glucose minimum media agar at 37C for three days.

extract_protocol: Neutrophil lysates were homogenized using QIAshredder columns then mixed with Rnase-free 70% ethanol and purified using the Rneasy Mini Kit. RNA concentrations were measured using NanoDrop One and 1% agarose gels were used to verify integity.

treatment_protocol: Ibrutinib was dissolved in 0.1% DMSO to 0.3 uM concentration and was added to neutrophils 30 minutes before infection or TNFalpha treatment.

value: Primary neutrophils

tag: disease state

value: Healthy adult

value: TNFa and Af


title: TNFa and Af 1 Sample 22


title: TNFa and Af 2 Sample 23


title: S2-Zld_DMSO_R2


title: 15286X074_blastomere_567B_type_IVF_cell_number_2

description: cellnumber 2


title: [DDB_PD_036]_[SDT107_ZnHigh]_[Fed-batch]_[16h]_[R1]


title: 15286X075_blastomere_568A_type_IVF_cell_number_2

description: cellnumber 2


title: [DDB_PD_036]_[SDT107_ZnHigh]_[Batch]_[0h]_[R2]


title: 15286X076_blastomere_568B_type_IVF_cell_number_2

description: cellnumber 2


title: 15286X072_blastomere_566B_type_IVF_cell_number_2

description: cellnumber 2


title: Embryo_DeGradCBP_R4

source_name: Embryo (15min into NC14)

value: Embryo (15min into NC14)


title: [DDB_PD_036]_[SDT107_ZnHigh]_[Batch]_[0h]_[R1]


title: [DDB_PD_036]_[SDT107_ZnHigh]_[Fed-batch]_[16h]_[R2]


title: [DDB_PD_023]_[DDB16_ZnHigh]_[Fed-batch]_[15h]_[R2]


title: Embryo_DeGradCBP_R3


title: [DDB_PD_023]_[DDB16_ZnHigh]_[Fed-batch]_[15h]_[R1]


title: S2-Zld_DMSO_R1


title: IBT, TNFa, and Af 3 Sample 18

value: IBT, TNFa, and Af


title: 15286X073_blastomere_567A_type_IVF_cell_number_2

description: cellnumber 2


title: S2-Zld_A-485_R1


title: 15286X071_blastomere_566A_type_IVF_cell_number_2

description: cellnumber 2


title: TNFa 1 Sample 19

value: TNFa


title: TNFa 2 Sample 20


title: TNFa 3 Sample 21


title: 15286X070_blastomere_565B_type_IVF_cell_number_2

description: cellnumber 2


title: Embryo_DeGradCBP_R1


title: IBT, TNFa, and Af 2 Sample 17


title: IBT, TNFa, and Af 1 Sample 16


title: [DDB_PD_023]_[DDB16_ZnCtrl]_[Fed-batch]_[15h]_[R2]

value: Escherichia coli cells


title: [DDB_PD_036]_[SDT107_ZnLow]_[Batch]_[0h]_[R2]


title: [DDB_PD_023]_[DDB16_ZnCtrl]_[Fed-batch]_[15h]_[R1]


title: 15286X069_blastomere_565A_type_IVF_cell_number_2

description: cellnumber 2


title: 15286X068_blastomere_564B_type_IVF_cell_number_2

description: cellnumber 2


title: Embryo_GFPCBP_R4


title: Embryo_GFPCBP_R5


title: Embryo_DeGradCBP_R2


title: Embryo_GFPCBP_R3


title: [DDB_PD_023]_[DDB16_ZnHigh]_[Fed-batch]_[6h]_[R2]


title: 15286X067_blastomere_564A_type_IVF_cell_number_2

description: cellnumber 2


title: IBT and TNFa 3 Sample 15

value: IBT and TNFa


title: 15286X066_blastomere_563B_type_IVF_cell_number_2

description: cellnumber 2


title: IBT and TNFa 1 Sample 13


title: Embryo_GFPCBP_R2


title: IBT and TNFa 2 Sample 14


title: [DDB_PD_023]_[DDB16_ZnCtrl]_[Fed-batch]_[6h]_[R1]


title: Embryo_GFPCBP_R1


title: 15286X064_blastomere_562B_type_IVF_cell_number_2

description: cellnumber 2


title: Embryo_ctrl_Dark_R4

value: his2avRFP III

value: Dark


title: 15286X065_blastomere_563A_type_IVF_cell_number_2

description: cellnumber 2

value: IVF


title: [DDB_PD_023]_[DDB16_ZnHigh]_[Batch]_[0h]_[R2]


title: IBT and Af 2 Sample 11

value: IBT and Af


title: Embryo_ctrl_Dark_R3


title: IBT and Af 1 Sample 10


title: [DDB_PD_023]_[DDB16_ZnHigh]_[Batch]_[0h]_[R1]


title: Embryo_ctrl_Dark_R2


title: [DDB_PD_023]_[DDB16_ZnCtrl]_[Batch]_[0h]_[R2]


title: 15286X062_blastomere_561B_type_IVF_cell_number_2

description: cellnumber 2


title: [DDB_PD_023]_[DDB16_ZnHigh]_[Fed-batch]_[6h]_[R1]


title: IBT 3 Sample 9

value: IBT


title: 15286X061_blastomere_561A_type_IVF_cell_number_2

description: cellnumber 2


title: [DDB_PD_023]_[DDB16_ZnCtrl]_[Fed-batch]_[6h]_[R2]


title: IBT 2 Sample 8


title: IBT 1 Sample 7


title: IBT and Af 3 Sample 12


title: Embryo_ctrl_Dark_R1


title: 15286X059_blastomere_560A_type_IVF_cell_number_2

description: cellnumber 2


title: 15286X060_blastomere_560B_type_IVF_cell_number_2

description: cellnumber 2


title: 15286X063_blastomere_562A_type_IVF_cell_number_2

description: cellnumber 2


title: Embryo_ctrl_BlueLight_R3

value: Blue light


title: [DDB_PD_036]_[DDB35_ZnCtrl]_[Fed-batch]_[16h]_[R1]


title: Af 3 Sample 6

value: Af


title: Embryo_ctrl_BlueLight_R4


title: 15286X057_blastomere_559A_type_IVF_cell_number_2

description: cellnumber 2


title: [DDB_PD_038]_[SDT158_GenRed]_[Fed-batch]_[3h]_[R2]


title: [DDB_PD_036]_[DDB35_ZnCtrl]_[Batch]_[0h]_[R2]


title: Af 2 Sample 5


title: 15286X058_blastomere_559B_type_IVF_cell_number_2

description: cellnumber 2


title: Af 1 Sample 4


title: 15286X056_blastomere_558B_type_IVF_cell_number_2

description: cellnumber 2


title: [DDB_PD_036]_[DDB35_ZnCtrl]_[Batch]_[0h]_[R1]


title: [DDB_PD_023]_[DDB16_ZnCtrl]_[Batch]_[0h]_[R1]


title: DMSO 3 Sample 3

value: DMSO


title: [DDB_PD_036]_[DDB35_ZnCtrl]_[Fed-batch]_[16h]_[R2]


title: [DDB_PD_036]_[SDT107_ZnCtrl]_[Fed-batch]_[16h]_[R2]


title: DMSO 2 Sample 2


title: [DDB_PD_036]_[SDT107_ZnCtrl]_[Fed-batch]_[16h]_[R1]


title: Embryo_CRY2CBP_Dark_R3

value: CRY2nej;his2avRFP III


title: [DDB_PD_036]_[SDT107_ZnCtrl]_[Batch]_[0h]_[R1]


title: Embryo_ctrl_BlueLight_R1


title: 15286X053_blastomere_557A_type_IVF_cell_number_2

description: cellnumber 2


title: Embryo_CRY2CBP_Dark_R2


title: 15286X054_blastomere_557B_type_IVF_cell_number_2

description: cellnumber 2


title: [DDB_PD_022]_[HMP3427_crash_30L]_[Fed-batch]_[12h]_[R1]


title: DMSO 1 Sample 1

value: Primary neutrophils


title: Adult day 14 untreated

city: Houston

first: JP

last: McGinnis

state: TX

address: 5306 Creekbend Dr

department: Neurosurgery

institute: Baylor College of Medicine

description:
Library name: 3v4-620-STL-d14-untransd_S1
10X Genomics

data_processing:
The demultiplexing, barcode processing, gene counting, and aggregation were made using the Cell Ranger software.
Assembly: GrCH38
Supplementary files format and content: HDF5

extract_protocol:
For the tissue sections that received barcoded viral libraries (total titer 2.1E9 in 4 µL PBS per tissue slice), 14 days after virus application the tissue was gently removed from its well, flash frozen in liquid nitrogen, and stored at -80 oC. On the day of processing, frozen tissue was dissociated using GentleMACS nuclei isolation protocol (nuclei isolation buffer [Miltenyi Biotec, cat# 130-128-024], Protector RNAse Inhibitor [Millipore Sigma, cat# 3335402001], GentleMACS C tubes [Miltenyi Biotec, cat# 130-093-237], GentleMACS Octo Dissociator [Miltenyi Biotec, cat# 130-096-427], MACS SmartStrainers 70um [Miltenyi Biotec, cat# 130-098-462], MACS SmartStrainers 30um [Miltenyi Biotec, cat# 130-098-458]). In brief, samples were placed in 2 mL of Miltenyi Nuclei Isolation Buffer and Protector RNAse Inhibitor in GentleMACS C tubes. Samples then underwent the preprogrammed “nuclei isolation” program on a GentleMACS Octo Dissociator. Immediately after dissociation, samples were strained through a 70um MACS SmartStrainer and collected in a 15 ml tube, centrifuged at 300xg for 5 minutes at 4°C. The supernatant was extracted and discarded, and the resulting pellet resuspended in 1mL of ice-cold PBS. Resuspended samples were then run through a 30um MACS SmartStrainer, centrifuged, and resuspended in ~250-500 µL. Nuclei were then FACS sorted using DAPI on a Sony MA900 in the Baylor Cytometry and Cell Sorting Core.
The single-cell gene expression libraries were prepared according to the Chromium Single Cell Gene Expression 3’v3.1 instruction (PN-1000121, PN-1000120, PN-1000213, 10x Genomics). Briefly, single cells, reverse transcription (RT) reagents, Gel Beads containing barcoded oligonucleotides, and oil were loaded on a Chromium controller (10x Genomics) to generate single-cell GEMS (Gel Beads-In-Emulsions) where full-length cDNA was synthesized and barcoded for each molecule of mRNA (UMI) and each single cell (cell barcode). Subsequently, the GEMS were broken and cDNA from each single cell was pooled. Following cleanup using Dynabeads MyOne Silane Beads, cDNA is amplified by PCR. The amplified product was fragmented to optimal size before end-repair, A-tailing, and adaptor ligation. The final library was generated by amplification.

value: Brain

value: cultured 14 days


title: 15286X052_blastomere_547B_type_IVF_cell_number_2

description: cellnumber 2


title: Embryo_CRY2CBP_Dark_R1

value: Embryo (15min into NC14)


title: [DDB_PD_022]_[HMP3427_crash_30L]_[Fed-batch]_[4h]_[R1]


title: Embryo_CRY2CBP_BlueLight_R2


title: Pediatric day 14 untreated

description:
Library name: 3v4-5-6-d14U_S1
10X Genomics


title: 15286X051_blastomere_547A_type_IVF_cell_number_2

description: cellnumber 2


title: Adult day 14 with vector library

description:
Library name: 3v4-620-STL-d14-BC_S1
10X Genomics

source_name: Brain with AAVs

value: Brain with AAVs

value: 14 AAV library


title: 15286X055_blastomere_558A_type_IVF_cell_number_2

description: cellnumber 2


title: Embryo_CRY2CBP_BlueLight_R1


title: 15286X050_blastomere_546B_type_IVF_cell_number_2

description: cellnumber 2