title: Kdm5bOE_2C_40h_74

city: Munich

first: Tamas

last: Schauer

address: Feodor-Lynen-Straße 21

department: Institute of Epigenetics and Stem Cells

institute: Helmholtz Zentrum München

data_processing:
Sequencing reads were aligned to the mm10 genome using bowtie2 (version 2.3.5) with the --local option. Duplicates were marked using samtools (version 1.9)and reads were filtered by keeping only properly paired reads, removing duplicates and selecting those whose mapping quality was higher or equal to 20. Bed files of the read coordinates were generated with bedtools (version 2.29.0) bamtobed command. Using bedtools intersect, read counts were obtained for contiguous 50kb genomic bins.
The window counts were first normalised to RPM and then each bin by its respective average of all samples within the same stage, aiming to correct for the mappability biases intrinsic to the genomic regions. Outlier regions were then masked, specifically the windows of the lower 5th percentile and the upper 1st percentile values. To correct for low mappability, the windows were segmented with the R package copynumber (version 1.28.0) to keep the segments with the highest 95% of values. The data were centred by the mean and scaled by the interquartile range for each cell and smoothed using a median filter with a running window width of 15 windows, followed by a segmentation with the R package copynumber. Finally, using the function normalmixEM from R package mixtools (version 1.2.0), the segmented values were used to fit a mixture model with two components to identify replicated and non-replicated window populations.
Assembly: mm10
Supplementary files format and content: tab-separated txt file with binary replication status
Library strategy: Single-cell Repli-seq

source_name: 2-cell embryo + Kdm5b

growth_protocol: Zygotes were collected from the oviduct and cumulus cells were removed upon brief incubation in M2 media containing hyaluronidase. Zygotes were placed in drops of KSOM and cultured at 37 ºC with 5% CO2.

extract_protocol:
Early stage zygotes were collected and cultured until they reached the S-phase at each developmental stage, based on their time after hCG injection. Embryos were collected at different time points to achieve sampling over the entire S-phase. For the parthenogenetic embryos and IVF-derived zygotes, the timing of S-phase was calculated based on the time after activation and insemination, respectively. Zona pellucida was removed by exposure to acid Tyrode and each blastomere was dissociated by gentle pipetting after trypsin treatment. For the Repli-seq with physically isolated pronuclei, we distinguished maternal and paternal pronucleus based on their size and their relative position to the second polar body and isolated either of them using micromanipulation. The remaining zygote containing a single pronucleus was also collected after removal of polar body so that both pronuclei from the same zygote were further processed for Repli-seq.
Individual blastomeres or pronuclei were placed into 8-strip PCR tubes containing lysis buffer and extracted DNA was fragmented by heat incubation. Fragmented DNA was tagged by the universal primer (5’-TGTGTTGGGTGTGTTTGGKKKKKKKKKKNN-3’) and amplified with WGA primer sets which have individual barcode. Amplified DNA was purified by the QIAquick 96 PCR Purification Kit (QIAGEN) and concentration was determined by the NanoDrop (Thermo Scientific). Equal amount of DNA from each samples (up to 96 samples) were pooled and 1ug of them was ligated with the illumina adaptors using the NEBNext Ultra II DNA Library Prep Kit (NEB). Illumina sequence (NEBNext Multiplex Oligos for Illumina; NEB) were added to the adaptor- ligated samples by the PCR. Clean up and size selection of the PCR product was done using SPRIselect (Beckman Coulter) and the quality of the library was confirmed by 2100 Bioanalyzer with the High Sensitivity DNA Kit (Agilent).

treatment_protocol: For induction of parthenogenetic embryos, MII-stage oocytes were collected from superovulated females without mating. After removal of cumulus cells, oocytes were treated with 10 mM Sr2+ for 2 hours in Ca2+-free CZB medium and then incubated in KSOM. For generation of IVF-derived zygote, MII oocytes from F1 female mice (C57Bl/6J × CBA) were inseminated with activated spermatozoa obtained from the caudal epididymides of adult DBA/2J male mice. To inhibit both minor and major ZGA, embryos were treated with 0.1mg/mL a-amanitin or 100uM DRB from 17 hphCG injection until their collection time. For Kdm5b expression, 2ug/uL of in vitro synthesised Kdm5b mRNA was micro-injected in to zygotes at 18 hphCG.

value: 2-cell embryo + Kdm5b

value: (C57BL/6J xCBA) x DBA/2J

value: Kdm5b mRNA


title: Kdm5bOE_2C_40h_72

status: Public on Oct 16 2023

type: SRA

country: Germany

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: tissue

tag: genotype

tag: treatment


title: Kdm5bOE_2C_40h_71


title: Kdm5bOE_2C_40h_73


title: Kdm5bOE_2C_40h_70


title: Kdm5bOE_2C_40h_68


title: Kdm5bOE_2C_40h_67


title: Kdm5bOE_2C_39h_64


title: Kdm5bOE_2C_40h_69


title: Kdm5bOE_2C_39h_59


title: Kdm5bOE_2C_39h_60


title: Kdm5bOE_2C_39h_63


title: Kdm5bOE_2C_39h_58


title: Kdm5bOE_2C_39h_56


title: Kdm5bOE_2C_39h_54


title: Kdm5bOE_2C_39h_57


title: Kdm5bOE_2C_39h_55


title: Kdm5bOE_2C_39h_66


title: Kdm5bOE_2C_39h_62


title: Kdm5bOE_2C_38h_52


title: Kdm5bOE_2C_39h_53


title: Kdm5bOE_2C_39h_61


title: Kdm5bOE_2C_38h_50


title: Kdm5bOE_2C_38h_51


title: Kdm5bOE_2C_38h_49


title: Kdm5bOE_2C_38h_47


title: Kdm5bOE_2C_38h_46


title: Kdm5bOE_2C_38h_45


title: Kdm5bOE_2C_39h_65


title: Kdm5bOE_2C_38h_42


title: Kdm5bOE_2C_38h_43


title: Kdm5bOE_2C_38h_44


title: Kdm5bOE_2C_38h_40


title: Kdm5bOE_2C_38h_41


title: Kdm5bOE_2C_38h_39


title: Kdm5bOE_2C_38h_37


title: Kdm5bOE_2C_38h_35


title: Kdm5bOE_2C_38h_38


title: Kdm5bOE_2C_37h_28


title: Kdm5bOE_2C_38h_34


title: Kdm5bOE_2C_37h_31


title: Kdm5bOE_2C_37h_29


title: Kdm5bOE_2C_38h_33


title: Kdm5bOE_2C_37h_26


title: Kdm5bOE_2C_38h_36


title: Kdm5bOE_2C_37h_32


title: Kdm5bOE_2C_37h_27


title: Kdm5bOE_2C_36h_9


title: Kdm5bOE_2C_38h_48


title: Kdm5bOE_2C_37h_25


title: Kdm5bOE_2C_36h_7


title: Kdm5bOE_2C_36h_24


title: Kdm5bOE_2C_36h_23


title: Kdm5bOE_2C_36h_22


title: Kdm5bOE_2C_36h_5


title: Kdm5bOE_2C_37h_30


title: Kdm5bOE_2C_36h_21


title: Kdm5bOE_2C_36h_20


title: Kdm5bOE_2C_36h_18


title: Kdm5bOE_2C_36h_19


title: Kdm5bOE_2C_36h_17


title: Kdm5bOE_2C_36h_8


title: Kdm5bOE_2C_36h_16


title: Kdm5bOE_2C_36h_15


title: Kdm5bOE_2C_36h_6


title: Kdm5bOE_2C_36h_14


title: Kdm5bOE_2C_36h_12


title: Kdm5bOE_2C_36h_13


title: Kdm5bOE_2C_34h_4


title: Kdm5bOE_2C_36h_10


title: Kdm5bOE_2C_34h_1


title: DRB_2C_40h_70

source_name: 2-cell embryo + DRB

value: 2-cell embryo + DRB

value: DRB


title: Kdm5bOE_2C_34h_3


title: Kdm5bOE_2C_34h_2


title: DRB_2C_40h_67


title: DRB_2C_40h_71


title: DRB_2C_40h_68


title: DRB_2C_40h_65


title: DRB_2C_40h_62


title: DRB_2C_40h_63


title: DRB_2C_39h_60


title: DRB_2C_40h_61


title: DRB_2C_39h_57


title: DRB_2C_39h_56


title: DRB_2C_39h_59


title: DRB_2C_39h_55


title: DRB_2C_39h_58


title: DRB_2C_39h_53


title: DRB_2C_39h_54


title: DRB_2C_40h_72


title: Kdm5bOE_2C_36h_11


title: DRB_2C_40h_69


title: DRB_2C_40h_66


title: DRB_2C_39h_51


title: DRB_2C_38h_46


title: DRB_2C_38h_47


title: DRB_2C_38h_48


title: DRB_2C_38h_45


title: DRB_2C_38h_42


title: DRB_2C_38h_43


title: DRB_2C_40h_64


title: DRB_2C_39h_52


title: DRB_2C_37h_39


title: DRB_2C_37h_38


title: DRB_2C_38h_41


title: DRB_2C_37h_40


title: DRB_2C_37h_36


title: DRB_2C_37h_37


title: DRB_2C_37h_35


title: DRB_2C_39h_50


title: DRB_2C_37h_31


title: DRB_2C_37h_30


title: DRB_2C_37h_28


title: DRB_2C_37h_29


title: DRB_2C_37h_32


title: DRB_2C_37h_27


title: DRB_2C_37h_34


title: DRB_2C_37h_26


title: DRB_2C_37h_25


title: DRB_2C_36h_24


title: DRB_2C_39h_49


title: DRB_2C_36h_23


title: DRB_2C_36h_22


title: DRB_2C_38h_44


title: DRB_2C_36h_19


title: DRB_2C_35h_16


title: DRB_2C_36h_20


title: DRB_2C_36h_18


title: DRB_2C_36h_17


title: DRB_2C_35h_9


title: DRB_2C_35h_15


title: DRB_2C_37h_33


title: DRB_2C_35h_14


title: DRB_2C_35h_13


title: DRB_2C_35h_11


title: DRB_2C_35h_12


title: DRB_2C_35h_10


title: DRB_2C_34h_8


title: DRB_2C_36h_21


title: DRB_2C_34h_7


title: DRB_2C_34h_5


title: DRB_2C_34h_6


title: DRB_2C_34h_3


title: DRB_2C_34h_1


title: S858R Kidney 4 snRNA-seq

city: Birmingham

first: Jordan

last: Whitlock

email: jwhitlock@uab.edu, bnp0001@uab.edu

state: AL

address: 1900 University Boulevard

department: Cell, Developmental and Integrative Biology

country: USA

institute: The University of Alabama at Birmingham

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
We processed all 10X snRNA-seq data using 10X Genomics Cell Ranger (version 6.1.1) according to 10X Genomics standard protocols. We aligned sequencing reads to mus musculus (mm10) to generate feature-barcode matrices. The average paired-end sequencing depth was 81,000 reads per nuclei, with approximately 12,000 and 8,000 nuclei per sample for the kidney and cerebral cortex, respectively. We investigated raw sequencing data quality using FastQC (version 0.11.9).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

source_name: right kidney

extract_protocol:
We adapted and conducted single nuclei isolation for the kidney cortex as previously described by Kirita et al. PNAS 2020. We isolated nuclei using the Nuclei EZ Prep kit with Nuclei EZ Lysis buffer (Sigma #NUC-101) supplemented with cOmplete ULTRA tablets (Sigma# 05892791001), SUPERase IN (Thermosisher# AM2696), and Promega RNasin Plus (Fisher Promega #PRN2615). We minced whole kidney cortex into <1mm pieces and then homogenized them using a Dounce tissue grinder (Kimble# 8853000002) in 2 ml of cold Nuclei EZ Lysis buffer. We then filtered the homogenate through a 200-µm strainer (Pluriselect#:43-50200) and a 40-µm strainer (Pluriselect#:43-50040) and then centrifuged at 500 x g for 5 min at 4 ºC. We resuspended the pellet in 4ml of the buffer and incubated it on ice for 5 minutes. After centrifugation at the same time, temperature, and speed, we resuspended the pellet in Nuclei Suspension Buffer as described by Kirita et al. PNAS 2020.  We adapted our single nuclei isolation for cerebral cortex samples for mice from the previously described protocol for rats in Phillips et al. Cell Reports 2022 and sorted nuclei at the University of Alabama at Birmingham's (UAB) Comprehensive Flow Cytometry Core (CFCC) using fluorescence-activated cell sorting (FACS) on an Atlas BD ARIA II.
Per the standard 10X protocol, the UAB CFCC used the 10X Chromium Controller to partition kidney and cerebral cortex nuclei into droplets with a barcoded gel bead where nuclei were lysed, and RNA was reverse transcribed, creating cDNA encapsulated in each droplet. After fragmenting and amplifying cDNA, they added Illumina adapters using the Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3 (10X#: PN-1000121). The UAB Heflin Center for Genomic Sciences at the UAB Sequencing Core indexed and sequenced all samples on a NovaSeq 6000 (Illumina). For each sample, they loaded approximately 20,000 nuclei onto an S4 flow cell.

value: right kidney

tag: age

value: 6 weeks

tag: Sex

value: male


title: WT Kidney 5 snRNA-seq

description: 10x Genomics

value: C57BL6/J control


title: S858R Kidney 2 snRNA-seq

description: 10x Genomics


title: WT Kidney 3 snRNA-seq

description: 10x Genomics


title: S858R Cortex 13 snRNA-seq

description: 10x Genomics

source_name: right cerebral cortex

value: right cerebral cortex


title: WT Kidney 1 snRNA-seq

description: 10x Genomics


title: S858R Cortex 15 snRNA-seq

description: 10x Genomics


title: WT Cortex 4 snRNA-seq

description: 10x Genomics


title: WT Cortex 3 snRNA-seq

description: 10x Genomics


title: WT Cortex 2 snRNA-seq

description: 10x Genomics


title: 2 TSC Total RNA bulkRNA

city: Clemson

first: David

middle: Matthew

last: Feliciano

state: South Carolina

address: 132 Long Hall

department: Biological Sciences

institute: Clemson University

library_source: transcriptomic

data_processing:
Reads were trimmed for adapter sequences using FastQ Toolkit (v. 2.2.5).
Reads were aligned to UCSC mm10 using RNA-SEQ Alignment (which utilizes STAR, v. 2.6.1A) on BaseSpace (Illumina).
Aligned sequences were further analyzed on BaseSpace (llumina) using RNA-SEQ Differential Expression (v. 1.0.1 which utilizes DESEQ2).

molecule: total RNA

source_name: brain

growth_protocol: Brains were bisected into two sagittal hemispheres. The V-SVZ was micro-dissected in ice cold Neurobasal A (Gibco, #10888022) medium. 100 µl 0.25% Trypsin (Gibco, # 25200072) was added and incubated for 3 min at 37°C before the tissue was dissociated using three Pasteur pipettes having progressively decreasing bore sizes. 100 µl defined trypsin inhibitor (Gibco, # R007100) containing 0.01 mg/ml DNase1 was added, and the solution was centrifuged at 300 x g in an Eppendorf 5425 centrifuge. The pellet was resuspended in complete growth media (96.4% Neural basal A (Gibco, #10888022), 0.02% Mouse FGF-basic Recombinant protein (Invitrogen, #RP-8626), 0.02% Recombinant Mouse EGF (Gibco, #PMG8044), 0.5% Pen Strep (Gibco, #15140-122), 0.008% 25 mg/ml Heparin sodium salt (Sigma Aldrich, #H3393), 1% Glutamax (Gibco, #35050-061), 2% B-27 Supplement without vitamin A (Gibco, #12587) before plating in a dish coated with natural mouse Laminin (Gibco, 23017) and poly-D-lysine (Gibco, #A38904-01). Cultures were passaged at the appropriate confluency by incubating in 5 mL Accutase (Invitrogen, #00-4555-56) for 5 minutes at 37°C. The cells were then spun down for 5 minutes at 300 x g in an Eppendorf 5425 centrifuge and replated at an appropriate density. Cultures were passaged no more than three times.

extract_protocol:
Trizol was added to NSCs grown on culture plates. NSC lysate was removed, triturated, and placed on ice in 1.5 mL Eppendorf tubes. Chloroform was added to tubes after freezing at -80°C and vigorously shaken by hand for 15 seconds. Samples were incubated for 5 minutes at room temperature and then centrifuged at 12,000 x g at 4°C. The aqueous phase was used to precipitate RNA by adding isopropanol and incubated overnight at -20°C. Samples were centrifuged for 10 minutes at 12,000 x g at 4°C. Supernatant was removed and pellets were washed with 75% ethanol. Samples were spun at 7,500 x g for 5 minutes at 4°C. Supernatant was removed and pellet air dried and resuspended in dH2O. Samples were incubated with DNase I and buffer RDD. Samples were then subject to Qiagen MinElute Column clean up on an RNeasy MinElute spin column. Briefly, buffer RLT is added to samples and mixed followed by addition of 100% ethanol. Samples were mixed and transferred to RNeasy MinElute spin column in a collection tube. Samples were centrifuged for 15 seconds at 8,000 x g twice. Columns were placed into a fresh 2 mL collection tube and 80% ethanol is added to MinElute column. Samples are centrifuged at 8,000 x g for 2 minutes and spin column is placed into a new tube. Samples were subject to an additional centrifugation and RNA is eluted in RNase free water before library preparation.
Libraries were constructed using the NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (New England Biolabs Inc., #E7770S) and the NEBNext® Poly(A) mRNA Magnetic Isolation Module (New England Biolabs Inc., #E7490S).
These libraries were dual-indexed using the NEBNext® Multiplex Oligos for Illumina® (Dual Index Primers Set 1) (New England Biolabs Inc., #E7600S). The libraries were quantified and qualified using Qubit (Thermo-Fischer, #Q32852) and TapeStation (Agilent, # 5067-5579).

value: brain

tag: cell type

value: neural stem cell

value: Tsc2 mutant/mutant


title: DRB_2C_34h_4


title: DRB_2C_34h_2


title: S858R Kidney 6 snRNA-seq

description: 10x Genomics


title: 2 Control Total RNA bulkRNA

value: Tsc2 wild type/wild type


title: 1 TSC Total RNA bulkRNA


title: 3 Control Total RNA bulkRNA


title: 4 TSC scRNA

data_processing:
FASTQ files were preprocessed for quality and length and aligned to Mus musculus reference genome GRCm38 (mm10) using the counts command with --force-cells parameter set to 60000
Output from thecountscommand was exported into R for quality control, multi-sample integration, cell-type clustering, cell-type marker identification and differential expression within each cluster using the Seurat v4 single cell analysis platform. Differential expression lists were curated by removing mitochondrial encoded transcripts.
Assembly: GRCm38(mm10)

growth_protocol: Brains from were bisected into two sagittal hemispheres. The V-SVZ was micro-dissected in ice cold Neurobasal A (Gibco, #10888022) medium. 200 µl 0.25% Trypsin (Gibco, # 25200072) was added and incubated for 7 min at 37°C before the tissue was dissociated using three Pasteur pipettes having progressively decreasing bore sizes. Cells were sieved using a 70 µm cell strainer (Corning, #431751) and centrifuged at 300 x g in a Eppendorf 5425 centrifuge before isolation.

extract_protocol:
Cell pellets were resuspended in lysis buffer (0.25 M sucrose, 50 mM Tris/HCl (pH7.5, Sigma Aldrich, #93363), 5 mM MgCl2 (Sigma Aldrich, #M1028), 25 mM KCl (Sigma Aldrich, #P9333), 200 µg/ml CHX (VWR, #94271), 1X HALT protease inhibitor (Thermo Scientific, #87785), 1 mM dithiothreitol (DTT, Enzo, #ALX-280-001-G005), 100 U/ml recombinant RNAsin ribonuclease inhibitor (Promega, #N2511)) and incubated on ice for 15 minutes. Cells were then Dounce homogenized five times and spun down at 500 x g in a Eppendorf 5425 centrifuge. The pellet was frozen at -80°C until FAC sorting.  Nuclei were resuspended in 400 µl cold Nuclei Suspension Buffer (1% BSA, 0.2 U/µl RNase inhibitor (RNasin Plus, Promega) in 1X PBS). The nuclei suspension was loaded on to a Bio-Rad S3e Cell Sorter and 100k tdtomato positive nuclei were sorted into chilled Nuclei Suspension Buffer. Nuclei samples were transported on ice until gel-bead-in-emulsion (GEM) generation. GEM generation was performed using Chromium Next GEM Chip G Single Cell Kit (10x Genomics, #1000127). GEMs were created using a 10X Genomics Chromium controller (10X Genomics, #1000204).
Libraries were made after GEM generation in accordance with 10X Genomics Single Cell 3’ kit v3.1 (10x Genomics, #1000269) according to the manufacturer’s guidelines and Chromium Next GEM Single Cell 3’ v. 3.1 (Dual Index) protocol. The libraries were quantified and qualified using Qubit 4 Fluorometer (Thermo Fisher Scientific, #Q33238, 1X dsDNA, high sensitivity, 500 rxns (Thermo Fisher Scientific, #Q33231) and TapeStation 4150 (Aglient, #G2992AA, High Sensitivity D5000 ScreenTape Aglient, #5067-5592, High Sensitivity D5000 Ladder Agilent, #5067-5594. Final libraries were pooled on a NovaSeq 6000 SP v1.5 (300 cycles) flow cell (Illumina, #20028400) according to manufacturer’s instructions.


title: 1 Control Total RNA bulkRNA


title: 4 Control scRNA

value: Tsc2 wild


title: 1 TSC scRNA


title: 2 TSC scRNA


title: S858R Cortex 1 snRNA-seq

description: 10x Genomics


title: 3 TSC Total RNA bulkRNA


title: 3 Control scRNA


title: 3 TSC scRNA


title: 1 Control scRNA


title: 2 Control scRNA


title: 4 TSC Polyribosomal RNA

library_source: other

molecule: other

source_name: Brain

growth_protocol: Brains from were bisected into two sagittal hemispheres. The V-SVZ was micro-dissected in ice cold Neurobasal A (Gibco, #10888022) medium. 100 µl 0.25% Trypsin (Gibco, # 25200072) was added and incubated for 3 min at 37°C before the tissue was dissociated using three Pasteur pipettes having progressively decreasing bore sizes. 100 µl defined trypsin inhibitor (Gibco, # R007100) containing 0.01 mg/ml DNase1 was added, and the solution was centrifuged at 300 x g in a Eppendorf 5425 centrifuge. The pellet was resuspended in complete growth media (96.4% Neural basal A (Gibco, #10888022), 0.02% Mouse FGF-basic Recombinant protein (Invitrogen, #RP-8626), 0.02% Recombinant Mouse EGF (Gibco, #PMG8044), 0.5% Pen Strep (Gibco, #15140-122), 0.008% 25 mg/ml Heparin sodium salt (Sigma Aldrich, #H3393), 1% Glutamax (Gibco, #35050-061), 2% B-27 Supplement without vitamin A (Gibco, #12587) before plating in a 100 mm dish coated with natural mouse Laminin (Gibco, 23017) and poly-D-lysine (Gibco, #A38904-01). Upon reaching confluency, cells were passaged by incubating in 5 mL Accutase (Invitrogen, #00-4555-56) for 5 minutes at 37°C. The cells were then spun down for 5 minutes at 300 x g in an Eppendorf 5425 centrifuge and replated at an appropriate density.

extract_protocol:
Primary NSC cultures were passaged once prior to isolations. 100 mg/ml (66.6uL) cycloheximide (CHX, VWR, #94271) was added to each dish and incubated at 37°C for 15 minutes. The cells were dissociated in 500 mL lysis buffer (0.25 M sucrose, 50 mM Tris/HCl (pH7.5, Sigma Aldrich, #93363), 5 mM MgCl2 (Sigma Aldrich, #M1028), 25 mM KCl (Sigma Aldrich, #P9333), 200 µg/ml CHX (VWR, #94271), 1X HALT protease inhibitor (Thermo Scientific, #87785), 1 mM dithiothreitol (DTT, Enzo, #ALX-280-001-G005), 100 U/ml recombinant RNAsin ribonuclease inhibitor (Promega, #N2511), scraped into a 1.5 mL microcentrifuge tube, and incubated for 15 minutes on ice. Lysates were homogenized five times with a Dounce homogenizer. 50 mL was removed and 150 mL TRIzol LS reagent (Ambion, #10296010) was added for RNA Total isolation. The remaining lysates were centrifuged for 10 minutes at 500 x g at 4°C. 10% sodium deoxycholate and 10% NP-40 was added, and the samples were incubated on ice for thirty minutes. Prepared lysates were loaded onto 10 mL continuous sucrose gradients that consisted of 17.5-50% sucrose (as well as 30 mM Tris-HCl (pH7.5, Sigma Aldrich, #93363), 30 mM MgCl2 (Sigma Aldrich, #M1028), 600 mM NaCl (Fisher Scientific, #BP358-10), 200 µg/ml CHX (VWR, #94271), 2 mM DTT (Enzo, #ALX-280-001-G005), and UltraPure DEPC treated H2O (Invitrogen, #750023). The gradients were balanced using lysis buffer and were centrifuged for 1.5 hours at 280,000 x g in a SW-41 Ti swinging bucket rotor with the acceleration speed set to max and the deceleration speed set to coast. Seven 1080 mL fractions were then removed from the top of the sucrose gradients leaving 3 mL of the heaviest sucrose fractions. TRIzol LS reagent (9 mL) (Ambion, #10296010) was added and stored at -80°C overnight. The solutions were then split into two equal parts and 1.2 mL of chloroform (Sigma Aldrich, #372978) was added to each tube. The tubes were incubated for three minutes before centrifugation at 12,000 x g for 15 minutes at 4°C. The aqueous layer was then removed and 3 mL isopropanol (Fisher Chemical, #A416-1) and 1 mL GlycoBlue Blue coprecipitant (Invitrogen, #AM9516) was added. The tubes were then moved to the -80°C freezer to precipitate overnight. Samples were then centrifuged for ten minutes at 12,000 x g at 4°C and the supernatants discarded. Pellets were resuspended in 6 mL 75% EtOH (Sigma Aldrich, #E7023) and vortexed before centrifugation for five minutes at 7,500 x g at 4°C. The supernatants were discarded, and the pellets allowed to air dry for 8 minutes before resuspension in 50 mL UltraPure Distilled water (Invitrogen, #10977-015). The samples were incubated for 15 minutes at 57°C in a water bath before being recombined into one polysomal RNA fraction each. Chloroform (Sigma Aldrich, #372978) was added to each cell lysate that was collected during polysomal profiling as a total RNA fraction. The tubes were incubated for three minutes before centrifugation at 12,000 x g for 15 minutes at 4C. The aqueous layer was then removed and 100 µL isopropanol (Fisher Chemical, #A416-1) and 1 mL GlycoBlue Blue co-precipitant (Invitrogen, #AM9516) was added. The tubes were then moved to the -80°C freezer to precipitate overnight. Samples were centrifuged for ten minutes at 12,000 x g at 4°C and the supernatants discarded. Pellets were resuspended in 200 µL 75% EtOH (Sigma Aldrich, #E7023) and vortexed before centrifugation for five minutes at 7,500 x g at 4°C. The supernatants were discarded, and the pellets allowed to air dry for 8 minutes before resuspension in 50 mL UltraPure Distilled water (Invitrogen, #10977-015). The samples were incubated for 15 minutes at 57°C in a water bath before library prep.
Libraries were constructed using the NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (New England Biolabs Inc., #E7770S) and the NEBNext® Poly(A) mRNA Magnetic Isolation Module (New England Biolabs Inc., #E7490S).
These libraries were dual-indexed using the NEBNext® Multiplex Oligos for Illumina® (Dual Index Primers Set 1) (New England Biolabs Inc., #E7600S). The libraries were quantified and qualified using Qubit (Thermo-Fischer, #Q32852) and TapeStation (Agilent, # 5067-5579).

value: Brain


title: 3 TSC Polyribosomal RNA


title: 1 TSC Polyribosomal RNA


title: 2 TSC Polyribosomal RNA


title: 4 TSC Total RNA


title: 3 TSC Total RNA


title: 2 TSC Total RNA


title: 3 Control Polyribosomal RNA


title: 2 Control Polyribosomal RNA


title: 2 Control Total RNA


title: 3 Control Total RNA


title: 4 Control Total RNA


title: Notch2 mutant chondrocytes, with TNFalpha_biol rep 4

city: Farmington

first: Ernesto

last: Canalis

state: CT

address: 263 Farmington Avenue

department: Orthopaedic Surgery

institute: UConn Health

data_processing:
Raw reads were trimmed with Sickle (Version 1.33), with a quality threshold of 30 and length threshold of 45, following that the trimmed reads were mapped to Mus Musculus genome (GRCm38 ensembl release 97) with HISAT2 (version 2.1.0).
The resulting SAM files then converted into BAM format using samtools (version 1.9), and the PCR duplicates were removed using PICARD (http://broadinstitute.github.io/picard/).
The counts were generated against the features with htseq-count.
The differential expression of genes between conditions was evaluated using DESeq2.
Covariates were introduced in the DESeq2 analysis to increase the accuracy of results, and genes showing less than 10 counts across the compared samples were excluded from the analysis.
Genes with a false discovery rate (FDR) < 0.05 were considered significant and used in the downstream analysis.
Assembly: Mus Musculus genome (GRCm38 ensembl release 97)
Supplementary files format and content: COUNTS File (*.counts) and counts

source_name: Chondrocytes

growth_protocol: Chondrocytes were cultured with Dulbecco's Modified Eagle's medium including 10% fetal bovine serum in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Total RNA was extracted from chondrocytes with the RNeasy Mini kit (Qiagen, Valencia, CA)
Total RNA samples were prepared for mRNA-Sequencing using the Illumina TruSeq Stranded mRNA Sample Preparation kit following the manufacturer’s protocol (Illumina, San Diego, CA).
Libraries were validated for length and adapter dimer removal using the Agilent TapeStation 4200 D1000 High Sensitivity assay (Agilent Technologies), and then they were quantified and normalized using the dsDNA High Sensitivity Assay for Qubit 3.0 (Thermo Fisher Scientific).
Sample libraries were prepared for Illumina sequencing by denaturing and diluting the libraries per manufacturer’s protocol (Illumina).
All samples were pooled into one sequencing pool, equally normalized, and run as one sample pool across the Illumina NextSeq 500 using version 2.5 chemistry.
Target read depth was achieved for each sample with paired end 75bp reads.

treatment_protocol: The cells were deprived in serum free medium for TNFalpha treatment groups only, and then were treated with TNFalpha 50 ng/ml for 6 hours.

value: Chondrocytes

value: Notch2 mutant

value: pooled male and female

value: TNF alpha (50ng/ml)

tag: time

value: 6 hours


title: 1 Control Polyribosomal RNA


title: Notch2 mutant chondrocytes, with TNFalpha_biol rep 1


title: Notch2 mutant chondrocytes, with TNFalpha_biol rep 2


title: Wild type chondrocytes, with TNFalpha_biol rep 4

value: Wild type


title: 1 TSC Total RNA


title: 1 Control Total RNA


title: 4 Control Polyribosomal RNA


title: Wild type chondrocytes, with TNFalpha_biol rep 2


title: Wild type chondrocytes, with TNFalpha_biol rep 1


title: Notch2 mutant chondrocytes, with vehicle_biol rep 4

value: Vehicle, PBS


title: Notch2 mutant chondrocytes, with TNFalpha_biol rep 3


title: Wild type chondrocytes, with vehicle_biol rep 4


title: Notch2 mutant chondrocytes, with vehicle_biol rep 3


title: Notch2 mutant chondrocytes, with vehicle_biol rep 1


title: Notch2 mutant chondrocytes, with vehicle_biol rep 2


title: Wild type chondrocytes, with TNFalpha_biol rep 3


title: Wild type chondrocytes, with vehicle_biol rep 3


title: Wild type chondrocytes, with vehicle_biol rep 1


title: Zygote_26h_48

source_name: Zygote

treatment_protocol: For induction of parthenogenetic embryos, MII-stage oocytes were collected from superovulated females without mating. After removal of cumulus cells, oocytes were treated with 10 mM Sr2+ for 2 hours in Ca2+-free CZB medium and then incubated in KSOM. For generation of IVF-derived zygote, MII oocytes from F1 female mice (C57Bl/6J × CBA) were inseminated with activated spermatozoa obtained from the caudal epididymides of adult DBA/2J male mice. To inhibit both minor and major ZGA, embryos were treated with 0.1mg/mL a-amanitin from 17 hphCG injection until their collection time.

value: Zygote

value: (C57BL/6J x CBA) x DBA/2J


title: Zygote_26h_46


title: Zygote_26h_47


title: Zygote_26h_45


title: Zygote_26h_44


title: Zygote_26h_42


title: Zygote_25h_39


title: Zygote_26h_41


title: Zygote_25h_40


title: Zygote_25h_38


title: Zygote_25h_36


title: Zygote_25h_33


title: Zygote_24h_80


title: Zygote_24h_79


title: Zygote_25h_35


title: Wild type chondrocytes, with vehicle_biol rep 2


title: Zygote_24h_78


title: Zygote_24h_77


title: Zygote_24h_74


title: Zygote_24h_76


title: Zygote_24h_75


title: Zygote_24h_30


title: Zygote_24h_32


title: Zygote_24h_29


title: Zygote_24h_31


title: Zygote_24h_73


title: Zygote_26h_43


title: Zygote_24h_28


title: Zygote_24h_27


title: Zygote_23h_24


title: Zygote_24h_25


title: Zygote_24h_26


title: Zygote_25h_37


title: Zygote_23h_23


title: Zygote_23h_22


title: Zygote_25h_34


title: Zygote_23h_21


title: Zygote_23h_20


title: Zygote_23h_19


title: Zygote_23h_17


title: Zygote_22h_72


title: Zygote_22h_69


title: Zygote_22h_71


title: Zygote_22h_70


title: Zygote_22h_68


title: Zygote_22h_66


title: Zygote_22h_65


title: Zygote_21h_9


title: Zygote_21h_63


title: Zygote_21h_62


title: Zygote_21h_58


title: Zygote_21h_59


title: Zygote_21h_57


title: Zygote_21h_60


title: Zygote_21h_64


title: Zygote_21h_15


title: Zygote_21h_13


title: Zygote_21h_16


title: Zygote_21h_14


title: Zygote_23h_18


title: Zygote_21h_12


title: Zygote_21h_10


title: Zygote_21h_11


title: Zygote_20h_56


title: Zygote_20h_5


title: Zygote_20h_7


title: Zygote_20h_6


title: Zygote_22h_67


title: Zygote_20h_8


title: Zygote_20h_55


title: Zygote_20h_52


title: Zygote_20h_54


title: Zygote_20h_53


title: Zygote_21h_61


title: Zygote_20h_51


title: Zygote_20h_50


title: Zygote_20h_49


title: Zygote_20h_4


title: Zygote_20h_2


title: Zygote_20h_1


title: Zygote_20h_3


title: Parthenote_9h_32

source_name: Parthenote

value: Parthenote

value: (C57BL/6J x CBA)F1


title: Parthenote_9h_30


title: Parthenote_9h_31


title: Parthenote_9h_29


title: Parthenote_9h_28


title: Parthenote_9h_25


title: Parthenote_9h_26


title: Parthenote_9.5h_88


title: Parthenote_9.5h_87


title: Parthenote_9.5h_85


title: Parthenote_9.5h_84


title: Parthenote_9h_27


title: Parthenote_9.5h_81


title: Parthenote_9.5h_86


title: Parthenote_9.5h_82


title: Parthenote_8h_24


title: Parthenote_9.5h_83


title: Parthenote_8h_22


title: Parthenote_8h_20


title: Parthenote_8h_21


title: Parthenote_8h_23


title: Parthenote_8h_19


title: Parthenote_8h_18


title: Parthenote_8.5h_79


title: Parthenote_8.5h_78


title: Parthenote_8h_17


title: Parthenote_8.5h_76


title: Parthenote_8.5h_77


title: Parthenote_8.5h_75


title: Parthenote_8.5h_73


title: Parthenote_8.5h_74


title: Parthenote_7h_15


title: Parthenote_7h_16


title: Parthenote_7h_9


title: Parthenote_7h_12


title: Parthenote_7h_11


title: Parthenote_7h_10


title: Parthenote_7h_14


title: Parthenote_7h_13


title: Parthenote_7.5h_71


title: Parthenote_7.5h_68


title: Parthenote_7.5h_70


title: Parthenote_7.5h_69


title: Parthenote_7.5h_66


title: Parthenote_8.5h_80


title: Parthenote_7.5h_65


title: Parthenote_6h_7


title: Parthenote_6h_8


title: Parthenote_6h_6


title: Parthenote_7.5h_67


title: Parthenote_6h_5


title: Parthenote_6h_4


title: Parthenote_6h_3


title: Parthenote_6h_2


title: Parthenote_6h_1


title: Parthenote_6.5h_64


title: Parthenote_7.5h_72


title: Parthenote_6.5h_63


title: Parthenote_6.5h_62


title: Parthenote_6.5h_61


title: Parthenote_6.5h_60


title: Parthenote_6.5h_59


title: Parthenote_6.5h_58


title: Parthenote_5.5h_55


title: Parthenote_5.5h_54


title: Parthenote_6.5h_57


title: Parthenote_5.5h_53


title: Parthenote_5.5h_52


title: Parthenote_5.5h_51


title: Parthenote_5.5h_50


title: Parthenote_5.5h_49


title: Parthenote_12h_56


title: Parthenote_12h_55


title: Parthenote_12h_53


title: Parthenote_12h_52


title: Parthenote_12h_54


title: Parthenote_12h_50


title: Parthenote_12h_51


title: Parthenote_12h_49


title: Parthenote_11h_48


title: Parthenote_11h_47


title: Parthenote_11h_46


title: Parthenote_11h_44


title: Parthenote_10h_40


title: Parthenote_11h_42


title: Parthenote_11h_43


title: Parthenote_10h_39


title: Parthenote_10h_38


title: Parthenote_10h_37


title: Parthenote_10h_36


title: Parthenote_10h_35


title: Parthenote_10h_33


title: Parthenote_10.5h_96


title: Parthenote_10h_34


title: Parthenote_5.5h_56


title: Parthenote_10.5h_95


title: Parthenote_10.5h_94


title: Parthenote_10.5h_92


title: Parthenote_10.5h_93


title: Parthenote_10.5h_90


title: Parthenote_11h_45


title: Parthenote_10.5h_89


title: Parthenote_11h_41


title: P_21-25h_52

source_name: paternal PN

value: paternal PN


title: P_21-25h_9


title: P_21-25h_50


title: P_21-25h_51


title: P_21-25h_7


title: P_21-25h_8


title: P_21-25h_6


title: P_21-25h_5


title: P_21-25h_4


title: P_21-25h_47


title: P_21-25h_46


title: P_21-25h_49


title: P_21-25h_45


title: P_21-25h_44


title: P_21-25h_42


title: P_21-25h_41


title: P_21-25h_39


title: P_21-25h_38


title: Parthenote_10.5h_91


title: P_21-25h_34


title: P_21-25h_35


title: P_21-25h_31


title: P_21-25h_32


title: P_21-25h_30


title: P_21-25h_2


title: P_21-25h_29


title: P_21-25h_27


title: P_21-25h_43


title: P_21-25h_20


title: P_21-25h_25


title: P_21-25h_24


title: P_21-25h_21


title: P_21-25h_22


title: P_21-25h_3


title: P_21-25h_26


title: P_21-25h_19


title: P_21-25h_1


title: P_21-25h_37


title: P_21-25h_18


title: P_21-25h_33


title: P_21-25h_17


title: P_21-25h_14


title: P_21-25h_13


title: P_21-25h_40


title: P_21-25h_15


title: P_21-25h_10


title: Mol_90-96h_7

source_name: Morula

value: Morula


title: Mol_90-96h_6


title: P_21-25h_11


title: Mol_90-96h_9


title: Mol_90-96h_5


title: Mol_90-96h_4


title: Mol_90-96h_47


title: Mol_90-96h_48


title: P_21-25h_16


title: Mol_90-96h_46


title: P_21-25h_12


title: Mol_90-96h_37


title: Mol_90-96h_38


title: Mol_90-96h_8


title: Mol_90-96h_44


title: Mol_90-96h_39


title: Mol_90-96h_41


title: Mol_90-96h_40


title: Mol_90-96h_3


title: Mol_90-96h_43


title: Mol_90-96h_45


title: Phaffia rhodozyma cells, S3

city: Hangzhou

first: Guoliang

last: Bao

address: No. 182 Tianmushan Road

country: China

institute: Hangzhou medical college

description: SVSC_Transcript_differential_expression.xlsx

data_processing:
A cDNA library constructed by technology from the pooled RNA from < sample description > samples of < research species > was sequenced run with Illumina Novaseq TM 6000 sequence platform.
The FASTAQ format data was first processed with the fastap software (https://github.com/OpenGene/fastp), and the clean reads with adapters, poly-N, and low-quality reads removed were obtained
The HISAT2 (https://ccb.jhu.edu/software/hisat2) was used to map reads to the reference genome of P. rhodozyma CBS6938 (Genebank No. GCA_014706385.1)
StringTie was used to estimate the expression levels of all transcripts through the FPKM value
The R package GOseq was used to conduct GO enrichment analysis of the DEGs with a significant p value <0.05
The KOBAS software was used to enrich signiﬁcant DEGs in the KEGG pathway
Assembly: NCBI_Xden1（GCA_001007165.2）
Supplementary files format and content: Excel file includes FPKM values for each Sample

organism: Phaffia rhodozyma

source_name: yeast cell

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) according to the manufacturer's procedure. Then 10 ug of total RNA was extracted according to the RNA-Seq sample preparation kit for constructing sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: yeast cell

value: Salicylic acid


title: M2_MTX_B: MTX-M-MØ macrophage donor2 rep2

city: Madrid

first: Amaya

middle: Rocío

last: Puig Kröger

state: Madrid

address: Dr. Esquerdo 46

department: Immunology

country: Spain

institute: Hospital General Universitario Gregorio Marañón

data_processing:
BGISEQ-500 platform
Low quality reads (More than 20% of the bases qualities are lower than 10), reads with adaptors and reads with unknown bases (N bases more than 5%) were filtered to get the clean reads. Sequences were mapped to GRCh38 genome using  Bowtie2 with the following parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant  -p 1 -k 200
Gene expression levels were determined with software RSEM
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include Entrez Gene ID and FPKM values for each Sample

organism: Homo sapiens

source_name: macrophages

growth_protocol: Human Peripheral Blood Mononuclear Cells (PBMC) were isolated from buffy coats from three healthy donors over a Lymphoprep gradient according to standard procedures. Monocytes were purified from PBMC by magnetic cell sorting using anti-CD14 microbeads (>95% CD14+ cells). Monocytes (0.5 x 10^6 cells/ml, >95% CD14+ cells) were cultured  in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) for 7 days in the presence of 10 ng/ml M-CSF to generate M-CSF-polarized macrophages (M-MØ).

extract_protocol:
Total RNA was extracted using the NucleoSpin RNA kit (Macherey-Nagel, Düren, Germany). Qualitative analysis of total RNAs were performed in a bioanalizer Agilent 2100.
RNA libraries were prepared for sequencing using standard BGI protocols

treatment_protocol: Freshly isolated CD14+ monocytes were cultured for 7 days in RPMI 10% FBS containing M-CSF after an initial exposure (at day 0) to 5 micromolar of the antifolate methotrexate (MTX).

value: Monocyte-derived M-CSF macrophages

value: MTX-treated


title: Phaffia rhodozyma cells, C2

value: nothing


title: Mol_90-96h_28


title: Mol_90-96h_31


title: Mol_90-96h_29


title: Mol_90-96h_30


title: Mol_90-96h_2


title: Mol_90-96h_33


title: Mol_90-96h_32


title: Mol_90-96h_35


title: Mol_90-96h_36


title: Phaffia rhodozyma cells, C1


title: Phaffia rhodozyma cells, C3


title: Phaffia rhodozyma cells, S1


title: ATP7B_m_Cu_1

city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

country: Italy

institute: Tigem

description:
Transcriptome profile of cua-1 (H828Q) strain treated with CuCl2, biological rep1
ATP7B_m_Cu_1

data_processing:
Illumina NovaSeq 6000 base call (BCL) files were converted in fastq file through bcl2fastq
Alignment was performed with STAR 2.6.0a The expression levels of genes were determined with HTseq-counts 0.9.1
Assembly:   ce11
Supplementary files format and content: The expression levels of genes were determined with HTseq-counts 0.9.1

organism: Caenorhabditis elegans

source_name: not known

growth_protocol: Worms were grown and handled following standard procedures, under uncrowded conditions, at 20°C, on NGM (Nematode Growth Medium) agar plates seeded with Escherichia coli strain OP50

extract_protocol:
RNA was extracted after a growth of three days on a NGM  agar plate for each condition
Total RNA was quantified using the Qubit 4.0 fluorimetric Assay (Thermo Fisher Scientific).
Libraries were prepared from 125 ng of total RNA using the NEGEDIA Digital mRNA-seq research grade sequencing service (Next Generation Diagnostic srl; https://doi.org/10.1038/s41598-017-14892-x) which included library preparation, quality assessment and sequencing on a NovaSeq 6000 sequencing system using a single-end, 100 cycle strategy (Illumina Inc.).
NEGEDIA Digital mRNA-seq

treatment_protocol: Syncronyzed worms were grown on 100-mm NGM plates for three days  without or with 100 uM of copper. Worms were washed with M9 buffer and then resuspended in Trizol reagent and flash frozen with liquid nitrogen.  Frozen worms were ground in dry-ice-cooled mortar and pestle and total RNA was extracted using chloroform/ethanol protocol.

tag: agent

value: not known


title: Phaffia rhodozyma cells, S2


title: M2_MTX_A: MTX-M-MØ macrophage donor1 rep1


title: Mol_90-96h_42


title: M2_MTX_C: MTX-M-MØ macrophage donor3 rep3


title: Mol_90-96h_34


title: CTR_Cu_4

description:
Transcriptome profile of c.elegans treated with CuCl2, biological rep4
CTR_Cu_4

value: control


title: ATP7B_m_Cu_4

description:
Transcriptome profile of cua-1 (H828Q) strain treated with CuCl2, biological rep4
ATP7B_m_Cu_4


title: M2_C: M-MØ macrophage donor3 rep3

value: untreated


title: M2_B: M-MØ macrophage donor2 rep2


title: M2_A: M-MØ macrophage donor1 rep1


title: CTR_noCu_3

description:
Transcriptome profile of c.elegans, biological rep3
CTR_noCu_3


title: CTR_noCu_4

description:
Transcriptome profile of c.elegans, biological rep4
CTR_noCu_4


title: ATP7B_m_noCu_4

description:
Transcriptome profile of cua-1 (H828Q) strain , biological rep4
ATP7B_m_noCu_4


title: ATP7B_m_Cu_3

description:
Transcriptome profile of cua-1 (H828Q) strain treated with CuCl2, biological rep3
ATP7B_m_Cu_3


title: ATP7B_m_Cu_2

description:
Transcriptome profile of cua-1 (H828Q) strain treated with CuCl2, biological rep2
ATP7B_m_Cu_2


title: CTR_Cu_2

description:
Transcriptome profile of c.elegans treated with CuCl2, biological rep2
CTR_Cu_2


title: CTR_Cu_3

description:
Transcriptome profile of c.elegans treated with CuCl2, biological rep3
CTR_Cu_3


title: CTR_Cu_1

description:
Transcriptome profile of c.elegans treated with CuCl2, biological rep1
CTR_Cu_1


title: CTR_noCu_2

description:
Transcriptome profile of c.elegans, biological rep2
CTR_noCu_2


title: ATP7B_m_noCu_2

description:
Transcriptome profile of cua-1 (H828Q) strain , biological rep2
ATP7B_m_noCu_2


title: ATP7B_m_noCu_1

description:
Transcriptome profile of cua-1 (H828Q) strain , biological rep1
ATP7B_m_noCu_1


title: Day 1 adult on hsf-1 RNAi, biological rep 4

city: Ann Arbor

first: Bryndon

last: Oleson

state: MI

address: 1100 N. University Ave

institute: University of Michigan

data_processing:
CleanData (fastq format) to remove low quality reads and adapters with cutadapt and perl scripts in house
Reads mapped to genome of https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/002/985/GCF_000002985.6_WBcel235 using HISAT2
Transcripts assembled using StringTie, and assemblies merged using StringTie and gffcompare
mRNA expression profiling done using Stringtie
Differential mRNA expression using DESeq2. mRNAs with a FDR <0.05 and fold change >2 considered differentially expressed
Assembly: GCF_000002985.6_WBcel235
Supplementary files format and content: Excel files including FPKM values for each sample

source_name: Whole organism

extract_protocol:
RNA was extracted from frozen C. elegans pellets via mechanical homogenization in TRIzol, extraction via chloroform, and clean-up and concentration via a QIAGEN RNeasy column and Dnase treatment. 1-5 µg of RNA was used per sample.
Illumina TruSeq-stranded mRNA sample preparation protocol

value: Whole organism

value: Day 1

value: Day 1 adult on hsf-1 RNAi


title: Day 1 adult on ash-2 + hsf-1 RNAi, biological rep 2

value: Day 1 adult on ash-2 + hsf-1 RNAi


title: Day 1 adult on ash-2 + hsf-1 RNAi, biological rep 4


title: ATP7B_m_noCu_3

description:
Transcriptome profile of cua-1 (H828Q) strain , biological rep3
ATP7B_m_noCu_3


title: CTR_noCu_1

description:
Transcriptome profile of c.elegans, biological rep1
CTR_noCu_1


title: Day 1 adult on L4440 RNAi, biological rep 4

value: Day 1 adult on L4440 RNAi


title: Day 1 adult on L4440 RNAi, biological rep 3


title: Day 1 adult on ash-2 + hsf-1 RNAi, biological rep 3


title: Day 1 adult on L4440 RNAi, biological rep 1


title: HSC-derived NKT cells, rep3

city: Los Angeles

first: Wenbin

last: Guo

state: CA

address: 610 Charles E. Young Drive, TLSB 5000

institute: UCLA

description:
854_iNKT-TK
raw_counts.txt

data_processing:
The raw sequencing data underwent quality check using FastQC software (version 0.11.9), and fastp (version 0.23.2) was used to remove sequencing adapters and low-quality bases
The trimmed reads were mapped to the human reference genome (hg38) along with and annotation file gencode v32 using software STAR (version 2.7.9a)
gene count matrixes were obtained using featureCounts from Subread package (version 2.0.3)
Downstream data analysis was performed using R (version 4.2). For more details, please refer to the manuscipt
Assembly: hg38
Supplementary files format and content: raw_counts.txt: tab-delimited text file includes gene expression raw counts for each sample

source_name: AlloNKT

extract_protocol:
RNAs were isolated from each cell sample using a miRNeasy Mini Kit (QIAGEN).
Libraries were constructed using an Illumina TruSeq Stranded Total RNA Sample Prep kit.

value: AlloNKT


title: HSC-derived NKT cells, rep2

description:
784_iNKT-TK
raw_counts.txt


title: Day 1 adult on hsf-1 RNAi, biological rep 3


title: Day 1 adult on hsf-1 RNAi, biological rep 2


title: Day 1 adult on hsf-1 RNAi, biological rep 1


title: Day 1 adult on ash-2 RNAi, biological rep 4

value: Day 1 adult on ash-2 RNAi


title: Day 1 adult on ash-2 RNAi, biological rep 3


title: Day 1 adult on ash-2 RNAi, biological rep 2


title: Day 1 adult on ash-2 RNAi, biological rep 1


title: Day 1 adult on L4440 RNAi, biological rep 5


title: Day 1 adult on L4440 RNAi, biological rep 2


title: HSC-derived CAR19-engineered NKT cells, rep2

description:
784_CAR19_Bi
raw_counts.txt


title: PBMC-derived CD8 conventional T cells, rep2 (re-analyzed)

description:
SRR13381434
raw_counts.txt
Re-analysis of GSM5009495

source_name: PBMC-T

value: PBMC-T


title: PBMC-derived CD8 conventional T cells, rep7 (re-analyzed)

description:
SRR13381439
raw_counts.txt
Re-analysis of GSM5009500


title: PBMC-derived CD8 NKT cells, rep2 (re-analyzed)

description:
SRR13381425
raw_counts.txt
Re-analysis of GSM5009511

source_name: PBMC-NKT

value: PBMC-NKT


title: PBMC-derived CD8 conventional T cells, rep5 (re-analyzed)

description:
SRR13381437
raw_counts.txt
Re-analysis of GSM5009498


title: PBMC-derived NK cells, rep2 (re-analyzed)

description:
SRR13381423
raw_counts.txt
Re-analysis of GSM5009509

source_name: PBMC-NK

value: PBMC-NK


title: HSC-derived NKT cells, rep1

description:
768_iNKT-TK_083
raw_counts.txt


title: HSC-derived CAR19-engineered NKT cells, rep1

description:
687_CAR19_Bi
raw_counts.txt


title: Day 1 adult on ash-2 + hsf-1 RNAi, biological rep 1


title: HSC-derived BCAR-engineered IL15-enhanced NKT cells, rep3

description:
SS-B-iNKT15-3
raw_counts.txt


title: PBMC-derived CD8 conventional T cells, rep3 (re-analyzed)

description:
SRR13381435
raw_counts.txt
Re-analysis of GSM5009496


title: HSC-derived BCAR-engineered NKT cells, rep3

description:
854_BCAR_Bi
raw_counts.txt

source_name: AlloBCAR-NKT

value: AlloBCAR-NKT


title: HSC-derived BCAR-engineered NKT cells, rep1

description:
687_BCAR_Bi
raw_counts.txt


title: PBMC-derived CD8 conventional T cells, rep8 (re-analyzed)

description:
SRR13381440
raw_counts.txt
Re-analysis of GSM5009501


title: PBMC-derived CD8 conventional T cells, rep6 (re-analyzed)

description:
SRR13381438
raw_counts.txt
Re-analysis of GSM5009499


title: PBMC-derived CD8 conventional T cells, rep4 (re-analyzed)

description:
SRR13381436
raw_counts.txt
Re-analysis of GSM5009497


title: PBMC-derived CD8 conventional T cells, rep1 (re-analyzed)

description:
SRR13381433
raw_counts.txt
Re-analysis of GSM5009494


title: PBMC-derived CD8 NKT cells, rep3 (re-analyzed)

description:
SRR13381426
raw_counts.txt
Re-analysis of GSM5009512


title: WT_Ali3

city: Houston

first: Di

last: Zhao

state: Tx

address: Zayed Building Z7. 4018

institute: MD Anderson Cancer Center

data_processing:
Basecalling was done by Illumina HiSeq Control Software (version HD 3.4.0.38).
The reads were mapped to the human genome (hg38) by TopHat (version 2.0.10).
The number of fragments in each known gene from GENCODE Release 35 was enumerated using htseq-count from HTSeq package (version 0.6.0).
Genes with less than 10 fragments in all the samples were removed, and then the normalized fragment count for each gene was calculated by R/Bioconductor package DESeq (version 1.18.0).
Genome_build: hg38
Supplementary_files_format_and_content: The first column is Ensembl gene id. The second column is gene symbol. The other columns are normalized expression values (estimated by DESeq) for all the samples.

molecule: polyA RNA

source_name: BPH1_CHD1 Wildtype_Alisertib

growth_protocol: WT and CHD1 KO BPH1 cells were cultured in DMEM (Corning, #10-017-CV) supplemented with 10% FBS and 1% P/S.

extract_protocol:
Cells were lysed with TRIzol (Life Tech, Cat. #15596026), followed by RNA extraction with chloroform following the standard protocol and RNA purification using RNeasy Mini Kit (QIAGEN, Cat. #74104). Experiment was performed in triplicate.
Libraries were made using an Illumina TruSeq stranded mRNA kit.

treatment_protocol: WT and CHD1 KO BPH1 cells were treated with DMSO or Alisertib (10μM) for 24 hours. The experiment was performed in triplicate.

tag: tissue source

value: Prostate

value: Benign prostatic hyperplasia (BPH) epithelial cell line

value: CHD1 Wildtype

value: Alisertib


title: WT_Ali1


title: HSC-derived BCAR-engineered NKT cells, rep2

description:
768_BCAR_Bi
raw_counts.txt


title: PBMC-derived CD8 NKT cells, rep1 (re-analyzed)

description:
SRR13381424
raw_counts.txt
Re-analysis of GSM5009510


title: KO_Ali3

source_name: BPH1_CHD1 Knockout_Alisertib

value: CHD1 Knockout


title: KO_Ali1


title: HSC-derived BCAR-engineered IL15-enhanced NKT cells, rep2

description:
SS-B-iNKT15-2
raw_counts.txt


title: PBMC-derived NK cells, rep1 (re-analyzed)

description:
SRR13381422
raw_counts.txt
Re-analysis of GSM5009508


title: HSC-derived BCAR-engineered IL15-enhanced NKT cells, rep1

description:
SS-B-iNKT15-1
raw_counts.txt


title: WT_C2

source_name: BPH1_CHD1 Wildtype_DMSO

value: DMSO


title: WT_Ali2


title: Mol_90-96h_26

value: Morula

value: (C57BL/6J x CBA) x DBA/2J


title: KO_C2

source_name: BPH1_CHD1 Knockout_DMSO


title: KO_C3


title: WT_C1


title: KO_C1


title: WT_C3


title: Mol_90-96h_27


title: KO_Ali2


title: MEF_Nkiras1Nkiras2_doubleKO_EGF5h

type: RNA

city: Jersey City

first: Thomas

middle: S

last: Postler

state: New Jersey

address: 95 Greene Street 5-018

department: Discovery Science

institute: International AIDS Vaccine Initiative

hyb_protocol: NimbleGen protocol.

scan_protocol: NimbleGen protocol.

data_processing: Raw data were processed with NimbleScan v2.5 and analyzed with GeneSpring v11.0

source_name: mouse embryonic fibroblasts from Nkiras1-/- Nkiras2-/- mice, stimulated with 100 ng/ml EGF for 5 h

label_protocol: NimbleGen protocol.

growth_protocol: Standard cell culture

extract_protocol: RNA isolation with TRIzol

treatment_protocol: Stimulation with 100 ng/ml EGF for 5 h where indicated

value: MEFs

value: MEFs were generated on embryonic day 12.5

value: Nkiras1-/- Nkiras2-/-

value: EGF


title: MEF_Nkiras1KO_unstimulated

source_name: mouse embryonic fibroblasts from Nkiras1-/- Nkiras2+/+ mice, unstimulated

value: Nkiras1-/- Nkiras2+/+

value: unstimulated


title: Mol_90-96h_17


title: Mol_90-96h_22


title: Mol_90-96h_23


title: Mol_90-96h_16


title: Mol_90-96h_15


title: Mol_90-96h_24


title: Mol_90-96h_13


title: Mol_90-96h_1


title: Mol_90-96h_19


title: Mol_90-96h_25


title: MEF_Nkiras1Nkiras2_doubleKO_unstimulated

source_name: mouse embryonic fibroblasts from Nkiras1-/- Nkiras2-/- mice, unstimulated


title: Mol_90-96h_14

source_name: Morula


title: Mol_90-96h_18


title: Mol_90-96h_21


title: Mol_90-96h_10


title: MEF_Nkiras1KO_EGF5h

source_name: mouse embryonic fibroblasts from Nkiras1-/- Nkiras2+/+ mice, stimulated with 100 ng/ml EGF for 5 h


title: M_21-25h_6

source_name: maternal PN

value: maternal PN

value: (C57BL/6J x CBA)F1


title: Mol_90-96h_11


title: Mol_90-96h_12


title: M_21-25h_9


title: M_21-25h_5


title: Mol_90-96h_20


title: M_21-25h_8


title: M_21-25h_7


title: M_21-25h_51


title: M_21-25h_52


title: M_21-25h_4


title: M_21-25h_49


title: M_21-25h_47


title: M_21-25h_48


title: M_21-25h_46


title: M_21-25h_45


title: M_21-25h_43


title: M_21-25h_39


title: M_21-25h_42


title: M_21-25h_36


title: M_21-25h_37


title: M_21-25h_29


title: M_21-25h_26


title: M_21-25h_27


title: M_21-25h_32


title: M_21-25h_35


title: M_21-25h_28


title: M_21-25h_2


title: M_21-25h_41


title: M_21-25h_44


title: M_21-25h_21


title: M_21-25h_40


title: M_21-25h_19


title: M_21-25h_1


title: M_21-25h_3


title: M_21-25h_23


title: M_21-25h_20


title: M_21-25h_31


title: M_21-25h_34


title: M_21-25h_25


title: M_21-25h_15


title: M_21-25h_18


title: M_21-25h_17


title: M_21-25h_16


title: M_21-25h_14


title: M_21-25h_11


title: M_21-25h_13


title: M_21-25h_12


title: IVF_Zygote_9.5h_40

source_name: IVF Zygote

value: IVF Zygote


title: IVF_Zygote_9.5h_37


title: IVF_Zygote_9.5h_34


title: IVF_Zygote_9.5h_39


title: IVF_Zygote_9.5h_35


title: IVF_Zygote_8.5h_32


title: IVF_Zygote_9.5h_33


title: IVF_Zygote_9.5h_38


title: IVF_Zygote_9.5h_36


title: M_21-25h_10


title: IVF_Zygote_8.5h_31


title: IVF_Zygote_8.5h_30


title: IVF_Zygote_8.5h_29


title: IVF_Zygote_8.5h_28


title: IVF_Zygote_7.5h_64


title: IVF_Zygote_8.5h_25


title: IVF_Zygote_8.5h_26


title: IVF_Zygote_7.5h_63


title: IVF_Zygote_7.5h_62


title: IVF_Zygote_7.5h_61


title: IVF_Zygote_8.5h_27


title: IVF_Zygote_7.5h_60


title: IVF_Zygote_7.5h_24


title: IVF_Zygote_7.5h_59


title: IVF_Zygote_7.5h_58


title: IVF_Zygote_7.5h_22


title: IVF_Zygote_7.5h_23


title: IVF_Zygote_7.5h_21


title: IVF_Zygote_7.5h_20


title: IVF_Zygote_7.5h_19


title: IVF_Zygote_7.5h_17


title: IVF_Zygote_6.5h_9


title: IVF_Zygote_7.5h_18


title: IVF_Zygote_6.5h_53


title: IVF_Zygote_6.5h_52


title: IVF_Zygote_6.5h_51


title: IVF_Zygote_6.5h_15


title: IVF_Zygote_6.5h_56


title: IVF_Zygote_6.5h_49


title: IVF_Zygote_6.5h_16


title: IVF_Zygote_6.5h_50


title: IVF_Zygote_6.5h_54


title: IVF_Zygote_6.5h_55


title: IVF_Zygote_6.5h_13


title: IVF_Zygote_6.5h_14


title: IVF_Zygote_6.5h_11


title: IVF_Zygote_6.5h_12


title: IVF_Zygote_7.5h_57


title: IVF_Zygote_5.5h_7


title: IVF_Zygote_5.5h_5


title: IVF_Zygote_6.5h_10


title: IVF_Zygote_5.5h_8


title: IVF_Zygote_5.5h_6


title: IVF_Zygote_5.5h_2


title: IVF_Zygote_5.5h_3


title: IVF_Zygote_5.5h_1


title: IVF_Zygote_10.5h_72


title: IVF_Zygote_10.5h_69


title: IVF_Zygote_10.5h_70


title: IVF_Zygote_10.5h_71


title: IVF_Zygote_10.5h_68


title: IVF_Zygote_10.5h_48


title: IVF_Zygote_10.5h_65


title: IVF_Zygote_10.5h_67


title: IVF_Zygote_10.5h_66


title: IVF_Zygote_10.5h_47


title: IVF_Zygote_10.5h_46


title: IVF_Zygote_10.5h_43


title: IVF_Zygote_10.5h_44


title: ICM_96-100h_9

source_name: ICM

value: ICM


title: IVF_Zygote_10.5h_42


title: ICM_96-100h_79


title: ICM_96-100h_80


title: ICM_96-100h_8


title: IVF_Zygote_10.5h_41


title: ICM_96-100h_7


title: IVF_Zygote_5.5h_4


title: ICM_96-100h_77


title: ICM_96-100h_76


title: ICM_96-100h_71


title: ICM_96-100h_73


title: ICM_96-100h_78


title: ICM_96-100h_70


title: ICM_96-100h_68


title: ICM_96-100h_6


title: ICM_96-100h_69


title: ICM_96-100h_67


title: ICM_96-100h_66


title: IVF_Zygote_10.5h_45


title: ICM_96-100h_64


title: ICM_96-100h_65


title: ICM_96-100h_63


title: ICM_96-100h_62


title: ICM_96-100h_61


title: ICM_96-100h_74


title: ICM_96-100h_60


title: ICM_96-100h_58


title: ICM_96-100h_59


title: ICM_96-100h_72


title: ICM_96-100h_4


title: ICM_96-100h_47


title: ICM_96-100h_57


title: ICM_96-100h_5


title: ICM_96-100h_46


title: ICM_96-100h_45


title: ICM_96-100h_43


title: ICM_96-100h_44


title: ICM_96-100h_38


title: ICM_96-100h_42


title: ICM_96-100h_39


title: ICM_96-100h_41


title: ICM_96-100h_3


title: ICM_96-100h_28


title: ICM_96-100h_37


title: ICM_96-100h_31


title: ICM_96-100h_27


title: ICM_96-100h_2


title: ICM_96-100h_34


title: ICM_96-100h_33


title: ICM_96-100h_75


title: ICM_96-100h_32


title: ICM_96-100h_35


title: ICM_96-100h_25


title: ICM_96-100h_24


title: ICM_96-100h_17


title: ICM_96-100h_23


title: ICM_96-100h_21


title: ICM_96-100h_40


title: ICM_96-100h_22


title: ICM_96-100h_36


title: ICM_96-100h_16


title: ICM_96-100h_30


title: ICM_96-100h_14


title: ICM_96-100h_15


title: ICM_96-100h_18


title: ICM_96-100h_19


title: ICM_96-100h_20


title: ICM_96-100h_29


title: ICM_96-100h_13


title: ICM_96-100h_11


title: ICM_96-100h_10


title: ICM_102-104h_9


title: ICM_96-100h_26


title: ICM_102-104h_5


title: ICM_102-104h_56


title: ICM_96-100h_1


title: ICM_102-104h_54


title: ICM_102-104h_7


title: ICM_102-104h_48


title: ICM_102-104h_53


title: ICM_102-104h_52


title: ICM_102-104h_44


title: ICM_102-104h_8


title: ICM_102-104h_4


title: ICM_102-104h_51


title: ICM_102-104h_50


title: ICM_102-104h_49


title: ICM_102-104h_41


title: ICM_102-104h_40


title: ICM_102-104h_42


title: ICM_96-100h_12


title: ICM_102-104h_47


title: ICM_102-104h_45


title: ICM_102-104h_6


title: ICM_102-104h_35


title: ICM_102-104h_55


title: ICM_102-104h_3


title: ICM_102-104h_34


title: ICM_102-104h_37


title: ICM_102-104h_39


title: ICM_102-104h_38


title: ICM_102-104h_46


title: ICM_102-104h_32


title: ICM_102-104h_33


title: ICM_102-104h_43


title: ICM_102-104h_31


title: ICM_102-104h_36


title: ICM_102-104h_30


title: ICM_102-104h_24


title: ICM_102-104h_26


title: ICM_102-104h_22


title: ICM_102-104h_21


title: ICM_102-104h_2


title: ICM_102-104h_29


title: ICM_102-104h_23


title: ICM_102-104h_27


title: ICM_102-104h_1


title: ICM_102-104h_18


title: ICM_102-104h_17


title: ICM_102-104h_19


title: ICM_102-104h_25


title: ICM_102-104h_28


title: 8-Cell_69h_65

source_name: 8-cell embryo

value: 8-cell embryo


title: 8-Cell_72h_47


title: ICM_102-104h_12


title: 8-Cell_72h_44


title: ICM_102-104h_15


title: 8-Cell_72h_46


title: ICM_102-104h_14


title: 8-Cell_69h_66


title: ICM_102-104h_13


title: ICM_102-104h_16


title: 8-Cell_72h_48


title: ICM_102-104h_11


title: 8-Cell_72h_43


title: ICM_102-104h_20


title: ICM_102-104h_10


title: 8-Cell_72h_45


title: WT_NN_2: Colon macrophages from WT mice 2

city: Derio

first: Jose

middle: Luis

last: Lavin

state: Bizkaia

address: Parque Tecnológico de Bizkaia Building 502, Floor 0

institute: CIC bioGUNE

data_processing:
Basecalls performed using CASAVA version 1.8.2
Individual FASTQ files for each sample were merged prior to the quality control & filtering steps
Quality control of the reads was carried out using FASTQC software (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Reads were filtered from the adapter sequences and  their quality score using trim_galore software. (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and  only are retained those  with at least 20 phred quality score.
Reads were mapped to mm10 (Mus musculus) reference genome using STAR v2.5.4 (https://github.com/alexdobin/STAR).
Resulting BAM aligment files were used in as input for a Differential Expression Analysis pipeline based on DESeq2 BioconductoR package (https://bioconductor.org/packages/release/bioc/html/DESeq2.html).
Genome_build: mm10
Supplementary_files_format_and_content: Tables of raw counts, obtained from the BAM files of the samples in each comparative using Rsubread BioconductoR package (http://bioconductor.org/packages/release/bioc/html/Rsubread.html). These tables are in tab separated plain text format.

source_name: Colon macrophages

growth_protocol: Mice were breed and housed at the Animal Facility of CIC bioGUNE under controled conditions according to the animal care international gidelines.

extract_protocol:
Total RNA was extracted using Trizol reagent protocol.
Universal Plus mRNA-SeqNuGEN

treatment_protocol: Mice were treated with  a broad spectrum antibiotic during 7 days or not previously to DSS treatment for 6 days. Mice colon tissue was collected and macrophages were extracted using several washing steps and by enzymatic disruption mediated by collagenase type IV.

tag: strain

value: 8 weeks

value: Colon macrophages


title: WT_NN_1: Colon macrophages from WT mice 1


title: WT_NP_7: Colon macrophages from WT mice 4 Ant-DSS+


title: WT_PP_11: Colon macrophages from WT mice 11 Ant+DSS+


title: WT_NP_8: Colon macrophages from WT mice 5 Ant-DSS+


title: 8-Cell_69h_32


title: 8-Cell_72h_41


title: 8-Cell_72h_36


title: 8-Cell_72h_37


title: 8-Cell_72h_39


title: 8-Cell_69h_31


title: 8-Cell_72h_33


title: 8-Cell_72h_40


title: 8-Cell_69h_28


title: 8-Cell_72h_42


title: 8-Cell_72h_34


title: WT_PP_10: Colon macrophages from WT mice 10 Ant+DSS+


title: WT_NN_3: Colon macrophages from WT mice 3


title: 8-Cell_72h_38


title: WT_PP_12: Colon macrophages from WT mice 12 Ant+DSS+


title: WT_NP_9: Colon macrophages from WT mice 6 Ant-DSS+


title: 8-Cell_69h_30


title: 8-Cell_69h_25


title: 8-Cell_72h_35


title: 8-Cell_69h_29


title: 8-Cell_69h_27


title: KO_PP_23: Colon macrophages from MCJ deficient mice 9 Ant+DSS+


title: 8-Cell_69h_26


title: KO_NP_19: Colon macrophages from MCJ deficient mice 1 Ant-DSS+


title: 8-Cell_69h_23


title: KO_PP_22: Colon macrophages from MCJ deficient mice 8 Ant+DSS+


title: KO_NP_21: Colon macrophages from MCJ deficient mice 3 Ant-DSS+


title: 8-Cell_69h_20


title: KO_NP_20: Colon macrophages from MCJ deficient mice 2 Ant-DSS+


title: 8-Cell_69h_19


title: 8-Cell_69h_22


title: KO_NN_13: Colon macrophages from MCJ deficient mice 1


title: KO_PP_24: Colon macrophages from MCJ deficient mice 10 Ant+DSS+


title: 8-Cell_69h_21


title: Vehicle-2

city: Philadelphia

first: Serge

middle: Y.

last: Fuchs

state: PA

address: 316 Hill Veterinary School

institute: University of Pennsylvania

data_processing:
sequencing reads were aligned to the mouse genome mm10 with STAR v. 2.7.2 using default parameters
Expression levels for each gene were counted by VERSE v. 0.1.4, and exonic reads are retained for downstream analyses.
Normalization and differential expression (DE) analysis was conducted by DESeq2 v. 1.28.1.
Significantly enriched pathways (P-value < 0.05) were determined through gene set enrichment analysis (GSEA) integrated in the R/Bioconductor package “clusterProfiler” v. 3.14.3.
Assembly: mm10
Supplementary files format and content: normalized_count

source_name: tumor

growth_protocol: Tumor was s.c. injected into WT mice and let them to grow for 7  days

extract_protocol:
RNA was extraced from tumor tissue using Trizol agent kit
The library was constructed  using Illumina stranded mRNA Prep protocol

treatment_protocol: Vehicle of dCNP were injected s.c. into tumor bearing mice at 0.3 mg/kg

value: tumor

tag: cell line

value: cancer cell

value: WT

value: Vehicle


title: dCNP-3

value: dCNP


title: Vehicle-3


title: dCNP-1


title: 8-Cell_69h_24

value: (C57BL/6J x CBA) x DBA/2J


title: dCNP-2


title: 8-Cell_68h_60


title: 8-Cell_68h_64


title: 8-Cell_68h_59


title: 8-Cell_68h_58


title: 8-Cell_68h_61


title: 8-Cell_68h_63


title: 8-Cell_69h_17


title: 8-Cell_68h_62


title: 8-Cell_69h_18


title: ValLib_mouse_BIC_R3

city: Muenster

first: Michael

middle: J

last: Ziller

address: Busso-Peus-Str. 10

institute: University of Muenster

description: ValLib_countMatrix_final_barcode_raw.txt

data_processing:
Associating MPRA barcodes with sequence elements: In order to associate the 3’ barcodes with its corresponding sequence/variant tested, we performed paired end sequencing of the intermediate MPRA library prior to inserting the minP-nanoLuc cassette, sequencing 150 cycles from either end on a Illumina MiSeq. Resulting FASTQ files were the modified to clip the 16bp barcode at the end of the second read to be included in the sequence name. Subsequently, the reads were aligned against a custom build reference of the original sequences included in each MPRA library using bwa version 0.7.17(Li and Durbin, 2009) in paired end mode. Resulting .bam files were converted to table format, only retaining aligned reads harboring the expected variant at the center position and including less than 5 clipped or mismatched bases. Subsequently, reads were collapsed onto individual barcodes and only barcodes covered by at least 2 reads and uniquely associated with one sequence element were retained for further analysis.
Processing of 3’ sequencing data: 3’mRNA sequencing data obtained from MPRA experiments in iPSC derived neurons or primary mouse cortical cultures were processed with a custom python scripts to count occurence of individual barcodes discovered in the data. All reads were filtered based on quality metrics, only retaining reads with less than 5 bases below a phred score of 20 and proper backbone sequence elements at the expected positions of the read, e.g. presence of the restriction site TCT and GAC. Subsequently, all 16mer barcodes from the remaining reads were counted initially, but only those barcodes also present in the quality-controlled results of the barcode-pEE association sequencing of the MPRA plasmid library were kept for quantitative analysis.
Assembly: hg19
Supplementary files format and content: table with the following columns: Barcode – unique 16mer barcode of mRNA fragment  Eid – unique Id of reference enhancer element that this barcode associates to  variantMapped – Boolean variable indicating if the expected SNP was detected at the correct position in the association sequencing  reference_name – name of the reference sequence fragment, corresponds to fasta file for this library  chrom – chromosome of enhancer fragment  chromstart – start coordinate of putative enhancer fragment  chromend – end coordinate of putative enhancer fragment  allele – detected allele in this fragment   ref_bases – reference allele for SNP that is interrogated by this putative enhance fragment  alt_bases – alternative allele for SNP that is interrogated by this putative enhance fragment  type – type of fragment, e.g. control or SNP   count – tag count of this fragment in the original plasmid library, used for normalization  followed by observed tag counts for MPRA all tag  count libraries from the different cell types and conditions evaluated

source_name: primary cortical cultures

growth_protocol: iPSC derived neurons were generated via overexpression of pro-neural transcription factor Ngn2 plus small molecules and differentiated for 49 days on murine astrocytes. NPCs were differentiated based on the protocol from (Qi et al., 2017) with slight modifications. Primary mouse cortical cultures were generated from E15.5 mice cultured in vitro over a total of 12 days.

extract_protocol:
All cell types were directly lysed with lysis buffer (Quick-RNA Miniprep Kit, R1054, Zymogen). To increase the yield of the total RNA purification, QIAshredder columns (79654, Qiagen) were used before total RNA isolation. On-column DNAse digest was performed to digest DNA residues. Concentration of total RNA was measured by NanoDrop before performing mRNA isolation with the Poly(A)Purist MAG kit (AM1922, ThermoFisher Scientific) according to manufacturer’s protocol. Purification with glycogen was omitted and mRNA was directly isolated from the beads.
Association Seq: The fragments were amplified at the pMPRA1-enhancer-barcode stage in order to associate enhancer and their respective barcodes. The same forward primer (5’ AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT 3’) was used for all amplifications, while the reverse primer (5’CAAGCAGAAGACGGCATACGAGAT NNNNNNNNGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTGGTGCCAGAACATTTCTCTG3’) was barcoded (for barcode sequences see Table S7). 100 pg plasmid DNA, 1x Q5 Hot Start High-Fidelity 2x Master Mix (M0494L, NEB) and 0.5 µM reverse and forward primer were mixed and DNA was amplified at the following conditions: 98°C for 30 s, 16 cycles of [98°C for 10 s, 60°C for 30 s, 72°C for 20 s], and a final extension step for 2 min at 72°C. 8 PCR reactions were pooled and purified with Agencourt Ampure XP magnetic beads (A63881, Beckman Coulter) with a double sided selection with 0.55x and subsequently 0.35x of the volume of the pooled PCR product. Purification and clean-up were performed according to manufacturer’s recommendations. The correct fragment size and the concentration of the library were analyzed with the Bioanalyzer (High Sensitivity DNA Analysis, 5067-4626, Agilent). Library quantification was performed in triplicates with an RT-qPCR on the Illumina sequencing adapters according to manufacturer’s protocol (KAPA Library Quantification) on a Roche LightCycler® 480 System. 6-10 % PhiX were spiked into the final library of 6-10 pmol. Paired-end (150 bp each side) sequencing was performed with the MiSeq Reagent Kit (v2, 300-cycles, MS-102-2002, Illumina).  TagCountSeq: 30 µl mRNA were reverse transcribed into cDNA with 2 µl SuperScript IV reverse transcriptase (18090050, ThermoFisher Scientific) and 8 µl SuperScript™ IV VILO™ Master Mix (11756050, ThermoFisher Scientific): 25°C for 10 min, 50°C for 30 min and 85°C for 5 min. In order to analyze the activity of the enhancer, the barcodes were amplified from the cDNA: The PCR protocol described beforehand was used, but the cycle number was increased from 16 to 22 cycles. 0.5 µl cDNA were used for each of the 8 individual PCR reactions. The reverse primer was barcoded (barcode sequences Table S7). Sequence of primers: FW 5’AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT3’ and RV 5’CAAGCAGAAGACGGCATACGAGATNNNNNNNNGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTttatcgacgagcgcctg3. As described above, PCR reactions were pooled and purified. Libraries were pooled equimolar according to their concentrations measured with the bioanalyzer.

treatment_protocol: Human iPSC derived glutamatergic iNeurons were infected during the splitting procedure on day 4. 1.5 - 4 µl MPRA-virus per million cells was added to the dislocated neurons for half an hour at RT. Cell differentiation proceeded then normally. NPCs were infected on day5 and then cultivated for another 3 days. 15-25 million neurons, 8 million NPCs, or 8 million primary neurons were infected per condition.

value: primary cortical cultures

value: primary mouse neurons

value: BIC


title: KO_NN_14: Colon macrophages from MCJ deficient mice 2


title: ValLib_mouse_BIC_R2


title: ValLib_mouse_BIC_R4


title: 8-Cell_68h_57


title: 8-Cell_67h_9


title: Vehicle-1


title: 8-Cell_67h_8


title: 8-Cell_67h_7


title: 8-Cell_67h_6


title: Foxa2_HiChIP_GW

city: Charlottesville

first: Irina

last: Bochkis

state: VA

address: 1340 Jefferson Park Ave Jordon Hall 5030

department: Pharmacology

institute: University of Virginia

data_processing:
HiChIP paired-end reads were aligned to mm10 genome assembly using the HiC-Pro pipeline using bowtie2 (version 2.2.9) and with mapping quality filter 15. Default settings were used to remove singleton, multi-mapped and duplicate reads. Reads were assigned to MboI (^GATC) and HinfI (G^ANTC) restriction fragments and filtered for valid interactions using min and max size parameters of 100 and 100,000, and binned interaction matrices were generated.
Bin pairs of the interaction matrix with statistically significant contact signals were identified using Fit-Hi-C. Genome wide intra-chromosomal bin pairs were filtered for an interaction distance between 20kb and 2Mb, and default Fit-HiC settings were used to calculate false discovery rate (FDR) values for each bin-pair in a given HiChIP experiment. Bin size of 50kb and  FDR cutoff < 0.001 were used to identify significant contacts.
TADs were called with HiCExplorer. Hi-C contact matrix was used as input. TAD-separation scores were calculated for all bins. The TAD-separation scores were evaluated and the cutoff p-values < 0.05 were applied to select the TAD boundaries.
Compartments were called using cworld. Genomic bins of reference genome were generated at 250kb. The command matrix2compartment command was used to extract the compartment A/B profiles with default settings.
The hichipper (version 0.7.7)  was used to identify the Foxa2-anchored chromatin loops. The HiC-Pro matrix output, restriction digested mm10 genome assembly and ChIP-Seq Foxa2 binding sites  from Kain et al, Molecular Metabolism, 2021  were used as input to identify chromatin loops extending from regions occupied by Foxa2. The default parameter settings were used with minimum distance of 5000 and maximum peak padding width of 2000000.
Assembly: mm10
Library strategy: HiChIP-Seq

source_name: liver

extract_protocol:
About ~200 mg of each mouse liver tissue was pulverized using Covaris CryoPrep System with impact level setting 3. Pulverized tissues were washed with cold 1xPBS and pelleted by centrifugation at 1,000xg at 4˚C for 5 min.  HiChIP experiments were performed with vehicle- and ligand-treated mouse liver tissues using the Arima-HiC+ Kit (Arima Genomics, Cat. A101020) according to manufacturer's  protocol.   Foxa2‐specific rabbit antiserum (Seven Hills Bioreagents, WRAB‐1,200) was used for immunoprecipitation.
HiChIP libraries were prepared using Accel-NGS 2S Plus DNA Library Kit for Illumina Platforms (Swift Biosciences, Cat# 21024) and Accel-NGS 2S Indexing Kit (Set A) for illumine Platforms (Swift Biosciences, Cat# 26148)

treatment_protocol: Mice were treated once with GW4064, FXR agonist, using oral gavage. Control mice were treated with vehicle (20 mL propylene glycol/5 mL Tween 80 solution). Agonist was added to the vehicle for experimental treatment.  Animals on both control and experimental treatments were sacrificed 4 h after gavage.

value: liver

value: wildtype


title: 8-Cell_67h_5

extract_protocol:
Early stage zygotes were collected and cultured until they reached the S-phase at each developmental stage, based on their time after hCG injection. Embryos were collected at different time points to achieve sampling over the entire S-phase. For the parthenogenetic embryos and IVF-derived zygotes, the timing of S-phase was calculated based on the time after activation and insemination, respectively. Zona pellucida was removed by exposure to acid Tyrode and each blastomere was dissociated by gentle pipetting after trypsin treatment. For the Repli-seq with physically isolated pronuclei, we distinguished maternal and paternal pronucleus based on their size and their relative position to the second polar body and isolated either of them using micromanipulation. The remaining zygote containing a single pronucleus was also collected after removal of polar body so that both pronuclei from the same zygote were further processed for Repli-seq.
Individual blastomeres or pronuclei were placed into 8-strip PCR tubes containing lysis buffer and extracted DNA was fragmented by heat incubation. Fragmented DNA was tagged by the universal primer (5’-TGTGTTGGGTGTGTTTGGKKKKKKKKKKNN-3’) and amplified with WGA primer sets which have individual barcode. Amplified DNA was purified by the QIAquick 96 PCR Purification Kit (QIAGEN) and concentration was determined by the NanoDrop (Thermo Scientific). Equal amount of DNA from each samples (up to 96 samples) were pooled and 1ug of them was ligated with the illumina adaptors using the NEBNext Ultra II DNA Library Prep Kit (NEB). Illumina sequence (NEBNext Multiplex Oligos for Illumina; NEB) were added to the adaptor- ligated samples by the PCR. Clean up and size selection of the PCR product was done using SPRIselect (Beckman Coulter) and the quality of the library was confirmed by 2100 Bioanalyzer with the High Sensitivity DNA Kit (Agilent).


title: 8-Cell_67h_3


title: ValLib_mouse_baseline_R4

value: baseline


title: 8-Cell_67h_2


title: Foxa2_HiChIP_veh

value: vehicle


title: 8-Cell_67h_4


title: AS-patient H125

city: Hannover

first: Valentin

last: Burkart

state: Lower Saxony

address: Carl-Neuberg-Strasse 1

department: Institute for Molecular and Cell Physiology

institute: Hannover Medical School

data_processing:
BCL files were converted to FASTQ files using bcl2fastq Conversion Software version v2.20.0.422 (Illumina).
Raw data processing was conducted by use of nfcore/rnaseq (v 1.4.2). The pipeline uses Nextflow ( v20.01.0) workflow tool and includes read trimming (Trim Galore! v0.6.4), alignment (STAR v2.6.1d), and counting (featureCounts  v1.6.4).
Normalization and differential expression analysis was performed on the internal Galaxy (version 20.05) instance with DESeq2 (Galaxy Tool Version 2.11.40.6) with default settings except for “Output normalized counts table”, which was set to “Yes” and all additional filters were disabled (“Turn off outliers replacement”, “Turn off outliers filtering”, and “Turn off independent filtering” set “Yes”).
Assembly: GRCh38.p13; release 34
Supplementary files format and content: Tab-delimited text files include normalized espression values as a matrix table for all or a part of the samples (DESeq2 output)

source_name: left ventricular cardiac tissue

extract_protocol:
Total RNA was extracted from cardiac tissue samples ground in a cryomortar using the Monarch® Total RNA Miniprep Kit (T2010S; New England Biolabs) according to the manufacturers protocol.
40ng of total RNA per sample (differing for sample N2859 = 31ng, N2864 = 37ng, N2868 = 35ng, N2869 = 37ng, and N2872 = 32ng) were utilized as input for mRNA enrichment procedure with ‘NEBNext® Poly(A) mRNA Magnetic Isolation Module’ (E7490L; New England Biolabs) followed by stranded cDNA library generation using ‘NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina’ (E7760L; New England Biolabs). All steps were performed as recommended in user manualE7760 (Version 1.0_02-2017; NEB) except that all reactions were downscaled to 2/3 of initial volumes. Furthermore, one additional purification step was introduced at the end of the standard procedure, using 1x ‘Agencourt® AMPure® XP Beads’ (#A63881; Beckman Coulter, Inc.).  cDNA libraries were barcoded by dual indexing approach, using ‘NEBNext Multiplex Oligos for Illumina – 96 Unique Dual Index Primer Pairs’ (6440S; New England Biolabs). All generated cDNA libraries were amplified with 12 cycles of final pcr.   Equal molar amounts of individually barcoded libraries were pooled for a common sequencing run. The library pools were denatured with NaOH and were finally diluted to 2pM according to the Denature and Dilute Libraries Guide (Document # 15048776 v02; Illumina). 1.3 ml of denatured pool was loaded on an Illumina NextSeq 550 sequencer using a High Output Flowcell for single reads (20024906; Illumina). Sequencing was performed with the following settings: Sequence reads 1 and 2 with 38 bases each; Index reads 1 and 2 with 8 bases each.

value: left ventricular cardiac tissue

tag: disease state

value: aortic stenosis

value: male


title: ValLib_mouse_BIC_R1


title: MYBPC3trunc patient H44

value: hypertrophic cardiomyopathy

value: female


title: AS-patient H130


title: 8-Cell_67h_16

data_processing:
Sequencing reads were aligned to the mm10 genome using bowtie2 (version 2.3.5) with the --local option. Duplicates were marked using samtools (version 1.9)and reads were filtered by keeping only properly paired reads, removing duplicates and selecting those whose mapping quality was higher or equal to 20. Bed files of the read coordinates were generated with bedtools (version 2.29.0) bamtobed command. Using bedtools intersect, read counts were obtained for contiguous 50kb genomic bins.
The window counts were first normalised to RPM and then each bin by its respective average of all samples within the same stage, aiming to correct for the mappability biases intrinsic to the genomic regions. Outlier regions were then masked, specifically the windows of the lower 5th percentile and the upper 1st percentile values. To correct for low mappability, the windows were segmented with the R package copynumber (version 1.28.0) to keep the segments with the highest 95% of values. The data were centred by the mean and scaled by the interquartile range for each cell and smoothed using a median filter with a running window width of 15 windows, followed by a segmentation with the R package copynumber. Finally, using the function normalmixEM from R package mixtools (version 1.2.0), the segmented values were used to fit a mixture model with two components to identify replicated and non-replicated window populations.
Assembly: mm10
Supplementary files format and content: tab-separated txt file with binary replication status
Library strategy: Single-cell Repli-seq

value: 8-cell embryo


title: 8-Cell_67h_1


title: ValLib_mouse_TTX_R2

value: TTX


title: ValLib_mouse_baseline_R2


title: 8-Cell_67h_15


title: ValLib_mouse_baseline_R1


title: 8-Cell_67h_12


title: MYBPC3trunc patient H36


title: 8-Cell_67h_13


title: ValLib_mouse_baseline_R3


title: ValLib_mouse_TTX_R3


title: ValLib_mouse_TTX_R1


title: 8-Cell_67h_11


title: 8-Cell_67h_10


title: MYBPC3trunc patient H59


title: eQTLLib_mouse_baseline_R3

description: eQTLLib_countMatrix_final_barcode_raw.txt


title: MYBPC3trunc patient H51


title: 8-Cell_66h_55


title: eQTLLib_mouse_TTX_R4


title: 8-Cell_67h_14


title: Donor H108


title: Donor H88


title: eQTLLib_mouse_TTX_R2


title: eQTLLib_mouse_TTX_R1


title: eQTLLib_mouse_TTX_R3


title: 8-Cell_66h_50


title: 8-Cell_66h_49


title: 8-Cell_66h_52


title: 8-Cell_66h_51


title: 8-Cell_66h_54


title: 8-Cell_66h_53


title: 4-Cell_56h_72

source_name: 4-cell embryo

value: 4-cell embryo


title: 4-Cell_56h_70


title: 4-Cell_56h_71


title: AS-patient H69


title: 8-Cell_66h_56


title: eQTLLib_mouse_BIC_R3


title: MYBPC3trunc patient H45


title: 4-Cell_56h_69


title: AS-patients H126


title: AS-patient H66


title: 4-Cell_56h_68


title: 4-Cell_56h_67


title: eQTLLib_mouse_BIC_R4


title: MYBPC3trunc patient H84


title: eQTLLib_mouse_BIC_R2


title: eQTLLib_mouse_baseline_R2


title: 4-Cell_56h_65


title: 4-Cell_56h_66


title: 4-Cell_56h_48


title: Donor H113


title: 4-Cell_56h_47


title: Donor H103


title: eQTLLib_mouse_baseline_R1


title: Donor H89


title: kdm5[140] RG_rep4

city: Bronx

middle: Francis

last: Rogers

state: NY

address: 1300 Morris Park Ave, Ullmann 809

department: Genetics

institute: Albert Einstein College of Medicine

description: 50% males, 50% females

data_processing:
Novogene performed data processing including QC, reference genome mapping via Hisat2 (v2.0.5), assembly via StringTie (v1.3.3b), quantification via featureCounts (v1.5.0-p3), and differential expression analysis via DESeq2 (1.20.0)
Assembly: dm6
Supplementary files format and content: counts, FPKM, log2FoldChange differential expression, and gene characterization

organism: Drosophila melanogaster

source_name: ring gland

growth_protocol: Flies were grown on standard media at 25ºC

extract_protocol:
Trizol extraction of total RNA from dissected ring glands was performed according to manufacturer's instructions. Animals were matched by developmental stage of wandering third instar larva. n = 80 ring glands per replicate.
Total RNA was submitted to Novogene for library construction and sequencing. At Novogene, polyA enrichment was performed to prepare mRNA libraries. Libraries were evaluated for quality using the Agilent Bioanalyzer 2100 system. Sequencing was performed on an Illumina NovaSeq PE150 sequencing platform (2 x 150bp) cycles.

treatment_protocol: No treatment

tag: developmental stage

value: wandering third instar larva

value: ring gland

value: pooled male and female


title: kdm5[140] RG_rep3

description: 50% males, 50% females


title: eQTLLib_mouse_BIC_R1

value: primary cortical cultures

value: primary mouse neurons


title: kdm5[140] RG_rep2

description: 50% males, 50% females


title: 4-Cell_56h_46

city: Munich

last: Schauer

address: Feodor-Lynen-Straße 21

institute: Helmholtz Zentrum München

value: (C57BL/6J x CBA) x DBA/2J


title: 4-Cell_56h_41


title: 4-Cell_56h_45


title: 4-Cell_56h_43


title: 4-Cell_56h_44


title: 4-Cell_54h_39


title: DevLib_mouse_BIC_R4

description: DevLib_countMatrix_final_barcode_raw.txt

value: BIC


title: DevLib_mouse_TTX_R2


title: 4-Cell_54h_37


title: 4-Cell_54h_38


title: DevLib_mouse_TTX_R1


title: kdm5[140] RG_rep1

description: 50% males, 50% females


title: DevLib_mouse_TTX_R3


title: 4-Cell_54h_35


title: 4-Cell_54h_40


title: 4-Cell_54h_36


title: WT RG_rep4

description: 50% males, 50% females


title: DevLib_mouse_BIC_R2


title: 4-Cell_54h_34


title: DevLib_mouse_baseline_R3

value: baseline


title: 4-Cell_54h_33


title: 4-Cell_54h_32


title: 4-Cell_56h_42


title: WT RG_rep3

description: 50% males, 50% females


title: 4-Cell_54h_31


title: DevLib_mouse_baseline_R2


title: 4-Cell_54h_30


title: 4-Cell_54h_29


title: CTCF ChIP-seq, lens fiber

first: William

last: Chang

address: 1301 Morris Park Ave

department: Ophthalmology

data_processing:
Reads were aligned with bwa. HiC: bwa-mem with default settings. ChIP-seq: bwa aln/samse with default settings.
HiC: contact maps were created from reads with MAPQ > 30  with a maximum resolution of 5kb with the ENCODE HiC pipeline (https://github.com/ENCODE-DCC/hic-pipeline), based on Juicer.
HiC: loops and topologically-associated domains (TADs) were called within the ENCODE pipeline using the HiCCUPs and Arrowhead algorithms, respectively.
HiC: A/B compartment analysis was performed using dcHiC to calculate, select, and normalize principal components of the Pearson correlation of the contact matrix at 10kb resolution
ChIP-seq: peaks were called with MACS2 using default settings.
Assembly: mm10
Supplementary files format and content: .hic (contact maps)
Supplementary files format and content: .bedpe (chromatin loops)
Supplementary files format and content: .bed (TADs)
Supplementary files format and content: .bedGraph (A/B compartment scores)
Supplementary files format and content: .bw (ChIP-seq read density)
Supplementary files format and content: .narrowPeak (ChIP-seq peaks)

source_name: lens

growth_protocol: HiC: v6.5 mESCs derived by Dr. Rudolph Jaenisch (gifted by Dr. Meelad Dawlaty) were used. Cells were grown under feeder-free conditions on 0.2% gelatin and supplemented with LIF (24 ng/mL). Each replicate contained ~2.0 x 106 cells.

extract_protocol:
HiC: Lenses were dissected at P0.5 and then micro-dissected into lens epithelium and lens fiber under a dissection microscope. Each replicate of lens tissue was comprised of either 30 lens epithelium, or 30 lens fiber samples. Samples were kept on dry ice for the duration of the micro-dissection process. Samples were then homogenized using a disposable pestle tissue grinder. Homogenized tissues were fixed in 2.0% formaldehyde for 10 mins at room temperature. Formaldehyde was quenched with 0.125 M glycine to stop the reaction. The crosslinking method for mESCs was the same. ChIP-seq: 200 P0.5 lenses were obtained from CD-1 mice, microdissected into lens epithelium and lens fibers and stored in liquid nitrogen prior the use as we described earlier (Sun et al. 2015).
The Hi-C library was generated using the Arima-HiC kit according to the manufacturers protocols (A510008) and performed by the NYU Langone Health Genome Technology Center. The ChIP-seq library was generated by Active Motif: Immunoprecipitation was performed on 6 µg chromatin from microdissected lens cells with 5 µl anti-CTCF antibody (ActiveMotif cat. # 61311, lot #11219006).

value: lens

value: fiber


title: DevLib_mouse_BIC_R1


title: WT RG_rep1

description: 50% males, 50% females


title: 4-Cell_54h_27

first: Tamas


title: 4-Cell_53h_64


title: 4-Cell_54h_26


title: 4-Cell_53h_63


title: 4-Cell_53h_61


title: 4-Cell_54h_28


title: DevLib_mouse_baseline_R1


title: 4-Cell_53h_60


title: DevLib_mouse_TTX_R5


title: MADM mammary tumor #12

first: Kevin

middle: A.

last: Janes

address: Box 800759 Health System

department: Department of Biomedical Engineering

data_processing:
Adapters were trimmed using fastq-mcf in the EAutils package (version ea-utils.1.1.2-779) with the following options: -q 10 -t 0.01 -k 0 (quality threshold 10, 0.01% occurrence frequency, no nucleotide skew causing cycle removal).
Data were aligned to the murine transcriptome (GRCm38.84) using HISATv2 (version 2.1.0) with options for paired-end reads. HISAT read counts were converted to transcripts and normalized to transcripts per million (TPM) using StringTie (version 2.1.6).
Supplementary files format and content: .csv file contains the transcript per million (TPM) estimated abundances for each gene per sample

source_name: Mammary gland

extract_protocol:
50 mg tumor was homogenized with Trizol, phenol-chloroform extracted, and purified with the RNEasey Mini Kit.
TruSeq Stranded mRNA kit

tag: animal id

value: Mammary gland

value: Tumor

value: MADM RG;GR alleles, mixed background


title: CTCF ChIP-seq, lens epithelium

value: epithelium


title: 4-Cell_53h_59


title: 4-Cell_54h_25


title: WT RG_rep2

description: 50% males, 50% females


title: MADM mammary tumor #11


title: C3-TAg luminal (scRNA-seq)

city: New York

first: Wenjun

address: 1301 Morris Park

department: Cell Biology

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: mouse mammary gland

extract_protocol:
10X Genomics Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 following the manufacter’s instructions.
10,000 cells per sample were submitted to Einstein Genomics Core for library preparation using 10X Genomics Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 following the manufacter’s instructions.

value: mouse mammary gland

value: mammary luminal cells

value: FVB/NJ

value: 3.5 months old


title: 4-Cell_53h_62

value: 4-cell embryo


title: DevLib_mouse_baseline_R4


title: MADM mammary tumor #10


title: 4-Cell_53h_58


title: 4-Cell_52h_9


title: 4-Cell_53h_57


title: MADM mammary tumor #9


title: WT luminal (scRNA-seq)

description: 10x Genomics


title: 4-Cell_52h_24


title: 4-Cell_52h_22


title: 753_149_Lung - Bleomycin 56d - old

city: Biberach

first: Katrin

last: Fundel-Clemens

address: Birkendorfer 65

institute: Boehringer Ingelheim

data_processing:
Basecalling has been done with bcl2fastq v2.20.0.422.
Alignment has been performed with STAR v2.5.2 using hg38 genome reference.
Read counts has been obtained with featureCounts v1.5.1.
Demultiplexing was performed using bcl2fastq v2.20.0.422 from Illumina (https://emea.support.illumina.com/downloads/bcl2fastq-conversion-software-v2-20.html).  Sequencing reads from the RNA-seq experiment were processed with a pipeline building upon the implementation of the ENCODE “Long RNA-seq” pipeline (also described in (Schlager et al., 2020)): filtered reads were mapped against the Homo sapiens (human) genome hg38/GRCh38 (primary assembly, excluding alternate contigs) using the STAR (v2.5.2b) aligner (Dobin et al., 2013) allowing for soft clipping of adapter sequences.   For quantification, we used transcript annotation files from Ensembl version 86, which corresponds to GENCODE 25 for human. Gene expression levels were quantified with the above annotations, using RSEM (v1.3.0) (Li and Dewey, 2011) and featureCounts (v1.5.1) (Liao, Smyth and Shi, 2014). Quality controls were implemented using FastQC (v0.11.5) [ Andrews, S. (2010). FastQC:  A Quality Control Tool for High Throughput Sequence Data [Online]. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ ], picardmetrics (v0.2.4) [ Slowikowski K. (2016): Available online at: https://github.com/slowkow/picardmetrics ] and dupRadar (v1.0.0) (Sayols, Scherzinger and Klein, 2016) at the respective steps.
Assembly: GRCm38.86
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Lungs

extract_protocol:
A total of 20 mg of tissue was used for RNA isolation using the Qiazol kit according to manufacturer´s protocol (Qiagen, Hilden, Germany). Quality of RNA was assessed by the Fragment Analyzer (Agilent Technologies, Santa Clara, CA, USA) using the SS RNA Kit (Agilent Technologies, Santa Clara, CA, USA).
RNA libraries for RNA-seq were prepared using Tru-seq mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Bleomycin or saline administration was performed in a hanging position with a Vasofix-Braunüle 22G (B.Braun, Melsungen, Germany). Young mice received 0.7 mg/kg of Bleomycin sulphate (Merck, Darmstadt, Germany) and old mice 0.63 mg/kg.

value: Lungs

value: Induced Pulmonary Fibrosis

value: old

value: Bleomycin

tag: day


title: MADM mammary tumor #8


title: 4-Cell_52h_23

value: (C57BL/6J x CBA) x DBA/2J


title: 753_148_Lung - Bleomycin 56d - old


title: MADM mammary tumor #7


title: 4-Cell_52h_19


title: 753_147_Lung - NaCl 56d - old

value: Healthy

value: NaCl


title: 753_146_Lung - NaCl 56d - old


title: 4-Cell_52h_20


title: 4-Cell_52h_16


title: 4-Cell_52h_18


title: 4-Cell_52h_15


title: MADM mammary tumor #6


title: 4-Cell_52h_14


title: MADM mammary tumor #4


title: 4-Cell_52h_13


title: MADM mammary tumor #3


title: 4-Cell_52h_17


title: 4-Cell_52h_12


title: 753_145_Lung - NaCl 56d - old


title: 753_144_Lung - NaCl 56d - old


title: 753_150_Lung - Bleomycin 56d - old


title: 4-Cell_52h_11


title: 4-Cell_52h_10


title: MADM mammary tumor #2


title: 4-Cell_52h_21


title: 753_143_Lung - NaCl 56d - old


title: MADM mammary tumor #5


title: 4-Cell_51h_56


title: MADM mammary tumor #1


title: 4-Cell_51h_55


title: Spatial_transcriptomics_Day_9_Aged

city: Chicago

first: Weiguo

last: Cui

state: IL

address: 303 E Chicago Ave

department: Pathology

institute: Northwestern University

data_processing:
Reads were aligned to mouse reference genome mm10
Assembly: mm10
Supplementary files format and content: Loupe Browser (v5.0, 10x Genomics) was used to identify which spatial sequencing capture area spots were in contact with tissue. Demultiplexing and alignment was performed with Space Ranger (v2.1, 10x Genomics) and the mm10 2020-A reference transcriptome (10x Genomics).
Library strategy: Visium spatial RNA sequencing

source_name: Lung

extract_protocol: 10x Genomics

value: Lung

value: C57BL/6 mice

tag: timepoint

value: Day 9

tag: infection

value: Flu PR8 infection

tag: condition

value: Aged


title: 753_141_Lung - Bleomycin 56d - old

tag: tissue


title: 4-Cell_51h_54

tag: genotype

tag: treatment


title: 4-Cell_51h_53


title: Spatial_transcriptomics_Day_9_Young

value: Young


title: 4-Cell_51h_52


title: U87_Input

city: Suzhou

first: Gen

last: Li

state: Jiangsu

address: No. 92 Zhongnan Street

institute: Children's Hospital of Soochow University

data_processing:
Raw Data of ChIP-Seq was aligned to the reference genome (UCSC hg38) using BWA-MEM (v0.7.17)
Peaks were identified using MACS2 (v2.2.7)
Assembly: hg38
Supplementary files format and content: peak text files
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a sonicator (M220, Covaris).
Libraries were prepared for sequencing using standard MGI 2000 protocols

value: Glioblastoma

tag: chip antibody


title: DevLib_mouse_TTX_R4

value: primary cortical cultures

tag: cell type

value: primary mouse neurons

value: TTX


title: Spatial_transcriptomics_Day_3_Aged

value: Day 3


title: U87_DMSO_H3K27ac

value: H3K27Ac (Abcam, #ab4729)

value: DMSO


title: 753_140_Lung - Bleomycin 56d - old

value: Lungs

value: Induced Pulmonary Fibrosis

tag: age

value: old

value: Bleomycin


title: U87_MZ1_H3K27Ac


title: Spatial_transcriptomics_Day_3_Young

value: Lung


title: 753_139_Lung - Bleomycin 56d - old