title: d9434.ALL (All HSC rep2)

data_processing:
HiSeq2000 using v3 chemistry. Software: Control v2.2.58, RTA 1.18.64. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch.
RNAseq reads were aligned to the mouse transcriptome prepared with the mm10 primary assembly and the Ensembl version 88 annotation using STAR version 2.5.3a (Dobin et al., 2013). Gene expression was summarized with RSEM version 1.3.0 (Li and Dewey, 2011) and samtools version 1.3 (Li et al., 2009).
Genome_build: mm10 with ensembl 88 annotation
Supplementary_files_format_and_content: ljette_size_counts.txt.gz is a tab separated text file of integer count data
Supplementary_files_format_and_content: ljette_size_l2tpm.txt.gz is a tab separated text file of log2 transcripts per million with a plus1 offset

growth_protocol: HSCs were isolated by harvesting bone marrow by flushing the long bones. Red blood cells were lysed in Ammonium-  Chloride-Potassium (ACK) buffer and samples were washed in Iscove’s Modified Dulbecco’s Medium  (IMDM) containing 2 % fetal bovine serum (FBS). Lineage positive cells were depleted using a mouse  lineage cell depletion kit (#130-090-858, Miltenyi Biotec) and the following antibodies from  BioLegend (CD150 [TC15-12F12.2] (PE/Cy7#115913, PE#115904), CD48 [HM48-1] (BV421#103427,  APC/Cy7(#103431), Sca-1 [D7] (PE/Cy7#108114), CD117 [2B8] (APC#105812)) and BD Biosciences  (CD150 [Q38-480] (PE#562651), Sca-1 [D7] (FITC #562058)) were used for staining. 7-AAD or  propidium Iodide was used for the identification of non-viable cells. Cells were sorted using an Aria I  cell sorter (Becton Dickinson). Size sorted HSCs were prepared using SSC-A and FSC-A. The gates to  isolate small and large HSCs were set so that they encompass the 10 % smallest and 10 % largest cells in  the HSC preparation, respectively. The medium gate was set to isolate HSCs of mean size +/- 10 %. HSC  size was determined based on FSC-A distribution using the FlowJo software package. Cytometerbased  HSC size fractionation was confirmed by measuring cell volume using a Multisizer-3 Coulter  Counter (Beckman Coulter) to determine the absolute cellular diameter and volume in every  experiment.

tag: size

value: All - no size fractionation


title: d7343.PD (PD rep3)

status: Public on Sep 19 2021

type: SRA

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

state: MA

country: USA

institute: Koch Institute

library_source: transcriptomic

data_processing:
HiSeq2000 using v3 chemistry. Software: Control v2.2.58, RTA 1.18.64. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch.
RNAseq reads were aligned to the mouse transcriptome prepared with the mm10 primary assembly and the Ensembl version 88 annotation using STAR version 2.5.3a (Dobin et al., 2013). Gene expression was summarized with RSEM version 1.3.0 (Li and Dewey, 2011) and samtools version 1.3 (Li et al., 2009).
Genome_build: mm10 with ensembl 88 annotation
Supplementary_files_format_and_content: ljette_treatment_counts.txt.gz is a tab separated text file of integer count data
Supplementary_files_format_and_content: ljette_treatment_l2tpm.txt.gz is a tab separated text file of log2 transcripts per million with a plus1 offset

molecule: total RNA

organism: Mus musculus

source_name: Hematopoietic Stem Cells (HSCs)

growth_protocol: HSCs were isolated by harvesting bone marrow by flushing the long bones. Red blood cells were lysed in Ammonium-  Chloride-Potassium (ACK) buffer and samples were washed in Iscove’s Modified Dulbecco’s Medium  (IMDM) containing 2 % fetal bovine serum (FBS). Lineage positive cells were depleted using a mouse  lineage cell depletion kit (#130-090-858, Miltenyi Biotec) and the following antibodies from  BioLegend (CD150 [TC15-12F12.2] (PE/Cy7#115913, PE#115904), CD48 [HM48-1] (BV421#103427,  APC/Cy7(#103431), Sca-1 [D7] (PE/Cy7#108114), CD117 [2B8] (APC#105812)) and BD Biosciences  (CD150 [Q38-480] (PE#562651), Sca-1 [D7] (FITC #562058)) were used for staining. 7-AAD or  propidium Iodide was used for the identification of non-viable cells. Cells were sorted using an Aria I  cell sorter (Becton Dickinson).

extract_protocol:
For RNA isolation, 10,000 HSCs in G0/1 were isolated in the absence of FBS and HSCs were sorted into 750 μL TrizolLS. During the sort, the collection  sample was vortexed every 10 min. Post-sort, the samples were brought to a total volume of 1 mL  with DEPC treated water. Samples were stored at -80 °C or directly used for RNA extraction. To  extract RNA, 200 μL chloroform was added to the sample and briefly vortexed at medium speed.  After 2 min at RT, the sample was centrifuged at 12,000 x g for 15 min at 4 °C. 400 μL of aqueous  phase was removed and put into 1,400 μL RLT buffer (Qiagen) with 14 μL β-mercaptoethanol and  mixed vigorously. 1 mL 100 % ethanol was added to each sample, mixed by pipetting, then loaded  onto RNeasy Micro Kit (Qiagen) columns.
Clontech v4 Low-Input RNA Kit

tag: strain

tag: tissue

value: Hematopoietic Stem Cells (HSCs)

tag: treatment

value: Mice treated with PD (Palbociclib) at 30.4 mg/kg body weight in 20 % DMSO, 40 % PEG 400 in PBS by intraperitoneally injected at a volume of 100 μL every 48h for 85  days.


title: d9433.ALL (All HSC rep1)


title: Zer.r

city: Christchurch

first: Anna

last: Pilbrow

address: 2 Riccarton Avenue

country: New Zealand

institute: University of Otago, Christchurch

data_processing:
Individual libraries were separated from multiplexed sequencing data (total yield=93.9Gb), adapter- and quality-trimmed and converted to FASTQ format with fastq-mcf (https://expressionanalysis.github.io/ea-utils/).
Paired-end reads <50 nucleotides were removed with the SolexaQA package (Cox et al. BMC Bioinformatics 2010;11:485) and the quality of the remaining reads verified using fastqc tools (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Sequence reads for all samples were aligned to the Ovis aries genome using Bowtie 2 (Langmead et al. Nat Methods 2012;9:357-9) and TopHat2 (Kim et al. Genome Biol 2013;14:R36).
Read counts for each transcript based on RefSeq and Ensembl annotations were extracted with Bedtools (Quinlan et al. Bioinformatics 2010;26:41-2). Those mapping to different isoforms of the same gene were combined to provide gene-level counts for comparative analysis.
Genome_build: Ovis aries genome (assembly version-3.1, http://www.ncbi.nlm.nih.gov/genome/83)
Supplementary_files_format_and_content: Data for individual genes are provided as raw read counts (not normalised for library size)

organism: Homo sapiens

extract_protocol:
Serial kidney biopsies were performed in duplicate prior to pacing (Baseline), on Day-14 of pacing (HF), and after 25-days (non-pacing) recovery (6 sheep, 5 x Baseline, 6 x Heart Failure and 5 x Recovery serial samples). For the first two procedures, the sheep were anaesthetized (as described above) and 2 adjacent percutaneous kidney biopsies taken under ultrasonic guidance (Philips iE33; Philips Ultrasound, WA, USA) using a 14g spring-loaded automated biopsy gun (BARD Peripheral Vascular, Inc., Tempe, USA). Final kidney samples were collected at study-end immediately following euthanasia (IV Pentobarb300 100mg/kg). On each occasion, one of the biopsies was fixed in 10% formalin (4oC overnight) for histological analysis, and the other snap frozen in liquid nitrogen and stored at -80oC for subsequent RNA extraction and RNA-Seq analysis. To maximise statistical power, the 5 x Baseline, 6 x Heart Failure and 5 x Recovery serial samples were supplemented with kidney samples collected post-mortem from animals sacrificed before, during or after the same pacing protocol. This provided a total of 14 x Baseline, 13 x HF and 8 x Recovery samples for RNA-Seq analysis.
Total RNA was extracted from frozen kidney biopsy samples and purified with RNeasy Midi Columns (Qiagen, Hilden, Germany).  RNA-Seq libraries were prepared using total RNA (500 ng input) and TruSeq stranded mRNA library prep kits (Illumina, San Diego, CA).

treatment_protocol: Nine adult Coopworth ewes (4-6 yrs; 47-69 kg; Lincoln University Farm, Canterbury, New Zealand) were instrumented via a left lateral thoracotomy as previously described (Rademaker et al. Am J Physiol 2007;293:H1536-1544) under general anaesthesia (induced by intravenous (IV) diazepam [1x0.5mg/kg] / IV ketamine [1x4mg/kg]; maintained with 2% isoflurane / 2L/min nitrous oxide / 2L/min oxygen) and using approved peri-/post-operative analgesia (IV carprofen [4mg/kg QD for >3 days]; IV buprenorphine [0.005-0.01mg/kg QD for >3 days]; intercostal bupivacaine [1x25mg] / intercostal lignocaine [1x100mg]) and antibiotics (IV cephazolin [2x20mg/kg]; IV enrofloxacin [1x2.5mg/kg]). Briefly, catheters were placed via the jugular vein and in the left atrium for blood sampling and measurement of central venous and left atrial pressures (CVP and LAP, respectively); Konigsberg pressure-tip transducers inserted in the aorta to record mean arterial pressure (MAP) and into the apex of the left ventricle (LV) to obtain heart rate, LV pressures and derivatives of pressure over time (dP/dt(max)); a Swan-Ganz thermodilution catheter (American Edwards) was placed in the pulmonary artery for measurement of cardiac output (CO); and a 7-French His-bundle electrode was stitched sub-epicardially to the LV for subsequent cardiac pacing. A bladder catheter was inserted per urethra to allow timed urine collections. Adequacy of anaesthesia was monitored via serial measurement of  heart rate, blood pressure, capillary refill time, mucous membrane colour, palpable blink response, jaw tone, anesthetic gas analysis, oxygen saturation and end-tidal CO2 levels. Animals recovered for at least 14-days before commencing the study protocol, and throughout the study were held in metabolic cages receiving a diet of Lucerne chaff and food pellets (providing ~75mmol sodium/day; ~150mmol potassium/day) with free access to water. The study followed a longitudinal repeated-measures design, with sampling conducted over a 5-day baseline period (Days -4-0) followed by 14-days of rapid LV pacing @220bpm to induce ADHF (Days 1-14-Pace), and then termination of pacing and 25-days recovery (Days 1-25-Recovery).

value: kidney

tag: time point

value: recovery


title: WT P3 rep2

city: Shanghai

first: Lingfang

last: Zhuang

state: Shanghai

address: 197 Rui Jin Road II

department: Department of Vascular & Cardiology

country: China

institute: Ruijin Hospital, Shanghai Jiao Tong University School of Medicine

data_processing:
Sequencing data were filtered with SOAPnuke (v1.5.2) to remove reads containing sequencing adapters and those with more than 1/5 low-quality base ratio. The resulting clean reads were saved in FASTQ format.
The transcriptional reads were mapped to the mm8 whole genome  using HISAT2 (v2.0.4) and STAR (v2.3.0).
fragments per kilobase million (FPKM) value using the DESeq2 were calculated.
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: WT P3_heart

extract_protocol:
WT and DYRK1B-Transgenic hearts were collected at 3-day and 8-week old mice and immediately frozen in liquid nitrogen. Total RNA was extracted from above tissues using Trizol according to standard protocols.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: cDNA encoding the full-length mouse DYRK1B transcript was cloned into a plasmid containing a cardiac-specific α-myosin heavy chain (αMHC) promotor. Then the transgenic mice and their WT littermates were sacrificed at 3-days and 8-week old for RNA-sequencing analysis.

value: Heart

tag: genotype

value: WT

tag: age

value: 3-day old


title: GFP-M

city: Beijing

first: Yong-Bin

last: Yan

address: Tsinghua University

department: School of Life Sciences

institute: Tsinghua University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence by Cutadapt , and discard low-quality sequence by Trimmomatic-0.36, then mapped to HG38 whole genome using STAR with parameters  --outSAMmapqUnique 255 --outFilterMismatchNoverLmax 0.3 --alignIntronMin 21 --alignIntronMax 0 --alignMatesGapMax 0 --outFilterMultimapNmax 10 --outSAMprimaryFlag OneBestScore --outSAMstrandField intronMotif --outSAMattributes Standard --outSAMtype BAM SortedByCoordinate --chimSegmentMin 0 --outReadsUnmapped Fastx --outFilterIntronMotifs RemoveNoncanonical --outWigType bedGraph --outFilterMismatchNoverReadLmax 1 --outSJfilterReads All -outSJfilterIntronMaxVsReadN 5000 10000 20000 --outFilterMatchNmin 0 --outFilterMatchNminOverLread 0.66 --outFilterScoreMinOverLread 0.66
Cuffdiff were used for calculating differential expression between flag-C and flag-M,GFP-C and GFP-M, P74-C and P74-M, D28A-C and D28A-M,P74-C and flag-C, D28A-C and flag-C,P74-M and flag-M, D28A-M and flag-M
Genome_build: HG38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample …

source_name: Renal epithelium cell

extract_protocol:
The cytosolic and ER fraction of each sample were prepared by sequential detergent extraction. Total RNAs were extracted using Trizol reagent.
RNA library was prepared for the total RNAs extracted from the cytosol and membrane fractions of HEK-293T cell by KAPA Stranded RNA-Seq Library Preparation Kit.

tag: cell type

value: HEK-293T cell

value: wild type

tag: fraction

value: ER


title: GFP-C

value: cytosol


title: Xt.r


title: CR059_S13

city: Lund

first: Johan

last: Jakobsson

address: Sölvegatan 17

department: Wallenberg Neuroscience Center

country: Sweden

institute: Lund University

description: iPS-derived chimpanzee neural forebrain progenitors

library_source: genomic

data_processing:
Library strategy: CUT&RUN
RNA-seq: raw base call files were converted to fastq and demultiplexed using bcl2fastq. The fastq files were mapped to hg38 and pantro6 reference genomes using STAR/2.5.0a with parameter --outFilterMismatchNoverLmax 0.03 and --sjdbGTFfile gencode.v27.annotation.gtf. When mapping to pantro6, the gencode.v27.annotation.gtf were lifted from hg38 coordinates to pantro6. Gene counts were quantified using featurecounts from Subread/1.5.0-p1, with -s 2, -p and -t exon parameters.
single-cell RNA-seq: raw basecall files were converted to fastq and demultiplexed using cellranger/2.1 mkfastq. Gene counting was done with cellranger count.
Genome_build: hg38
Supplementary_files_format_and_content: counts and coverage tracks

molecule: genomic DNA

organism: Pan troglodytes

growth_protocol: We used two human iPSC lines generated by mRNA transfection (RBRC-HPS0328 606A1 and RBRC-HPS0360 648A1, both from RIKEN; from here on referred to as HS1 and HS2, respectively). We used two chimpanzee iPSC lines: one generated by mRNA transfection (Sandra A, herein referred to as PT1) and the other with viral vector transduction (PR00818 PTCL-5, herein referred to as PT2) (Marchetto et al., 2013; Mora-Bermúdez et al., 2016). iPSCs were maintained on LN521-coated (0.7 µg/cm2; Biolamina) Nunc multidishes in iPS media (StemMACS iPS-Brew XF and 0.5% penicillin/streptomycin (Gibco)). Cells were passaged 1:2-1:6 every 2-4 days by being rinsed once with DPBS (Gibco) and dissociated using 0.5 mM EDTA (75 µl/cm2; Gibco) at 37 ºC for 7 minutes. Following incubation, EDTA was carefully aspirated from the well and the cells were washed off from the dish using washing medium (9.5 ml DMEM/F-12 (31330-038; Gibco) and 0.5 ml knockout serum replacement (Gibco)). The cells were then centrifuged at 400g for 5 minutes and resuspended in iPS brew medium supplemented with 10 µM Y27632 (Rock inhibitor; Miltenyi) for expansion.

extract_protocol: On the day of harvest, the cells were washed once with PBS, detached using Accutase, washed and resuspended in PBS. Briefly, 2x105 cells were washed twice (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine, 1x Roche complete protease inhibitors) and attached to pre-activated ConA-coated magnetic beads (Bangs Laboratories). Bead-bound cells were resuspended in 50 µL buffer (20 mM HEPES pH 7.5, 0.15 M NaCl, 0.5 mM Spermidine, 1x Roche complete protease inhibitors, 0.02% w/v digitonin, 2 mM EDTA) containing primary antibody (H3K9me3 (Ab8898, Abcam 1:50); H3k4me3 (Cat #39159, Active Motif 1;50) or IgG control antibody  (Ab97047, Abcam 1:50) at 4 ºC over-night. Washed with digitonin buffer, pA-MNase was added and incubated with the cells at 4 ºC for 1 h. Bead-bound cells were washed, resuspended in 100 µL digitonin buffer, and chilled to 0-2 ºC. Genome cleavage was stimulated by addition of 2 mM CaCl2 at 0 ºC for 30 min. The reaction was quenched by addition of 100 µL 2x stop buffer. After 10 min incubation at 37 ºC to release genomic fragments, cells and beads were pelleted by centrifugation (16,000 g, 5 min, 4 ºC) and fragments from the supernatant purified.

treatment_protocol: Differentiation to fbNPCs: iPSCs were grown to approximately 70-90% confluency and were then dissociated as usual for passaging. After centrifugation, the cells were resuspended in N2 medium (1:1 DMEM/F-12 (21331-020; Gibco) and Neurobasal (21103-049; Gibco) supplemented with 1% N2 (Gibco), 2 mM L-glutamine (Gibco), and 0.2% penicillin/streptomycin). The cells were manually counted twice and plated at a density of 10,000 cells/cm2 in 250 µl medium/cm2 on LN111 Nunc  multidishes (1.14 µg/cm2; Biolamina). 10 µM SB431542 (Axon) and 100 ng/ml noggin (Miltenyi) for dual SMAD inhibition, and 10 µM Y27632 was added to the medium. The medium was changed every 2-3 days (N2 medium with SB431542 and noggin) until day 9 of differentiation, when N2 medium without SMAD inhibitors was used. On day 11, the cells were replated by washing twice with DPBS followed by adding StemPro accutase (75 µl/cm2; Gibco) for 10-20 minutes at 37 ºC. The dissociated cells were washed off with 10 ml wash medium, centrifuged for 5 minutes at 400g and resuspended in B27 medium (Neurobasal supplemented with 1% B27 without vitamin A (Gibco), 2 mM L-glutamine and 0.2% penicillin/streptomycin Y27632 (10 µM), BDNF (20 ng/ml; R&D), and L-ascorbic acid (0.2 mM; Sigma). The cells were counted and replated at 800,000 cells/cm2 on LN111- coated plastic in B27 medium (600 µl medium/cm2). The cells were kept in the same medium until day 14, after which new B27 medium was added (Grassi et al., 2020).

value: chimpanzee neural forebrain progenitor cells

tag: chip antibody

value: IgG

tag: days in culture

tag: molecule subtype

value: DNA released by antibody-targeted MNase


title: d9432.L (Large HSC rep2)

value: Large


title: CR058_S12


title: Ea.h

source_name: heart failure_kidney

value: heart failure


title: flag-C


title: d9431.L (Large HSC rep1)


title: Ha.h


title: d9429.M (Medium HSC rep2)

value: Medium


title: ESC Matr3KO diff rep3

city: Boston

first: Hye Ji

last: Cha

address: 1 Blackfan Circle

institute: Boston Children’s Hospital

data_processing:
Paired-end 100bp reads were generated using Illumina HiSeq 2500 sequencing platform for MEL cells, and single-end 75bp reads were generated using Illumina NextSeq500.
Sequencing reads were mapped to the mm10 mouse reference genome using STAR (v2.5.4a) and/or HISAT2.
Raw counts were produced using Htseq and/or a Python script downloaded from https://ccb.jhu.edu/software/stringtie/dl/prepDE.py.
Genome_build: mm10
Supplementary_files_format_and_content: Raw gene counts for every gene and every sample

source_name: Mouse embryonic stem cell

growth_protocol: MEL cells were cultured in Dulbecco's Modified Eagle's Medium (DMEM) with 10% fetal calf serum, 1% L-glutamine, and 2% penicillin/streptomycin at 37 °C in a humidified. atmosphere of 5% CO2. Mouse ES cells were maintained on mouse embryonic fibroblasts (Gibco MEFs) feeders in standard ES medium supplemented with 15% heat-inactivated fetal calf serum, 0.1 mM 2-mercaptoethanol, 2 mM L-glutamine, 0.1 mM non-essential amino acid, 1% of nucleoside mix, 50 U/ml Penicillin/Streptomycin, 1000U/ml recombinant leukemia inhibitory factor(LIF/ESGRO).

extract_protocol:
RNA was extracted using TRIzol reagent (Thermo Fisher) and the RNeasy Plus Mini Kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Mouse ES cells were differentiated in Iscove’s Modified Dulbecco Media (IMDM) supplemented with 10% heat-inactivated fetal calf serum, 2mmol L-glutamine, 4.5x10-4mol/L monothioglycerol, 0.5 mmol/L ascorbic acid, 200 μg/mL transferrin, 5% protein free hybridoma media (PFHM-II) and 50 U/ml Penicillin/Streptomycin.

value: Embryonic stem cell

value: Matr3 -/-

value: differentiated


title: flag-M


title: CR057_S11


title: d9428.M (Medium HSC rep1)

value: Hematopoietic Stem Cells (HSCs)


title: Dr.h

value: kidney


title: CR055_S9


title: d9425.S (Small HSC rep1)

value: Small


title: ESC Matr3KO unt rep3

value: untreated


title: CR056_S10


title: U2.h


title: WT P3 rep1

value: Heart

value: WT

value: 3-day old


title: Ant.h


title: CR054_S8


title: Nit.h


title: CR034_wo_S10


title: Patient 11 subcutaneous metastase

first: Yulong

last: Wang

address: 270 Dongan Road, Shanghai

department: Department of Head and Neck Surgery

institute: Fudan University Shanghai Cancer Center

description: subcutaneous metastase  patient 11

data_processing:
Cell Ranger (v3.0.1, 10X Genomics)
Genome_build: GRCh38
Supplementary_files_format_and_content: Filtered single-cell gene expression matrix and associated cell barcodes and gene features

molecule: polyA RNA

source_name: subcutaneous metastase

extract_protocol: The cell suspension of each sample was subjected to the Gel Bead Kit V3 (10x Genomics, Pleasanton, CA) for library preparation according to the standard protocols.

treatment_protocol: Fresh samples were resected and washed twice with 1x PBS (Gibco). Each sample was cut into approximately 1 mm3 pieces and enzymatically digested with 10 mL digestion medium containing 1 mg/mL collagenase and 1 U/mL Dispase II (Gibco). These samples were subsequently incubated at 37 ℃ for 50 min and were triturated with pipette per 15 min. The suspended cells were washed with 20% fetal bovine serum (FBS) in Dulbecco’s Modified Eagle Medium (DMEM) and filtered through a 40-µm Cell-Strainer nylon mesh (BD) and centrifuged at 700 × g for 10 min. After removing the supernatant, the cell pellet was washed twice with MACS buffer (PBS containing 1% FBS, 0.5% EDTA, and 0.05% gentamycin) and then re-suspended in the sorting buffer (PBS supplemented with 1% FBS).  Subsequently, the suspended cells were stained with DRAQ5 and DAPI (Sigma) to harvest nucleated living cells. After antibody incubation, the cells were washed twice with cold PBS and reconstituted in DMEM with 20% FBS. Cell sorting was performed with a MoFlo Astrios EQ Cell Sorter (Beckman Coulter). Unstained cells were routinely used to define FACS gating parameters and sorted into DMEM media supplemented with 20% FBS.

tag: patient id

value: Patient 11

value: subcutaneous metastase

value: Total thyroidectomy, three times of iodine ablation and TSH suppression


title: ESC Matr3KO unt rep2


title: d9426.S (Small HSC rep2)


title: Patient 11 right lymph node

description: right lymph node patient 11

source_name: lymph node metastase

value: lymph node

value: lymph node metastase


title: ESC WT diff rep2

value: wild type


title: 24h NICD+lgl-KD replicate 2

city: New Orleans

first: Wu-Min

last: Deng

state: LA

address: 1700 Tulane Avenue

department: School of Medicine, Department of Biochemistry

institute: Tulane University

data_processing:
Illumina Casava1.7 software used for base-calling
Single-ended fastq files for the whole-tissue RNA-Seq samples were aligned to Drosophila melanogaster Release 6 (Drosophila_melanogaster.BDGP6.28.100.chr_filtered.gtf) reference genome assembly using STAR (v2.7) aligner. featureCounts (Subread package) was run on individual bam files for the generation of count-matrix.
Genome index for single-cell analysis was built using the Drosophila melanogaster Release 6 (Drosophila_melanogaster.BDGP6.28.100.chr_filtered.gtf) reference genome assembly using 10X genomics cellranger (version 3.0.1) mkref pipeline. Sequenced reads were then mapped to this reference genome index. The cellranger count pipeline for alignment, filtering, barcode counting and UMI counting was used to generate the multidimensional feature-barcode matrix for single-cell RNA-Seq datasets.
Genome_build: dm6
Supplementary_files_format_and_content: csv files contain raw counts for each whole-genome RNA Seq sample.
Supplementary_files_format_and_content: 3 files were obtained after running cellranger pipeline (barcodes.tsv, features.tsv and matrix.mtx) on the single-cell RNA-Seq datasets. All these files are readable in R and were processed using the Seurat pipeline which resulted in the individual R object files for each corresponding dataset.

organism: Drosophila melanogaster

source_name: Whole ovarian tissue

growth_protocol: 100 adult ovaries from 50 female Drosophila melanogaster flies maintained at 25°C, with access to males and yeast supplements for 3 days

extract_protocol:
For bulk-RNA sequencing: Whole ovaries were extracted from 40 females in complete medium (Grace’s Insect Basal Medium supplemented with 15% FBS. The anterior part of the ovaries were carefully removed before stage 10 egg chambers. Samples were transferred to a steril Eppendorf tube and media was aspirated. Samples were flash frozen using liquid nitrogen and stored until day of the library preparation in -80°C. Total RNA was extracted using Trizol. For single-cell RNA sequencing: Whole ovaries were extracted from female flies that were dissected in complete medium (Grace’s Insect Basal Medium supplemented with 15% FBS) and were transferred to a tube containing 300 μL EBSS (no calcium, magnesium, and phenol red), followed by a gentle wash for 2 minutes. The EBSS was then removed and the tissue was dissociated in 100 μL Papain (50 U/mL in EBSS and previously heat activated in 37°C for 15 minutes) for 30 minutes. The suspension was mechanically dissociated every 3 minutes by gentle pipetting up and down. To quench the digestion, 500 μL complete medium was added to dissociated cells. The suspension was then passed through a 40 μL sterile cell strainer and centrifuged for 10 minutes at 700 RCF to remove large eggs with intact eggshell which cannot be dissociated and debris. Supernatant was removed and single cells were re-suspended in 100 μL. Cell viability was assayed using Trypan Blue and estimates of cell concentration were made using a hemocytometer. Cells were then further diluted to an approximate, final concentration of 2,000 cells/μL according to 10X Genomics recommendations.
Bulk sequencing libraries were made using the Ultra II Directional RNA library prep kit for Illumina using the protocol for NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB#E7490). Single-cell libraries were prepared using the Single Cell 3’ Library & Gel Bead Kit v2 and Chip Kit according to the recommended 10X Genomics protocol. Single cell suspension was loaded onto the Chromium Controller (10X Genomics). Library quantification assays and quality check analysis was performed using the 2100 Bioanalyzer instrument (Agilent Technologies). The library samples were then diluted to a 10nM concentration and loaded onto two lanes of the NovaSeq 6000 (Illumina) instrument flow cell for a 100-cycle sequencing run.

treatment_protocol: Flies were transferred to 29°C incubator for 1 (24h), 3 (72h) and 4 (96h) days depending on the dataset, and were subsequently dissected.

value: Ovary

value: 3 days after eclosion

value: tj>GAL4, UAS-Gal80TS>UAS-lglRNAi, UAS-NICD, UAS-Dcr2

value: 1 day in 29°C


title: CR032_wo_S8

value: chimpanzee neural forebrain progenitor cells

value: IgG

value: DNA released by antibody-targeted MNase


title: Patient 10 right lymph node

description: right lymph node patient 10

value: Patient 10

value: No treatment


title: CR031_wo_S7


title: Lim.b

value: kidney

value: baseline


title: Mi.b


title: Nov.b


title: ESC WT diff rep1

value: Embryonic stem cell

value: differentiated


title: ESC WT unt rep2

value: untreated


title: ESC Matr3KO diff rep1

value: Matr3 -/-


title: CR029_wo_S5


title: Kil.b


title: CR019_S9


title: ESC Matr3KO unt rep1


title: Patient 9 paratumor

description: paratumor patient 9

source_name: thyroid paratumor

value: Patient 9

value: thyroid gland

value: thyroid paratumor


title: Del.b


title: Patient 8 paratumor

description: paratumor patient 8

value: Patient 8


title: Osc.b


title: ESC WT unt rep1

value: wild type


title: CR018_S8


title: CR017_S7


title: Jul.b


title: HiC MEL diff Matr3KO rep2

data_processing:
Fastq reads were mapped using bwa-mem, and then classified, de-duplicated.
Low-quality reads were filtered out using pairtools (phred score<30) to achieve valid pairs.
Valid pairs were binned at 1kb, 2kb, 5kb, 10kb, 25kb, 50kb, 100kb, 250kb, 500kb and 1Mb resolutions to generate interaction matrices.
A and B compartments were defined by eigen vector decomposition on 100kb binned Hi-C data using the call-compartments function of the cooltools.
Genome_build: mm10
Supplementary_files_format_and_content: PC1 value tsv file

source_name: MEL cells

growth_protocol: MEL cells were cultured in Dulbecco's Modified Eagle's Medium (DMEM) with 10% fetal calf serum, 1% L-glutamine, and 2% penicillin/streptomycin at 37 °C in a humidified. atmosphere of 5% CO2

extract_protocol:
5 million MEL cells were crosslinked with 1% formaldehyde for 10 minutes, quenched with glycine, and then lysed.
Illumina TruSeq adapted were ligated, cleaned-up and amplified using Illumina PCR master mix.

value: Erythroleukemia cells

value: treated with 2%DMSO


title: Patient 10 tumor

description: tumor patient 10

source_name: thyroid tumor

value: thyroid tumor


title: Patient 8 tumor

description: tumor patient 8


title: Patient 9 tumor

description: tumor patient 9


title: Patient 7 right lymph node

description: right lymph node patient 7

value: Patient 7

value: lymph node

value: lymph node metastase

value: Hemi-thyroidectomy and TSH suppression


title: D2.OR in 3D rep3

city: L'Hospitalet de Llobregat

first: Xavier

last: Solé

address: Av. Gran Via 199-203

department: Oncology Data Analytics Program

country: Spain

institute: Catalan Institute of Oncology

description:
D2OR_3D_B3
FCHKJCFBBXX_L7_HKMOUiqiEAAHRAAPEI-211

data_processing:
Quality control with FastQC v.0.11.4
Read trimming by quality and adapter removal with Trimmomatic v.0.32
Removal of reads with miscalls (Ns) using an in-home python (v.2.7.13) script
Allignment to GENCODE mouse release 15 (GRCm38) with STAR v.2.5.3.a
Quantification with RSEM v.1.3.0
Genome_build: GRCm38
Supplementary_files_format_and_content: Matrix of TPM counts for every gene and sample
Supplementary_files_format_and_content: tab-delimited text files from RSEM output

source_name: D2.OR in 3D

extract_protocol:
RNA was extracted from the pellet using the Nucleospin kit (BioKé) protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: Breast cancer cell line

tag: culture


title: HiC MEL diff parental rep2


title: D2.OR in 3D rep1

description:
D2OR_3D_B1
FCHKJCFBBXX_L8_HKMOUiqiEAALRAAPEI-216


title: D2.OR in 3D rep2

description:
D2OR_3D_B2
FCHKJCFBBXX_L6_HKMOUiqiEAADRAAPEI-207


title: ciPS_cPT_d14_s2

description:
iPS-derived chimpanzee neural forebrain progenitors
Merged_MultiMapping_Hg38.PanTro6_allGenes_h48_cPT.txt
mRNA4

data_processing:
RNA-seq: raw base call files were converted to fastq and demultiplexed using bcl2fastq. The fastq files were mapped to hg38 and pantro6 reference genomes using STAR/2.5.0a with parameter --outFilterMismatchNoverLmax 0.03 and --sjdbGTFfile gencode.v27.annotation.gtf. When mapping to pantro6, the gencode.v27.annotation.gtf were lifted from hg38 coordinates to pantro6. Gene counts were quantified using featurecounts from Subread/1.5.0-p1, with -s 2, -p and -t exon parameters.
single-cell RNA-seq: raw basecall files were converted to fastq and demultiplexed using cellranger/2.1 mkfastq. Gene counting was done with cellranger count.
Genome_build: hg38
Supplementary_files_format_and_content: counts and coverage tracks

extract_protocol:
On the day of harvest, the cells were washed once with PBS and lysed with 350 µl RLT buffer with 1% mercaptoethanol (Thermo Fisher). RNA was extracted using the RNeasy mini kit (Qiagen) according to manufacturer’s protocol. The quality and concentration of the RNA was analyzed using 2100 Bioanalyzer (RNA nano; Agilent) and Qubit (RNA HS assay kit).
TruSeq RNA Library Prep kit v2 (Illumina)

value: chimpanzee neural forebrain progenitor cells

value: polyA RNA


title: HiC MEL unt Matr3KO rep2

value: untreated


title: ciPS_C6_d14_scRNA

extract_protocol: HS1 and PT1 were differentiated to day 14, washed twice with DPBS, and dissociated with Accutase for approximately 10 minutes, followed by centrifugation at 400 × g for 5 minutes in wash medium. All pipetting was done very gently to avoid cell death. The pellets were resuspended in 1 ml PBS with 0.04% BSA (Sigma) and filtered through 100 µm cell strainers (Falcon) twice. Cells were resuspended in order to yield a concentration of approximately 1000 cells/µl. The single-cell libraries were prepared with Chromium Single Cell A chip kit and Chromium Single Cell 3’ Library & Gel Bead kit v2 (10× Genomics), quality controlled, and quantified using Qubit ds DNA HS and Bioanalyzer High Sensitivity DNA Assay prior to sequencing. The samples were sequenced for 26 cycles on read 1 and 98 cycles on read 2 using the Illumina NextSeq 500.


title: ciPS_cPT_d14_s1

description:
iPS-derived chimpanzee neural forebrain progenitors
Merged_MultiMapping_Hg38.PanTro6_allGenes_h48_cPT.txt
mRNA3


title: HiC MEL unt parental rep2


title: D2.OR in 2D rep2

description:
D2OR_2D_B2
FCHKJCFBBXX_L6_HKMOUiqiEAABRAAPEI-205

source_name: D2.OR in 2D


title: ESC Diff Rad21 rep2

data_processing:
ChIP sequencing was performed using Illumina HiSeq2500 or NextSeq500.
Sequencing reads were aligned to the assembly of the mouse genome mm10 using Bowtie2 with the default parameters.
Duplicate reads were removed using Picard Tools (http://broadinstitute.github.io/picard/).
Peaks were called using Model-based Analysis of ChIP-Seq (MACS2).
Genome_build: mm10
Supplementary_files_format_and_content: peak files

extract_protocol:
Cells were crosslinked and nuclei were prepared using truChIP Chromatin Shearing Reagent Kit (Covaris).
Purified ChIP DNA was processed to generate libraries using the NEBNext ChIP-seq Library Prep Master Mix, NEBNext Ultra DNA Library Prep Kit for Illumina (New England BioLabs), ThruPLEX DNA-Seq Kit (Rubicon Genomics), or Accel-NGS 2S Plus DNA Library Kit (Swift Biosciences) according to the manufacturer’s instructions.

value: Embryonic stem cell

value: differentiated


title: Patient 5 paratumor

description: paratumor patient 5

value: Patient 5

value: thyroid gland

value: No treatment


title: Patient 5 right lymph node

description: right lymph node patient 5


title: D2.OR in 2D rep3

description:
D2OR_2D_B3
FCHKJCFBBXX_L7_HKMOUiqiEAAFRAAPEI-209


title: Patient 5 tumor

description: tumor patient 5


title: ESC Matr3KO Rad21 rep2

value: Matr3 -/-


title: ciPS_C6_d16_batch2

description:
iPS-derived chimpanzee neural forebrain progenitors
RNAseq_H6_C6_map_hg38_pt6.tab
277


title: ESC parental Rad21 rep2

value: wild type


title: D2.OR in 2D rep1

description:
D2OR_2D_B1
FCHKJCFBBXX_L8_HKMOUiqiEAAJRAAPEI-213


title: Patient 4 subcutaneous metastase

description: subcutaneous metastase  patient 4

value: Patient 4

value: subcutaneous metastase

value: Iodine ablation and TSH suppression


title: CR016_S6

value: IgG

value: DNA released by antibody-targeted MNase


title: ciPS_C6_d15_batch2

description:
iPS-derived chimpanzee neural forebrain progenitors
RNAseq_H6_C6_map_hg38_pt6.tab
274


title: D2A1 in 3D rep3

description:
D2A1_3D_B3
FCHKJCFBBXX_L7_HKMOUiqiEAAGRAAPEI-210

source_name: D2A1 in 3D


title: ciPS_C6_d14_batch2

description:
iPS-derived chimpanzee neural forebrain progenitors
RNAseq_H6_C6_map_hg38_pt6.tab
271


title: ESC Diff Rad21 rep1


title: Patient 3 right lymph node

description: right lymph node patient 3

value: Patient 3

value: lymph node

value: lymph node metastase


title: Patient 6 right lymph node

description: right lymph node patient 6

value: Patient 6

value: Total thyroidectomy and TSH suppression


title: ESC Matr3KO diff rep2

value: Embryonic stem cell


title: Patient 3 left lymph node

description: left lymph node patient 3


title: ESC Matr3KO Rad21 rep1

value: untreated


title: D2A1 in 3D rep1

description:
D2A1_3D_B1
FCHKJCFBBXX_L8_HKMOUiqiEAAKRAAPEI-214

value: Breast cancer cell line


title: ciPS_C6_d13_batch2

description:
iPS-derived chimpanzee neural forebrain progenitors
RNAseq_H6_C6_map_hg38_pt6.tab
268

value: chimpanzee neural forebrain progenitor cells

value: polyA RNA


title: D2A1 in 3D rep2

description:
D2A1_3D_B2
FCHKJCFBBXX_L6_HKMOUiqiEAACRAAPEI-206


title: Patient 3 paratumor

description: paratumor patient 3

value: thyroid gland

value: thyroid paratumor

value: No treatment


title: ESC parental Rad21 rep1

value: wild type


title: ESC Matr3KO CTCF rep2

value: Matr3 -/-


title: D2A1 in 2D rep3

description:
D2A1_2D_B3
FCHKJCFBBXX_L7_HKMOUiqiEAAERAAPEI-208

source_name: D2A1 in 2D


title: ciPS_C6_d15_batch1

description:
iPS-derived chimpanzee neural forebrain progenitors
RNAseq_H6_C6_map_hg38_pt6.tab
262


title: ESC parental CTCF rep2


title: D2A1 in 2D rep2

description:
D2A1_2D_B2
FCHKJCFBBXX_L6_HKMOUiqiEAAARAAPEI-202


title: S08: smxl5obe3_GFP-

city: Heidelberg

first: Thomas

last: Greb

address: Im Neuenheimer Feld 360

department: Centre for Organismal Studies

country: Germany

institute: Heidelberg University

data_processing:
bowtie2 (v2.2.6) was used for mapping.
Output sam files were converted to bam files and then trimed with "-q 2" and "1 2 3 4 5" parameters in samtools (v0.1.19) to remove mitochondrial and chloroplast sequence.
Output bam files were treated with picard MarkDuplicates (2.25.5) to remove duplicated reads. Then, output files were passed through samtools view again, to obtain 40 M reads (targeted) for further analysis.
bigWig files were generated by bamCoverage in deepTools (v3.5.1) from bam files with 10bp bin size.
bam files were converted to TagDirectory by homer (v4.10.3), and peak calling were done by findPeaks in homer with "-region -minDist 150" option
Genome_build: Arabidopsis TAIR 10 (Arabidopsis_thaliana.TAIR10.28.dna.toplevel.fa)
Supplementary_files_format_and_content: bigWig files are generated from 40M reads bam files for coverage tracks.
Supplementary_files_format_and_content: Peak text files

organism: Arabidopsis thaliana

source_name: seedling nuclei

growth_protocol: Arabidopsis were grown on 1/2 MS agar plate for three weeks in long days (8h light 16h dark, constant 21°C).

extract_protocol:
Approximately 1 g of Arabidopsis seedlings were collected in a 60 mm petri dish and thoroughly chopped using a razor blade for five minutes in nucleus isolation buffer (1x NIB Sigma-Aldrich, #CELLYTPN1) supplemented with 10µg/ml Hoechst 33342 (Sigma-Aldrich, #B2261) as the final concentration. Next, the samples were incubated 15 minutes in a dark cold room while gently shaking. After the incubation, petri dishes were washed with additional 1 ml of NIB to properly clean the plate. Using wide-bored pipet tips, the nucleus suspension was applied to a 50 µm nylon-mesh filter (Sysmex, #04-004-2327) mounted into a 30 µm nylon-mesh filter (Sysmex, #04-004-2326) at the top, both inserted into 2 ml Protein LoBind tubes (Eppendorf #0030108132). The filtered material was passed through a 5 ml Round Bottom Polystyrene FACS tube (Corning, #352235). 15,000 nuclei for each sample were then sorted into a DNA LoBind tubes (Eppendorf) with 300 µL collection buffer (15 mM TRIS-HCl ph 7.5, 20 mM NaCl, 80 mM KCl, 0,1 % Triton) by a BD FACSAriaTM IIIu cell sorter using a 100 µm sort nozzle and a 30kHz drop drive frequency according to their GFP signal levels. The gate for GFP + nuclei was set using a WT Col as reference. Next, samples were centrifuged at 3000 g for 10 minutes at 4 degrees. The supernatant was partially removed and the nuclei resuspended in 300 µL Tris-Mg buffer (Tris HCl pH8 10mM, MgCl2 5mM). A second washing step was performed using centrifugation at 1000 g for 10 minutes at 4 degrees and the supernatant was removed completely. For tagmentation, the TDE1 (Nextera Tn5 Transposase) Tagment DNA Enzyme (Illumina kit #20034198) was immediately applied to the samples by resuspending the nuclei in the transposition reaction mix and the suspension was incubated for 30 minutes at 37 degrees while gently shaking.
The samples were then purified (NEB, Monarch Nucleic Acid Purification Kit #20034198), and 12 µl of transposed DNA was amplified by PCR (8 µl H2O, 2.5 µl 25µM Custom Nextera PCR primer 1 (Buenrostro et al., 2013), 2.5 µl 25 µM Custom Nextera PCR Primer 2 and 25 µl NEB Next High Fidelity 2x PCR Master Mix(NEB, #M0541) with 1 cycle of (72°C for 5 min, 98°C for 30 sec) and 16 cycles of (98°C for 10 sec, 63°C for 30 sec, 72°C for 1 min). Library was cleaned up using the Coulter Agencourt AMPure XP kit (Beckman-Coulter, #10136224) applying a 1:1 vol:vol (PCR product:beads) and eluted in 15 µl 15 mM Tris.

tag: ecotype

tag: cell population

value: GFP negative (SMXL5pro:H4-GFP)

value: seedling nuclei


title: ESC Matr3KO CTCF rep1


title: ESC Diff CTCF rep1

value: differentiated


title: ciPS_C6_d13_batch1

description:
iPS-derived chimpanzee neural forebrain progenitors
RNAseq_H6_C6_map_hg38_pt6.tab
256


title: ciPS_C6_d14_batch1

description:
iPS-derived chimpanzee neural forebrain progenitors
RNAseq_H6_C6_map_hg38_pt6.tab
259


title: D2A1 in 2D rep1

description:
D2A1_2D_B1
FCHKJCFBBXX_L8_HKMOUiqiEAAIRAAPEI-212


title: ESC parental CTCF rep1


title: MEL Diff Rad21 rep2

value: Erythroleukemia cells

value: treated with 2%DMSO


title: S07: smxl5obe3_GFP+

value: GFP positive (SMXL5pro:H4-GFP)


title: NASH_24w, rep1

city: New York

first: Chengguo

last: Wei

state: NY

address: 1428 Madison Ave1468 Madison Ave

department: Medicine

institute: Icahn School of Medicine at Mount Sinai

data_processing:
The RNA-seq data were analyzed by following the procedure described below.
Briefly,  after sequence quality filtering at a cut-off of a minimum quality score Q20 in at least 90%  bases for the paired-end 150bp FASTQ sequencing data, the good-quality reads aligned  to Reads were processed and aligned to the University of California Santa Cruz (UCSC)  Mus musculus reference genome and transcriptome (build mm10) using the Burrows-  Wheeler Aligner (bwa). The reads that are uniquely aligned to the exon and splicing  junction sites for each transcript were combined to calculate an expression level for a  corresponding transcript and further normalized based on reads per kilobase per million  reads to compare transcription levels among samples.
The transcripts with a low raw  read count <100 in all the samples were excluded for downstream analysis. Gene  expression value was transformed to the log 2 base scale. Principle Component Analysis  (PCA) was first performed to assess the sample correlations using the expression data  of all the genes. The differentially expressed genes in NASH mice compared with control  mice were identified by the R package limma test. A specific gene was considered  differentially expressed if the P-value was ≤0.05.
The Gene Ontology and pathway  analysis for the differentially expressed genes were then performed with a fold change cutoff of ≥1.5 using INGENUITY© IPA (www.ingenuity.com/products/ipa) and the online  tool Enrichr. The read coverage of gene functional elements was also visualized by the  Integrative Genome Viewer tool (www.broadinstitute.org/igv/) from the genome alignment  file. Heatmap analysis was performed for the top 50 differentially expressed genes after  the median center was transformed using Multi-Experiment Viewer software.

source_name: Kidney cortices

extract_protocol:
Total RNA was isolated from kidney cortices by using the RNeasy mini kit (Qiagen 74104)  according to the manufacturer's protocol. RNA concentrations were quantified using a  Nanodrop Spectrophotometer at a wavelength of 260nm.
Only samples with an RNA  integrity value of > 7.5 were used for mRNA sequencing at the CLC Genomics and  Epigenomics Core Facility at Weil Cornell Medical College for library construction and sequencing.

treatment_protocol: Control for 12 weeks (mice were fed with normal  diet and corn oil for 12 weeks; 6 mice: 3 male and 3 female), NASH for 12 weeks (mice  were treated with WD and CCl4 for 12 weeks; 6 mice: 3 male and 3 female), Control mice  at 24 weeks were fed with normal diet and corn oil (8 mice: 4 males and 4 females), NASH  mice at 24 weeks were treated with WD and CCl4 (10 mice: 5 males and 5 females).

value: Kidney cortices

value: Western diet and treated with CCl4 24 weeks


title: S06: smxl4smxl5_GFP-


title: NASH_24w, rep3


title: NASH_24w, rep2


title: NASH_12w, rep3

value: Western diet and treated with CCl4 12 weeks


title: ciPS_C6_d16_batch1

description:
iPS-derived chimpanzee neural forebrain progenitors
RNAseq_H6_C6_map_hg38_pt6.tab
265


title: Patient 3 tumor

description: tumor patient 3

value: Patient 3

value: thyroid tumor


title: NASH_12w, rep2


title: MEL Matr3KO Rad21 rep2

value: untreated


title: MEL parental Rad21 rep2


title: S03: smxl5_GFP+


title: Con_24w, rep3

value: Normal diet 24 weeks


title: S01: WT_GFP+

value: Wild type


title: MEL Diff Rad21 rep1


title: NASH_12w, rep1


title: MEL Diff CTCF rep2


title: O2_LacZ_63days_S2

description:
Organoids (LacZ, g2 and g3) were collected for single nuclei sequencing at 2 and 4 months. At harvest, organoids were dissected out of the Matrigel, frozen on dry ice and stored at -80°C. In order to reduce bias in the downstream analysis due to organoid heterogeneity, they were frozen 5 by 5 per time point and batch. The nuclei isolation protocol has been described in detail elsewhere (Sodersten et al., 2018). In brief, the organoids were thawed and homogenized in cold lysis buffer (0.32 M sucrose, 5 mM CaCl2, 3 mM MgAc, 0.1 mM Na2EDTA, 10 mM Tris-HCl, pH 8.0, 1 mM DTT) using a tissue douncer (Wheaton). The homogenate was carefully layered on top of a sucrose solution (1.8 M sucrose, 3 mM MgAc, 10 mM Tris-HCl, pH 8.0, and 1 mM DTT) before centrifugation at 30,000 × g for 2 hours and 15 min. Pelleted nuclei were softened for 10 min in 100 ml of nuclear storage buffer (15% sucrose, 10 mM Tris-HCl, pH 7.2, 70 mM KCl, and 2 mM MgCl2) before resuspended in 400 ml of dilution buffer (10 mM Tris-HCl, pH 7.2, 70 mM KCl, and 2 mM MgCl2) and run through a cell strainer (70 mm). Cells were run through the FACS (FACS Aria, BD Biosciences) at 4°C with low flowrate using a 100 mm nozzle (reanalysis showed >99% purity), sorting 8,500 nuclei per sample which were then loaded onto 10X Genomics Single Cell 3’ Chip along with the reverse transcription mastermix following the manufacturer’s protocol for the Chromium Single Cell 3′ Library (10X Genomics, PN-120233) to generate single-cell gel beads in emulsion. cDNA amplification was done as per the guidelines from 10x Genomics and sequencing libraries were generated with unique sample indices (SI) for each sample. Libraries for samples were multiplexed and sequenced on a Novaseq using a 150-cycle kit using the recommended read length.
human cerebral organoids

data_processing:
single-nuclei RNA-seq: raw basecall files were converted to fastq and demultiplexed using cellranger/2.1 mkfastq. Gene counting was done with cellranger count.
Genome_build: hg38

growth_protocol: To generate the human cerebral-like organoids we used three hIPSC6-derived lines, one control line (guide against LacZ) and two ZNF558 KD lines (g2 and g3). We used a protocol based by the one by Lancaster et al. with minor modifications (Lancaster et al., 2013). Starting from the plated cells, they were first washed once with DPBS-/-, then detached from the wells with 500 μl of Accutase with an incubation at 37° C for 5 minutes. The cells were then transferred in 5 ml of washing medium (5% KSR in DMEM F12 +/+) and centrifuged for 5 minutes at 400 x g (RT; acceleration/deceleration 8). After removing the supernatant, the pellet was resuspended in 1-2 ml of mTeSR1 (Stemcell Technologies) enriched with ROCK Inhibitor (RI) 10μM (1:1000 from stock concentration 10 mM). The cells in the cell suspension were then counted, and 8000 cells/well were plated in a 96-wells plate (Costar, Ultra Low Attachment, round bottom; REF 7007) with 250 μl of mTeSR1 and RI 10 μM. This is considered day -5 of the differentiation of the iPSCs-derived hFB organoids. At day -3 and -1 the medium was changed (150 μl and 200 μl of mTeSR1, respectively). At day 0 the cells are fed with Neural Induction Medium (NIM; DMEM/F12 media, N2 Supplement (1:100), L-Glutamine (2mM), Penicillin/Streptomycin (1:500), Non-Essential Amino acids (1:100) and Heparin (2ug/ml).) enriched with 3% KSR. At day 2, 4, and 6, the organoids were fed with NIM with no added KSR. At day 7 “cavities” for the organoids embedding were prepared by putting parafilm on an empty tip holder (with sterile surface facing up) and pressing every hole to form a little basin. The structure was sterilized with a 30-minutes UV cycle and left inside the hood until the next day. Matrigel was left to thaw overnight at 4° C. On day 8 the organoids were embedded: the parafilm was cut in half, then each organoid was transferred in one “cavity” with a cut P1000-tip; the media surrounding the organoid was removed, trying to place it in the center of the “cavity”. The organoids were then covered with 30-50 μl of Matrigel (Corning) avoiding any bubble and incubated at 37° C for 25 minutes to allow the Matrigel to solidify. The organoids were then transferred in Corning REF 3471 6-wells plates with flat bottom containing 3 ml/well of Cortical Differentiation Medium (CDM; F12 Media (-Glut) (48.5%), Neurobasal (48.5%), N2 Supplement (1:200), B27 Supplement (-Vit.A, 1:100), L-Glutamine (2mM), Penicillin/Streptomycin (1:500), Non-Essential Amino acids (1:200), Beta MercaptoEtOH (50uM) and Insulin (2.5 ug/mL)). To detach the organoids from the parafilm, the latter was removed from the tip holder and the “dimples” were turned inside-out; drops of CDM then were used to let the organoids fall into the wells. In the end, in every well there were about 4 ml of medium. On day 10 and 12 of the differentiation, the medium was changed exchanging 3 ml/well for 3 ml of fresh CDM. On day 15, 17, 19, 21 and 23, ~4 ml the medium was replaced with 4 ml of Improved Differentiation Medium + A (IDM, F12 Media (-Glut) (48.5%), Neurobasal (48.5%), N2 Supplement (1:200), B27 Supplement (+Vit.A, 1:50), L-Glutamine (2mM), Penicillin/Streptomycin (1:500), Non-Essential Amino acids (1:200), Beta MercaptoEtOH (50uM), Insulin (2.5 ug/mL) and Ascorbic Acid (400uM)). From day 25, the medium was changed every 3 days with 3-4 ml of Cortical Terminal Differentiation Medium (CTDM, F12 Media (-Glut) (48.5%), Neurobasal (48.5%), N2 Supplement (1:200), B27 Supplement (+Vit.A) – (1:50) 800uL, L-Glutamine (2mM), Penicillin/Streptomycin (1:500), Non-Essential Amino acids (1:200), Beta MercaptoEtOH (50uM), Insulin (2.5 ug/mL) and Ascorbic Acid (400uM), BDNF (10ng/uL), cAMP (200uM), GDNF (10ng/uL)). All the diameter measurements of the organoids were taken with the Measure tool from the software GIMP 2.10. The chosen measuring unit was mm.

extract_protocol:
Organoids (LacZ, g2 and g3) were collected for single nuclei sequencing at 2 and 4 months. At harvest, organoids were dissected out of the Matrigel, frozen on dry ice and stored at -80°C. In order to reduce bias in the downstream analysis due to organoid heterogeneity, they were frozen 5 by 5 per time point and batch. The nuclei isolation protocol has been described in detail elsewhere (Sodersten et al., 2018). In brief, the organoids were thawed and homogenized in cold lysis buffer (0.32 M sucrose, 5 mM CaCl2, 3 mM MgAc, 0.1 mM Na2EDTA, 10 mM Tris-HCl, pH 8.0, 1 mM DTT) using a tissue douncer (Wheaton). The homogenate was carefully layered on top of a sucrose solution (1.8 M sucrose, 3 mM MgAc, 10 mM Tris-HCl, pH 8.0, and 1 mM DTT) before centrifugation at 30,000 × g for 2 hours and 15 min. Pelleted nuclei were softened for 10 min in 100 ml of nuclear storage buffer (15% sucrose, 10 mM Tris-HCl, pH 7.2, 70 mM KCl, and 2 mM MgCl2) before resuspended in 400 ml of dilution buffer (10 mM Tris-HCl, pH 7.2, 70 mM KCl, and 2 mM MgCl2) and run through a cell strainer (70 mm). Cells were run through the FACS (FACS Aria, BD Biosciences) at 4°C with low flowrate using a 100 mm nozzle (reanalysis showed >99% purity), sorting 8,500 nuclei per sample which were then loaded onto 10X Genomics Single Cell 3’ Chip along with the reverse transcription mastermix following the manufacturer’s protocol for the Chromium Single Cell 3′ Library (10X Genomics, PN-120233) to generate single-cell gel beads in emulsion. cDNA amplification was done as per the guidelines from 10x Genomics and sequencing libraries were generated with unique sample indices (SI) for each sample. Libraries for samples were multiplexed and sequenced on a Novaseq using a 150-cycle kit using the recommended read length.
Chromium Single Cell 3′ (10x)
single nuclei RNA-seq

value: human cerebral organoids

tag: months in culture


title: O2_LacZ_4M_S8


title: O2_g3_63days_S4


title: Con_24w, rep1

tag: strain


title: O2_g3_4M_S10


title: MEL Matr3KO CTCF rep2


title: O2_g2_63days_S3


title: HT-22 Mouse hippocampal neuronal cell- Glutamate with PP treatment 24h

city: Pathumwan

first: Shuqin

last: Cao

state: Bangkok

address: 154 Rama I Road Chula Soi 12

department: Allied Health Sciences

country: Thailand

institute: Chulalongkorn University

data_processing:
The RNA-seq was performed according to BGISEQ experiment flow chart. Firstly, purify total RNA samples by enrich mRNA or deplete rRNA and get the mRNA fragments. Synthesis cDNA and adding A-tailing and bubble adapter ligation before running PCR.
Transcriptomic date were analyzed by merging novel coding transcripts with reference transcripts, with clean reads obtained using Bowtie2. The gene expression levels of each sample were calculated using RSEM. DEGs between the negative control and treated smaples were identified using the PossionDis algorithm.
In addition to the results from BGI, the overlaped genes between negative control and treated samples were selected using Microsoft Access based on double log2 (glutamate/control) and log2( P.edulis extracts and glutamate cotreatment/glutamate) ratio with predetermined cut-off parameters (p<0.05, FDR<0.05).

organism: Hippocampus

source_name: Mouse

growth_protocol: HT-22 cells were cultured in Dulbecco's modified Eagle medium supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin in a humidified 5% CO2 incubator at 37°C. For RNA extraction, HT-22 cells (150,000 cells/mL) were seeded in 6-well plates.

extract_protocol: Total RNA extracted using TRIzol reagent according to the manufacturer's instructions. Briefly, 1 mL of TRIzol lysate was mixed with 200 µL of ice-cold chloroform and centrifuged at 12,000 × g at 4°C for 15 min. Then, 400 µL of the aqueous phase was transferred and mixed with 500 µL of isopropyl alcohol, incubated for 15 min -20°C, and centrifuged at 12,000 × g at 4°C for 10 min. The resulting pellet was washed three times with 75% ethanol and centrifuged at 7,500 × g at 4°C for 5 min. Finally, the RNA pellet was dried at room temperature for 30 min before resuspension in 30 µL of RNase-free water. The amount of RNA was detected using a NanoDrop spectrophotometer at 260 nm.

treatment_protocol: This study includes 4 groups, which are untreated Control gorup; 5 mM Glutamate (24h) treated group; 5 mM Glutamate with P.edulis pulp extract (100 μg/mL) (24h) co-treated group; and 5 mM Glutamate with P.edulis peel extract (25 μg/mL) (24h) co-treated group

value: Hippocampal neuronal cell line

value: 5 mM Glutamate with P.edulis peel extract (25 μg/mL) 24h treatment


title: HT-22 Mouse hippocampal neuronal cell- Glutamate with FP treatment 24h

value: 5 mM Glutamate with P.edulis pulp extract (100 μg/mL) 24h treatment


title: O2_g2_4M_S9


title: MEL parental CTCF rep2

value: wild type


title: Con_12w, rep3

tag: tissue

value: Normal diet 12 weeks


title: O1_LacZ_4M_S5


title: HT-22 Mouse hippocampal neuronal cell- Glutamate treatment 24h

tag: treatment

value: Glutamate (5mM, 24h treatment)


title: MEL Matr3KO H3K27Ac rep2

value: Erythroleukemia cells

value: Matr3 -/-


title: MEL Diff CTCF rep1

value: treated with 2%DMSO


title: Con_12w, rep2

value: Kidney cortices


title: O1_g3_4M_S7


title: HT-22 Mouse hippocampal neuronal cell -Control

value: Vehicle (Untreat)


title: Con_24w, rep2


title: MEL parental H3K27Ac rep2


title: Con_12w, rep1


title: O1_g2_4M_S6


title: IgM-Rep4

status: Public on Sep 18 2021

city: Illkirch

first: Bernardo

last: Reina-San-Martin

address: 1, Rue Laurent Fries

country: France

institute: IGBMC- CNRS UMR 7104 - Inserm U 1258

data_processing:
Read counts extraction was performed using PoolQ from Broad Institute.
gRNA counts were normalized according as described in Jung, J et al. (2017) paper.
Ranking of candidate genes was performed using MaGeCK.
Genome_build: mm9
Supplementary_files_format_and_content: mBrie_PoolQ.txt (tab-delimited text file including target sequence and identifier)
Supplementary_files_format_and_content: S18186_ambiguous_counts.txt (tab-delimited text file including sequence of gRNAs and read counts-associated for each populations and replicates; gRNA counts)
Supplementary_files_format_and_content: mBrie_Analysis_Mageck.gene_summary.txt (tab-delimited text files including negative (not required for this screen) and positive selection screens results (score, p-value, fdr, rank, active sgrna, lfc); ranking of candidate genes)

source_name: B cell line CH12 stably expressing Cas9

growth_protocol: CH12 cells were cultured in RPMI supplemented with 10% FCS, HEPES (10 mM), penicillin-streptomycin (100 U/mL), Sodium Pyruvate (1 mM) and b-mercaptoethanol (50 µM).

extract_protocol:
IgM+ and IgA+ cells were sorted using anti-IgM and anti-IgA coupled magnetic beads. Genomic DNA from 24 million of cells was extracted using phenol/chloroform.
DNA libraries were prepared for sequencing using standard Illumina protocols
DNA-seq

treatment_protocol: In all replicates, CH12Cas9 cells transduced with mBrie library, selected with puromycin during 15 days and cultured with IL-4, TGF-b and anti-CD40 antibody during 72h

value: CH12Cas9 cells

value: B cell line CH12 stably expressing Cas9

tag: isotype

value: IgM+


title: IgA-Rep2

value: IgA+


title: IgA-Rep4


title: IgM-Rep2


title: IgM-Rep3


title: IgA-Rep1


title: IgM-Rep1


title: IgA-Rep3


title: TiKD cell line +tet at NMP - expt 2

city: Sheffield

first: Anestis

last: Tsakiridis

address: Western Bank

department: Biomedical Science

country: United Kingdom

institute: University of Sheffield

data_processing:
Illumina HiSeq Control Software (HCS) HD 3.4.0.38 was used for the data acquisition on the sequencing instrument.
On-instrument base-calling performed by the Illumina Real-Time Analysis (RTA) software 2.7.7.
BCL to BAM file conversion and demultiplexing with custom programmes (https://github.com/epigen/picard/) based on Picard tools 2.19.2 (https://broadinstitute.github.io/picard/)
Sequencing adapters were removed, and the low-quality reads were filtered using the fastp (0.20.1) software. Alignment of the short reads on GRCh38 was performed using Bowtie2 (2.4.1) with the “-very-sensitive” parameter. PCR duplicates were marked using samblaster (0.1.24), and the reads mapped to the ENCODE black-listed regions were discarded prior to peak calling.
To detect the open chromatin regions, we performed peak calling using the MACS2 (2.2.7.1) software with the “--nomodel”, “--keep-dup auto” and “--extsize 147” options. Finally, HOMER findMotifs (4.11) was used for motif enrichment analysis over the detected open chromatin regions.
Genome_build: GRCh38
Supplementary_files_format_and_content: peak lists in UCSC Genome Browser BED format

source_name: TiKD cell line +tet at NMP - expt 2

growth_protocol: hESCs were cultured routinely in feeder-free conditions in either Essential 8 (Thermo Fisher or made in-house) or mTeSR1 (Stem Cell Technologies) medium on laminin 521 (Biolamina) or Geltrex LDEV-Free reduced growth factor basement membrane matrix (Thermo Fisher).

extract_protocol:
Day 3 NMPs (50,000 cells) obtained from TBXT shRNA sOPTiKD hESC in the presence and absence of Tetracycline (three biological replicates) were harvested
After centrifugation, the pellet was carefully resuspended in the transposase reaction mix (12.5 μl 2xTD buffer, 2 μl TDE1 (Illumina), 10.25 μl nuclease-free water, and 0.25 μl 1% digitonin (Promega)) for 30 min at 37 °C. Following DNA purification with the MinElute kit eluting in 12 μl, 1 μl of eluted DNA was used in a quantitative PCR (qPCR) reaction to estimate the optimum number of amplification cycles.
The remaining 11 μl of each library were amplified for the number of cycles corresponding to the Cq value (i.e., the cycle number at which fluorescence has increased above background levels) from the qPCR. Library amplification was followed by SPRI (Beckman Coulter) size selection to exclude fragments larger than 1,200 bp. DNA concentration was measured with a Qubit fluorometer (Life Technologies). Library amplification was performed using custom Nextera primers.

treatment_protocol: hESCs were dissociated using Accutase solution (Merck Life Science) and plated at a density of approximately 50,000 cells/cm2 on vitronectin (Thermo Fisher)-coated culture plates in N2B27 basal medium containing 50:50 DMEM F12 (Merck Life Science / Neurobasal medium (Gibco) and 1x N2 supplement (Gibco), 1x B27 (Gibco), 1x GlutaMAX (Gibco), 1x MEM NEAA (Gibco), 2-Mercaptoethanol (50 μM, Gibco). N2B27 medium was supplemented with CHIR99021 (3 μM, Tocris), FGF2 (20 ng/ml, R&D Systems) and Rho-Associated Coil Kinase (ROCK) inhibitor Y-27632 2HCl (10 μM, Adooq Biosciences) with the latter being withdrawn from the differentiation medium after the first day of NMP induction. For TBXT inducible knockdown, NMP medium was supplemented with 1μg/ml tetracycline hydrochloride and replenished every other day.

tag: Sex

value: female

value: TBXT shRNA sOPTiKD hESC cell line

value: +tet

value: NMP-like axial progenitors


title: TiKD cell line -tet at NMP - expt 3

source_name: TiKD cell line -tet at NMP - expt 3

value: -tet


title: TiKD cell line +tet at NMP - expt 1

source_name: TiKD cell line +tet at NMP - expt 1


title: TiKD cell line -tet at NMP - expt 2

source_name: TiKD cell line -tet at NMP - expt 2


title: TiKD cell line -tet at NMP - expt 1

source_name: TiKD cell line -tet at NMP - expt 1


title: 2 Month Male 06 (L2-P19)

city: Irvine

first: Timothy

last: Downing

state: California

address: Samueli School of Engineering, University of California, Irvine

department: Dept. of Biomedical Engineering

institute: University of California, Irvine

data_processing:
The bismark pipeline of nfcore/methylseq:1.3 was used for quality-control, alignment and methylation calls with  as reference genome. (see here for more info: https://github.com/nf-core/methylseq)
Raw data QC: FastQC
Adapter sequence trimming : Trim Galore! (11 bp for both 3' end and 5' end and for both read 1 and read 2)
Alignment: Bismark
Methylation calls extraction: Bismark
The output methylation coverage CpGs are filtered with a minimum of 5x read depth
Genome_build: GRC38 (mm10)
Supplementary_files_format_and_content: The bedgraph files have four columns with the first column as chromosome number, the second and third columns are the start and end location of CpGs on chromosome, the fourth column is the methylation level in 0-1 range.

source_name: Mouse dorsal hippocampus

extract_protocol:
DNA was isolated, purified (260/280 ratio above 2.0) and digested at 4.5ug/sample with Msp1 (20U/uL, New England Biolabs). Samples were size selected for sequencinig and bisulfite converted.
Bisulfite converted DNA were size selected for 100-350bp and indexed using Swift Biosciences protocols.

tag: age

value: 2 month

value: Male

value: Mouse dorsal hippocampus


title: 2 Month Male 08 (L3-P18)


title: S04: smxl5_GFP-

tag: genotype

value: GFP negative (SMXL5pro:H4-GFP)

value: seedling nuclei


title: HEK293T cells, dko_rep2

city: Riverside

first: feng

last: tang

state: CA

address: 26861 Campus Point Dr., Moreno Valley

department: chemistry

institute: University of California, riverside

data_processing:
base calling analysis using the standard Illumina pipeline and sample de-multiplexing according to index read data
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using bowtie2
peaks were called using MACS2 with the following setting: macs2 callpeak -t -c -f BAM -g 2.7e+9 -n --outdir macs2
Genome_build: hg38
Supplementary_files_format_and_content: bed files were genereated using bedtools by overlaping the peaks of two replicates
Supplementary_files_format_and_content: wig files were generated using deeptools

source_name: HEK293T cells

growth_protocol: Cells were maintained in DMEM (Life Technologies) supplemented with 10% FBS (Invitrogen) and 1% penicillin/streptomycin at 37°C in a humidified incubator with 5% CO2. For genomic DNA extraction, the cells were harvested at 80% confluence. Cell lines used in this study were examined for a mycoplasma contamination test using e-Myco Mycoplasma PCR Detection Kit (Bulldog Bio. Inc.).

extract_protocol:
Cells were harvested and genomic DNA was extracted by Monarch® Genomic DNA Purification Kit (NEB, T3010S). Butylated hydroxytoluene (0.1 mM) (sigma) was added to prevent further DNA oxidation during DNA extraction. Genomic DNA was digested to 100–300 bp with NEBNext dsDNA Fragmentase (NEB, M0348) following the manufacturer’s guidelines.
The genomic DNA was labelled with  NTHL1 in  Tris-HCl buffer (50 mM, pH 7.0) with 1 mM EDTA, 1mM DTT, and 10 mM NaBH3CN at 37°C for 60 min. Mixtures of glycosylase and genomic DNA were enriched by incubating with 20 μL HisPur Ni-NTA Resin in 800 μL PBS with 20 μg single-stranded salmon sperm DNA. Then the mixture was placed at 4°C overnight. After centrifugation at 8000 rpm, the supernatant was discarded, the beads were washed twice with 1 mL PBS and then twice with 1 mL washing buffer (20 mM Tris-HCl pH 7.5，0.2% tween). NEB adaptor was ligated to double-stranded DNA on Ni-NTA resin to remove the free adaptor by beads washing. The ligation assay was performed by following the manufacturer’s guidelines. After completing the adaptor ligation, beads were washed twice with PBS and twice with washing buffer. After washing, DNA was eluted from the beads using 20 μL PBS with 500 mM imidazole at 37°C for 30 min with interval mixing at 1,200 rpm. The subsequent enrichment procedures (SDS-PAGE and membrane transfer) were the same as procedures described above. Purified DNA was subjected to qPCR and bioanalyzer analysis for quantification and verification. The library was then constructed using NEBNext Ultra DNA Library Prep Kit (NEB, E7103S) following the manufacturer’s instructions.

value: HEK293T cells

value: NTHL1-labeling, DPC-Seq


title: 2 Month Male 07 (L3-P17)


title: HEK293T cells, wt_rep2

value: wild type


title: 2 Month Male 03 (L2-P16)


title: 2 Month Male 04 (L2-P17)


title: TiKD cell line +tet at NMP - expt 3

source_name: TiKD cell line +tet at NMP - expt 3

tag: cell type


title: HEK293T cells, Input_rep2


title: HEK293T cells, dko_rep1


title: HEK293T cells, wt_rep1


title: 2 Month Male 10 (L3-P20)


title: 2 Month Male 05 (L2-P18)


title: HEK293T cells, Input_rep1


title: 2 Month Female 09 (L3-P16)

value: Female


title: 2 Month Female 05 (L3-P12)


title: 2 Month Female 07 (L3-P14)


title: 2 Month Female 08 (L3-P15)


title: Neutrophils-MSI-1436-rep I

city: Cold Spring Harbor

first: Nicholas

middle: K

last: Tonks

address: 1 Bungtown Rd

institute: Cold Spring Harbor Laboratory

data_processing:
The sequencing reads were aligned to customized mm10 gtf containing protein coding genes by using salmon 1.0.0 with default setting.
Expressed genes (TPM > 0.5 in either control or treatment) were subjected to differential gene expression analysis with DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM and fold change values for each Sample.

growth_protocol: Neutrophils isolated from Bone Marrow were plated into 6 cm petri dish, and incubate at 37°C for 30 min to allow attachment.

extract_protocol:
RNA was extracted using Trizol reagent.
The RNA-seq library was prepared with NEBNext Ultra™ II RNA Library Prep Kit (NET, E7770) for Illumina following manufacturer’s instruction.

treatment_protocol: Neutrophils purified from each mouse were either treated with saline or MSI-1436 for 2 hours.

value: Bone Marrow derived Neutrophils

value: Balb/c


title: Neutrophils-MSI-1436-rep III


title: 2 Month Male 02 (L2-P15)


title: Neutrophils-control-rep II

source_name: Neutrophils-control

value: Control


title: 2 Month Female 06 (L3-P13)


title: 20 Month Male 09 (L3-P10)

value: 20 month


title: 2 Month Female 02 (L2-P12)


title: 648T3

city: Lexington

first: Fan

last: Chen

state: Kentucky

address: 1095 V.A. Drive, HSRB 461

department: Toxicology and Cancer Biology

institute: University of Kentucky

description: Transplant

data_processing:
Sequencing and base-calling were performed by University of Kentucky Genomics core and BGI (Beijing Genomics Institute), respectively.
Sequencing reads were trimmed and filtered using Trimmomatic (V0.39) to remove adapters and low quality reads. Reads from human and mouse samples were mapped to Ensembl GRCm38 transcripts annotation (release 82), using RSEM (v1.3.2) and STAR (2.6.1d) with default settings.
Genome_build: GRCm38 release 82
Supplementary_files_format_and_content: tab-delimited text files including TPM, FPKM and expected_count for each gene

source_name: Mouse lung tumor organoids

growth_protocol: Murine 3D lung organoids were propagated in DMEM/F12 media containing 1x penicillin/streptomycin, 4mM L-glutamine, 10% fetal bovine serum and mixed 1:1 with growth factor-reduced Matrigel and lung mesenchymal endothelial cells, and pipetted into a 24-well 0.4 µm Transwell insert.

extract_protocol:
RNA from treated cell lines was extracted using Absolutely RNA Nanoprep kits (Agilent).
RNA libraries were prepared for sequencing using BGI or TruSeq standard Illumina protocols.

treatment_protocol: Murine 3D lung organoids were treated with Adeno-GFP or Adeno-Cre virus in vitro. Ad-Cre treated lung organoids were then orthotopically injected back to the trachea of immunocompromised mice.

tag: sorting type

value: Sca1 positive

value: Cre

tag: tissue origin

value: BASC mixed

tag: transplant

value: Yes

tag: seq platform

value: BGI std/DNBSEQ


title: 2 Month Male 01 (L2-P14)

value: 2 month

value: Male


title: 2 Month Male 09 (L3-P19)

value: Mouse dorsal hippocampus


title: 20 Month Male 08 (L3-P09)


title: 2 Month Female 04 (L3-P11)


title: 648T1

description: Transplant


title: 2 Month Female 03 (L2-P13)


title: 2 Month Female 01 (L2-P11)


title: Neutrophils-MSI-1436-rep II


title: KIm423

city: palo alto

first: John

last: Pluvinage

address: 3801 Miranda Ave Rm D3-131

institute: Stanford

data_processing:
cutadapt
STAR
SummarizedExperiment
tidyBulk
Genome_build: hg38
Supplementary_files_format_and_content: csv containing normalized counts

source_name: iMGL

growth_protocol: iMGL medium

extract_protocol:
Rneasy Micro Plus Kit
Smartseq v4 + Nextera XT

treatment_protocol: untreated or NPC CSF (10%) + antibody treatment

value: I1061T NPC1 knock-in mutant

tag: agent

value: anti-CD22 + NPC CSF


title: 648T2

description: Transplant

value: BASC bronchiolar


title: 646T1

description: Transplant


title: Neutrophils-control-rep III


title: 655T2

description: Transplant

value: NGFR negative


title: 20 Month Male 06 (L3-P07)


title: Neutrophils-control-rep I


title: 20 Month Male 03 (L3-P04)


title: KIm421


title: 20 Month Male 07 (L3-P08)


title: 20 Month Male 04 (L3-P05)


title: 20_540_T3_B

city: Washington

first: Sophie

middle: M

last: Colston

state: DC

address: 4555 Overlook Ave SW

department: CBMSE

institute: Naval Research Laboratory

data_processing:
Basecalling using Illumina RTA software v.1.18.54
Raw reads were trimmed of adapters/barcodes/primers and filtered on quality using CLC Genomics Workbench version 11.0.1
Reads were checked for quality using FASTQC v.0.11.8
Processed reads were mapped to a V. natriegens ATCC 14048 genome with the following parameters: mismatch cost = 2, insertion cost=2, deletion cost= 3, length fraction = 0.8, similarity fraction= 0.8. Fragment/read length less than 10 bp were discarded.
Differential expression was determined using an embedded Generalized Linear Model and dispersion estimate algorithm. Significant differential expression was assigned after applying the following thresholds: false discovery rate (FDR) p-value < 0.05, log2 fold change 3 |2|.
Genome_build: Processed reads were mapped to a V. natriegens ATCC 14048 draft genome NZ_ATFJ00000000.1
Supplementary_files_format_and_content: comma-separated values files; Name,Protein Inference,Product,Chromosome,Region,Expression value,TPM,Gene length

organism: Vibrio natriegens

source_name: bacterial cells

growth_protocol: V. natriegens was cultivated in modified M9 minimal media at 20C in a DasGip parallel bioreactor system

extract_protocol:
Total RNA was extracted using Lucigen MasterPureTM Complete DNA and RNA Purification Kit. Ribosomal RNA was removed using MICROBExpress.
Illumina-compatible cDNA libraries were constructed using the NEBNext Ultra Directional RNA Library Kit for Illumina.

treatment_protocol: Treatments included three different salinities: 0mM, 300 mM, and 540 mM NaCl, Samples were collected at three different time points.

value: 540 mM NaCl


title: 20 Month Male 05 (L3-P06)


title: KIiso1

value: isotype + NPC CSF


title: 20_540_T2_B


title: 20 Month Female 09 (L2-P09)

value: Female


title: KIiso2


title: 20 Month Female 05 (L2-P05)


title: 654T1

description: Transplant


title: 20 Month Male 02 (L3-P02)


title: 20 Month Female 06 (L2-P06)


title: 1000

description: in vivo

value: in vivo transformation


title: 20 Month Female 10 (L2-P10)

value: 20 month


title: 20 Month Male 01 (L3-P01)


title: 20_540_T1_B


title: 655T1

description: Transplant


title: 20 Month Female 08 (L2-P08)


title: KIuntr3

value: untreated


title: KIiso3


title: 20_300_T3_B

value: 300 mM NaCl


title: 20 Month Female 03 (L2-P03)


title: KIuntr2


title: 20 Month Female 07 (L2-P07)


title: 20 Month Female 04 (L2-P04)


title: KIm422


title: KIuntr1


title: 20_300_T2_B


title: 20_300_T1_B


title: 20 Month Female 01 (L2-P01)


title: WTm421

value: WT


title: liver tissue-CLP-GH010

first: George

last: Hasko

address: 630 West 168th Street

department: Anesthesiology

institute: Columbia University

data_processing:
Real-Time Analysis software (Illumina) was used for base calling.
bcl2fastq2 (version 2.19) was used for converting BCL to fastq format, coupled with adaptor trimming.
Pseudoalignment was performed to a kallisto index created from transcriptomes (Human: GRCh38; Mouse: GRCm38) using kallisto (0.44.0).
Testing for differentially expressed genes under various conditions was done using DESeq2 R package designed to test differential expression between two experimental groups from RNAseq counts data.
Signaling pathways were identified by Ingenuity Pathway Analysis (Qiagen IPA software).
Supplementary_files_format_and_content: DESeq2 and kallisto resutls files

source_name: Liver tissue

extract_protocol:
Frozen liver samples were submitted to Columbia Molecular Pathology/MPSR (HICCC) core where they were homogenized with Qiagen TissueLyser II, at 25/s oscillation frequency for 2 min. RNA was extracted with Qiagen miRNeasy mini kit following the instructions of the manufacturer, and RNA was eluted at a volume of 50 ul. RNA samples with RIN 8≥ were submitted to the JP Sulzberger Columbia Genome Center for RNAseq analysis.
Poly-A pull-down was used to enrich mRNAs from total RNA samples, followed by library construction using Illumina TruSeq chemistry. Libraries were sequenced using Illumina NovaSeq 6000. Samples were multiplexed in each lane, yielding a targeted number of paired end 100-bp reads for each sample.

value: CLP (cecal ligation and puncture) surgery

tag: disease state

value: CLP sepsis model

value: liver


title: WTm423


title: ESpCreA

description: EGFR

source_name: Mouse lung epithelial organoids

value: Sca1 positive alveolar

value: Cre

value: BASC alveolar

value: No

value: TruSeq std/HiSeq


title: ESpCreB

description: EGFR

value: Sca1 positive bronchiolar

value: BASC bronchiolar


title: 20_0_T2_B

value: 0 mM NaCl


title: ESpCre

description: EGFR

value: Sca1 positive

value: BASC mixed


title: 20 Month Female 02 (L2-P02)

value: 20 month

value: Female

value: Mouse dorsal hippocampus


title: liver tissue-sham-GH009

value: SHAM surgery

value: control


title: WTm422

value: WT

value: anti-CD22 + NPC CSF


title: 20_0_T1_B


title: 20_540_T3_A

value: 540 mM NaCl


title: WTiso3

value: isotype + NPC CSF


title: WTiso1


title: 20_540_T2_A


title: liver tissue-sham-GH008

value: liver


title: liver tissue-sham-GH007


title: 20_0_T3_B


title: 20_300_T3_A

value: 300 mM NaCl


title: MCF7-122_2

type: RNA

city: Ciudad de México

first: Isidro

middle: Xavier

last: Pérez-Añorve

state: Cuajimalpa

address: Vasco de Quiroga 487, Santa Fe

department: Posgrado en Ciencias Naturales e Ingeniería

country: Mexico

institute: Universidad AUtónoma Metropolitana Unidad Cuajimalpa

hyb_protocol: Samples were hybridized with Affymetrix GeneChip Human Gene 1.0 ST array (Affymetrix)

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix). GeneChips were scanned using The Genechip Scanner 3000 7G (Affymetrix , Santa Clara, USA).

data_processing:
Array signal intensitive were analyzed with the Affymetrix Expression Console using Signal Space Transformation-Robust Multichip Analysis (SST-RMA) for the background correction.
affymetrix-algorithm-name = rma-gene-default
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.4.1.46

label: biotin

label_protocol: WT Plus Reagents Kit was used to generate the biotinylated cRNA starting from 200ng of total RNA according to the manufacturer (Manual Target preparation for GeneChip Whole transcript (WT) expression arrays, Affymetrix).

growth_protocol: The MCF-7RR cell line was grown in DMEM Gibco® GlutaMAX™ supplemented with 10% fetal bovine serum and penicillin and streptomycin at 37°C in a 5% CO2 atmosphere

extract_protocol: Trizol method was used to extract the total RNA

treatment_protocol: MCF-7RR cell line was transfected at a concentration of 30nM of antagomiR-122. A scramble sequence at 30nM was used as a control and Lipofectamine 2000 was used as a transfection agent.

tag: cell line

value: breast cancer cells

tag: genotype/variation

tag: clone phenotype


title: 20_540_T1_A

tag: strain


title: WTiso2


title: liver tissue-CLP-GH012

value: CLP (cecal ligation and puncture) surgery

value: CLP sepsis model

tag: tissue


title: ESpGFP

description: Control

tag: treatment

value: GFP

value: No

value: TruSeq std/HiSeq


title: MCF7-RR_1

source_name: MCF-7 radioresistant

value: MCF-7 radioresistant


title: liver tissue-CLP-GH011


title: 2#M-LMSCs

city: suzhou

first: Zhiyuan

last: Zheng

address: 199,Ren ai Road

institute: Soochow University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using TopHat(version:2.0.9).
Strings (version: 1.3.0) were used to count the number of Fragments for each gene after TopHat alignment, and then normalized by TMM (trimmed mean of M values) method. Finally, the FPKM value of each gene was calculated.
Genome_build: mm10
Supplementary_files_format_and_content: Excel file include FPKM values for each Sample

source_name: lung MSCs

growth_protocol: LMSCs were cultured in DMEM medium supplemented with 10% FBS, 2 mM glutamine, 100 U/ml penicillin, and 100 g/ml streptomycin (all from Invitrogen).

extract_protocol:
Total RNA was extracted by customer following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: lung derived mesenchymal stromal cells

tag: passages

value: MMTV-PyMT


title: MCF7-RR_2


title: MCF7-122_1


title: Fsp1-Cre;Col1a1flox/flox mice

city: Houston

first: Yang

state: Texas

address: 1881 East Road

department: Cancer Biology

institute: UT-MD Anderson Cancer Center

data_processing:
Raw sequencing data from the Illumina platform were converted into Fastq files and aligned to the reference genome mm10 using the 10X Genomics Cell Ranger Pipeline
After the alignment, a matrix file containing the cell barcode identity and gene values was exported by the 10X Genomics Cell Ranger Pipeline
Matrix files for the samples were then processed and analyzed by Seurat R software 3.5.3
Genome_build: mm10
Supplementary_files_format_and_content: Processed data are in the CSV matrix format. Each group, either Fsp1-Cre;Col1a1flox/flox mouse bone marrow samples (n=2) or WT mouse bone marrow samples (n=2), has one combined matrix CSV file as processed data (Fsp1-Col1KO_combined_matrix.csv or WT_combined_matrix.csv)

source_name: Mouse bone marrow combined for single-cell RNA-seq

growth_protocol: Fsp1-Cre;Col1a1flox/flox mice and WT mice were housed under standard housing conditions.

extract_protocol:
Single-cell barcoding and library preparation were performed using the 10X Genomics’ Chromium controller and Single Cell 3’ Reagent Kits v2 according to the manufacturer’s instructions.
Following capture and lysis, cDNA was synthesized and amplified to construct Illumina sequencing libraries using the 10X Chromium v2 according to the manufacturer’s instructions.

treatment_protocol: All mice were housed under standard housing conditions at MDACC animal facilities, without any treatment.

value: bone marrow

tag: detailed genotype


title: ENpGFP

description: Control

value: NGFR positive

value: tracheal


title: 20_0_T3_A

value: 0 mM NaCl


title: WTuntr2

value: WT

value: untreated


title: 20_300_T1_A


title: ESnGFP

description: Control

value: Sca1 negative


title: 20_300_T2_A

value: 300 mM NaCl


title: WTuntr1


title: 1#M-LMSCs

tag: age


title: 2#L-LMSCs

value: 9-10 week


title: WT control mice

tag: genotype


title: 1#L-LMSCs

tag: cell type


title: ESnCre

description: EGFR

tag: sorting type

value: Cre


title: Pre-SR: mild radioresistant cells

city: Gyeongju

first: soyoung

last: Kim

address: Dongdae-ro 123

department: Department of Pharmacology

country: South Korea

institute: Dongguk university

description: Gene expression data from mild redioresistant SK-BR-3 breast cancer cells, which exposed to 5 cycle radiation

hyb_protocol: Following fragmentation, 5.5 ug of framented cDNA were hybridized for about 17 hr at 45℃ on Human Gene 2.0 ST array. The hybridized probe arrays were stained and washed with GeneChip® Hybridization, Wash and Stain Kit(900720, Thermo Fisher Scientific) using the Fluidics Station 450(Affymetrix).

scan_protocol: The stained GeneChips were scanned with a GeneChip® Scanner 3000+ 7G(Affymetrix) a 570 nm.

data_processing: The RMA algorithm was used for expression summary and signal calculation of Human Gene 2.0 ST array data. Sketch Quantile normalization was performed for the signal normalization.

source_name: human HER2-positive breast cancer cells irradiated with 40 Gy

label_protocol: The GeneChip® procedure for generation of the biotin-labeled single-stranded cDNA by in vitro transcription were performed according to the manufacturer's instructions from 200ng total RNA. Protocol performed using GeneChip™ WT PLUS Reagent Kit(902280, Thermo Fisher Scientific).

growth_protocol: Cell were cultured in Dulbecco Modified Eagle Medium (DMEM, Welgene) containing 10 % fetal bovine serum (Hyclone) and 1x Penicillin-Streptomycine solution (Welgene) using a 5% CO2 incubator at 37℃.

extract_protocol: Total RNA was extracted using easy-BLUE™ Total RNA Extraction kit (iNtRON Biotechnology Inc.) following to manufacturer’s instructions

treatment_protocol: Cells were exposed to 4 Gy twice a week and incubated for recovery from radiation-induced damage. Pre-SR and SR cells were exposed to 5 and 6 cycles of radiation, respectively.

tag: gender

value: Female

value: mammary gland, derived from metastatic site

tag: disease

value: pleural effusion

value: HER2-positive breast cancer


title: ENnCre

description: EGFR

value: NGFR negative

tag: tissue origin

tag: transplant

value: No

tag: seq platform

value: TruSeq std/HiSeq


title: ENpCre

description: EGFR


title: 46s

status: Public on Sep 17 2021

city: Balice near Krakow

first: Klaudia

last: Pawlina-Tyszko

address: Krakowska 1

department: Deaprtment of Animal Genomics and Molecular Biology

country: Poland

institute: National Research Institute of Animal Production

description: microRNA

data_processing:
demultiplexing: bcl2fastq
quality control: FastQC
trimming off the 3' adapter sequences: UEA sRNA WorkbenchV4.6
filtering: UEA sRNA WorkbenchV4.6; parameters: 17-25 nt in length, minimum abundance of at least 6 supporting reads, tRNA and rRNA sequences excluded.
mapping: the filtered reads were mapped to Sscrofa10.2 genome and miRBase 22.1, using miRCat tool embeded in UEA sRNA WorkbenchV4.6. The following parameters were applied - default animal parameters, except for: minimum abundance (6), minimum length (17 nt) and maximum length (25 nt).
differential expression analysis: DESeq2 (a Bioconductor R-project package)
Genome_build: Sscrofa10.2
Supplementary_files_format_and_content: FASTA files after filtering and adaptor trimming, generated with the use of UEA sRNA Workbench V4.6. They include the number of reads of detected sequences.

organism: Sus scrofa

source_name: porcine backfat

extract_protocol:
The quantity and quality of the obtained RNA were checked on a NanoDrop 2000 spectrophotometer (Thermo Scientific; Wilmington, USA) and on a TapeStation 2200 instrument (RNAScreen Tape, Agilent, Perlan Technologies, Poland).
microRNA libraries were prepared with the use of NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs; E7300L), according the standard protocol. Briefly, the first step was the 3’ adaptor ligation, followed by hybridization with the Reverse Transcription Primer and ligation with the 5’ adaptor. The RNA-adaptor ligation products were subjected to reverse transcription. Then, PCR amplification with 12 different indexed primers was performed to allow further multiplexing of the samples. The amplified samples were purified and size-selected on a Novex 6% TBE PAGE gel (Invitrogen). After the overnight elution from the gel, the libraries were precipitated and purified with ethanol (POCH). Next, they were subjected to a concentration measurement with a Qubit 2.0 Fluorometer (Thermo Fisher Scientific) and a size assessment with a 2200 TapeStation instrument (Agilent). The libraries were stored at -20°C at 10nM concentration until further use.

treatment_protocol: Immediately after slaughter, tissue samples were frozen in liquid nitrogen and stored at -80°C

tag: diet

value: cDDGS+beef tallow

value: backfat

tag: platform

value: HiScanSQ (Illumina)

value: male


title: 2#E-LMSCs

value: lung derived mesenchymal stromal cells

value: MMTV-PyMT

value: 6-7 week


title: 21s

description: microRNA

value: cDDGS+rapeseed oil

value: female


title: 22s

description: microRNA


title: 20_0_T1_A

value: 0 mM NaCl


title: 48s

description: microRNA


title: 45s

description: microRNA


title: 20_0_T2_A


title: 17s

description: microRNA


title: 20s

description: microRNA


title: 43s

description: microRNA


title: 41s

description: microRNA


title: 24s

description: microRNA


title: 1#E-LMSCs


title: 42s

description: microRNA


title: 7grIs

description: microRNA

value: no cDDGS+rapeseed oil


title: ENnGFP

description: Control

value: GFP

value: tracheal


title: 6s

description: microRNA


title: 8s

description: microRNA


title: 19s

description: microRNA


title: SK-BR-3: parental SK-BR-3 cells

description: Gene expression data from radiosensitive SK-BR-3 breast cancer cells

source_name: human HER2-positive breast cancer cells

value: Female

value: mammary gland, derived from metastatic site

value: pleural effusion

tag: cell line

value: HER2-positive breast cancer


title: SR: radioresistant cells

description: Gene expression data from radioresistant  SK-BR-3 breast cancer cells exibiting significant radioresistance, which exposed to 6 cycles radiation

source_name: human HER2-positive breast cancer cells irradiated with 48 Gy


title: 55s

description: microRNA

value: cDDGS+coconut oil


title: 52s

description: microRNA

value: backfat


title: 5s

description: microRNA

value: HiScanSQ (Illumina)


title: 53s

description: microRNA


title: 2s

description: microRNA

value: male


title: CTRL #01

city: Milan

first: Chiara

last: Balestrieri

address: Via Olgettina 58

department: Center for Omics Sciences

country: Italy

institute: IRCCS San Raffaele Scientific Institute

description:
genes.counts.txt
genes.edgeR_results.txt

data_processing:
Reads were quality filtered according to the Illumina pipeline, then were aligned to mouse genome build GRCm38/mm10 using using START version 2.6.0c. Only uniquely mapped reads were retained.
Gene expression counts were estimated using featureCounts  v0.6.1 (Rsubread version 1.6.1) , summarized across all exons , with option “largestOverlap”.
Differentially expressed genes were identified using EdgeR R-package v3.2.2.
Genome_build: GRCm38/mm10

source_name: Pancreatic spheroids

growth_protocol:
DMEM/F12 1:1 supplemented with 2.5 mM L-Glutamine, 15 mM HEPES Buffer (HyClone), 5 mg/ml D-glucose (Sigma Aldrich), 1.22 mg/ml nicotinamide (Sigma Aldrich), 5 nM 3,3,5-Tri-iodo-L-thyronine (Sigma Aldrich), 0.5 μM hydrocortisone Solution (Sigma Aldrich), 100 ng/ml cholera toxin (Sigma Aldrich), 0.5 % insulin-transferrin-selenium (Corning), 100 μg/ml penicillin/streptomycin (Gibco), 0.1 mg/ml soybean trypsin inhibitor (Sigma Aldrich), 20 ng/ml EGF (Peprotech), 25 μg/ml bovine pituitary extract (Invitrogen), and 5% Nu Serum IV Culture Supplement (BD)
See additional columns of the SAMPLES section

extract_protocol: Illumina Truseq. The poly-A containing mRNA molecules were purified using poly-T oligo-attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then go through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products are then purified and enriched with PCR to create the final cDNA library.

value: Pancreatic epithelial cells

value: Untreated


title: CTRL #03

treatment_protocol: See additional columns of the SAMPLES section


title: 1s

description: microRNA


title: H3K27Ac.CTRL

description: Chromatin IP against H3K27ac

data_processing:
Reads were pre-processing (filtering, quality trimming and adapter clipping) using Trimmomatic (version 0.38),  then reads were aligned to mouse genome build GRCm38/mm10 using Bowtie2 v2.2.6 with “–very-sensitive” preset of parameters. Reads that did not align to nuclear genome or aligned to mitocondrial genome were removed. PCR duplicates were removed using samtools.
Peak calling was performed using MACS 1.4 with the “--nomodel” and “--shiftsize 125” flags and arguments. Each IP was compared to input DNA.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: *.bed, list of the peaks called by MACS 1.4

extract_protocol: ChIP lysates were generated from 50x10^6 cells. Cells were fixed in 1% formaldehyde for 10min. Lysate was immunoprecipitated with 10ug of antibody. Antibodies were pre-bound overnight to 100ul of G protein-coupled paramagnetic beads in PBS/BSA 0.5%. Beads were then added to lysates (the preclearing step was omitted) and incubation was let to proceed overnight. Beads were washed 6 times in a modified RIPA buffer (50mM Hepes pH 7.6, 500mM LiCl, 1mM EDTA, 1% NP-40, 0.7% Na-deoxycholate) and once in TE containing 50mM NaCl. DNA was eluted in TE containing 2% SDS and crosslinks reversed by incubation overnight at 65ºC. DNA was then purified by AMPure XP SPRI (Beckman Coulter) and quantified using Quantifluor (Promega). ChIP DNA was prepared for HiSeq2000 Illumina sequencing using a standard protocol consisting in blunting, addition of dA overhangs, ligation of Illumina adapters, PCR with index primers and purification. A mixture of T4 DNA polymerase, DNA polymerase I and T4 kinase was used according to manufacturer’s instruction. Library preparation is carried out on SPRIworks Fragment Library System.

tag: growth protocol

value: DMEM/F12 1:1 supplemented with 2.5 mM L-Glutamine, 15 mM HEPES Buffer (HyClone), 5 mg/ml D-glucose (Sigma Aldrich), 1.22 mg/ml nicotinamide (Sigma Aldrich), 5 nM 3,3,5-Tri-iodo-L-thyronine (Sigma Aldrich), 0.5 μM hydrocortisone Solution (Sigma Aldrich), 100 ng/ml cholera toxin (Sigma Aldrich), 0.5 % insulin-transferrin-selenium (Corning), 100 μg/ml penicillin/streptomycin (Gibco), 0.1 mg/ml soybean trypsin inhibitor (Sigma Aldrich), 20 ng/ml EGF (Peprotech), 25 μg/ml bovine pituitary extract (Invitrogen), and 5% Nu Serum IV Culture Supplement (BD)

tag: antibody

value: Anti H3K27ac (Abcam, ab4729)


title: 3s

description: microRNA

tag: tissue

value: female


title: 54s

description: microRNA


title: H3K27Ac.PostCAE

description: Chromatin IP against H3K27ac

tag: treatment

value: Post caerulein-treated


title: PostCAE #01


title: 49s

description: microRNA


title: PostCAE #02


title: PostCAE #03


title: CTRL #02


title: PostCAE #04


title: input

description: Input


title: iKPC-3 ED U off dox

city: Newark

first: Pingping

last: Hou

state: New Jersey

address: 205 South Orange Ave

department: Microbiology, Biochemistry and Molecular Genetics

institute: Rutgers University

data_processing:
BCL (raw output of Illumina HigSeq) files are processed using Illumina’s Consensus Assessment of sequence And Variation (CASAVA) tool (http://support.illumina.com/sequencing/sequencing_software/casava.html) for demultiplexing/conversion to FASTQ format, which is the standard input for most aligners and downstream analytic tools.
FASTQ files of RNA samples are processed using both STAR (Dobin et. al. 2012) following the two-step alignment procedure and TopHat (Kim and Salzberg 2011) and Cufflinks (Trapnell et. al. 2010).
Additional RNA quantification is conducted using HTSeq (Anders et. al. 2014) analyses.
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: pancreatic cancer cells

growth_protocol: 10% FBS + RPMI media

extract_protocol:
Cells cultured in Matrigel were collected by using cell revovery solution (Corning, cat # 354253). RNA were extracted by Qiagen Rneasy Micro kit (cat # 74004) according to provided manufacturer’s protocols.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Doxycycline treatment at 1 ug/ml (Sigma) to activate KRAS* expression.

tag: strain

value: pancreatic ductal adenocarcinoma

value: Cre+ Tp53L/+ rtTA L/+ tetO-KRAS(G12D)+

tag: overexpressing

value: enzyme-dead USP21

value: off dox


title: iKPC-1 ED U off dox

tag: genotype