title: Adult Brain, CUT Tag ey-GFP GFP Ab pit stop high salt

data_processing:
Library strategy: CUT&Tag
The 10X samples were each processed (alignment, barcode assignment and UMI counting) with Cell Ranger ATAC (version 1.2.0) count pipeline.
For the ATAC samples the raw reads were first filtered and scanned for adapters using fastq‐mcf from the ea‐utils package. Read quality was then checked using FastQC. The reads were mapped to the Drosophila genome (dm6) using STAR. The outputted BAM file from STAR was then indexedand sorted using SAMtools. Using genomeCoverageBed from BedTools, the BAM file was converted to a BedGraph file. For fast, visualization in the IGV GenomeBrowser, the BedGraph file was further processed to a BigWig file using bedGraphtoBigWig.
Cut&Tag samples were processed similarly to ATAC-seq samples
TaDa sequencing data were mapped back to release 6.03 of the Drosophila genome using a previously described pipelines ( Marshall and Brand, 2015). Peaks were called and mapped to genes using a custom Perl program (available at https://github.com/tonysouthall/Peak_calling_DamID)
Genome_build: dm6 (dmel_r6.16_FB2017_03)
Supplementary_files_format_and_content: gff, narrowPeak, bigWig

extract_protocol:
D. melanogaster adult brains were dissected and transferred to a tube containing 100 µl ice cold DPBS solution. After centrifugation at 800 g for 5 min, the supernatant was replaced by 500 µl nuclei lysis buffer composed of 10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.1% Nonidet P40, 0.01% Digitonin, and 1% BSA, in Nuclease-free water. The following procedure was followed to extract the nuclei from the brain tissue: incubation in nuclei lysis buffer on ice for 5 min, transfer to a dounce tissue grinder tube (Merck), 25 strokes with pestle A, incubation on ice for 10 min, 25 strokes with pestle B. The lysis was stopped by adding 1 ml of wash buffer composed of 10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20 and 1% BSA, in Nuclease-free water. Nuclei were pelleted by centrifugation at 800 g for 5 min at 4°C and resuspended in 1x Nuclei Buffer (10x Genomics). Nuclei suspensions were passed through a 40 µM Flowmi filter (VWR Bel-Art SP Scienceware). Nuclei concentration was assessed by the LUNA-FL Dual Fluorescence Cell Counter. After centrifugation, supernatant was removed and isolated nuclei were resuspended in nuclear extraction (NE) buffer (EpiCypher CUT&Tag Protocol v1.5). Nuclei concentration was assessed by the LUNA-FL Dual Fluorescence Cell Counter. 100,000 nuclei in 100 µl NE buffer were used for each CUT&Tag reaction. All subsequent steps were followed according to the EpiCypher CUT&Tag Protocol v1.5. For each reaction, 11 µl of BioMag Plus Concanavalin A beads (ConA beads, Gentaur, Cat 86057-3) were washed twice with 100 µl cold Bead Activation buffer and then resuspended in 11 µl of cold Bead Activation buffer. To bind nuclei to the activated ConA beads, 100 µl of nuclei and 10 µl of activated ConA beads were incubated for 10 min at room temperature. After supernatant removal, nuclei-bead slurry was resuspended in 50 µl Antibody150 buffer. 0.5 µg of primary rabbit anti-GFP antibody (Abcam, Cat ab290) was added per sample and incubated overnight at 4°C. Beads were cleared and resuspended in 50 µl cold Digitonin150 buffer. 0.5 µg of anti-rabbit secondary antibody (EpiCypher, Cat 13-0047) was added per sample and incubated for 30 min at room temperature. While on a magnet, beads were washed twice with 200 µl cold Digitonin150 buffer. Beads were resuspended in cold Digitonin300 buffer and incubated for 1 hour at room temperature with 2.5 µl CUTANA pAG-Tn5 (EpiCypher, Cat 15-1017). To initiate tagmentation reaction, beads were resuspended in 50 µl cold Tagmentation buffer and incubated for 1 hour at 37°C. Beads were resuspended in 50 µl TAPS buffer and 5 µl SDS Release buffer was added to quench the tagmentation reaction. To release tagmented chromatin fragments into solution, samples were incubated for 1 hour at 58°C. 15 µl SDS quench buffer was added per sample. To amplify tagmented chromatin fragments, 2 µl each of individual barcoded P5 and P7 sequencing adapters (10 µM stock) and 25 µl non-hot start CUTANA High Fidelity 2x PCR Master Mix (EpiCypher, Cat 15-1018) were added and 18 cycles of CUT&Tag-specific PCR parameters were used (58°C for 5 min, 72°C for 5 min, 98°C for 45 sec, 98°C for 15 sec, 60°C for 10 sec, 72°C for 1 min). DNA cleanup was performed with 1.3 AMPure XP beads (Analis, Cat A63880) and DNA was eluted in 15 µl 0.1 TE buffer. The CUT&Tag libraries were analyzed on a Bioanalyzer (Agilent High Sensitivity DNA Chip, Cat 5067-4626) and sequenced on an Illumina NextSeq2000 instrument.
CUT&Tag

value: 3 day


title: Adult Brain, TADA_UAS-Dam_x_R16A06 sample1

status: Public on Aug 10 2021

type: SRA

city: LEUVEN

first: Stein

last: Aerts

address: Herestraat 49, bus 602

department: Center for Brain & Disease Research

country: Belgium

institute: KULeuven/VIB

description: final_peak_file_for_UAS-Dam-Mef2_x_R16A06-Gal4_2rep_FDR_0.01_with_peak_height_and_highest_associated_FDR.gff

library_source: genomic

data_processing:
Library strategy: DamID-seq
The 10X samples were each processed (alignment, barcode assignment and UMI counting) with Cell Ranger ATAC (version 1.2.0) count pipeline.
For the ATAC samples the raw reads were first filtered and scanned for adapters using fastq‐mcf from the ea‐utils package. Read quality was then checked using FastQC. The reads were mapped to the Drosophila genome (dm6) using STAR. The outputted BAM file from STAR was then indexedand sorted using SAMtools. Using genomeCoverageBed from BedTools, the BAM file was converted to a BedGraph file. For fast, visualization in the IGV GenomeBrowser, the BedGraph file was further processed to a BigWig file using bedGraphtoBigWig.
Cut&Tag samples were processed similarly to ATAC-seq samples
TaDa sequencing data were mapped back to release 6.03 of the Drosophila genome using a previously described pipelines ( Marshall and Brand, 2015). Peaks were called and mapped to genes using a custom Perl program (available at https://github.com/tonysouthall/Peak_calling_DamID)
Genome_build: dm6 (dmel_r6.16_FB2017_03)
Supplementary_files_format_and_content: gff, narrowPeak, bigWig

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: Adult Brain

extract_protocol:
Flies were allowed to lay eggs for 2 days at 18˚C in fly food vials. Vials containing those eggs were kept at 18˚C (restrictive temperature) until adult flies eclosed. They were then kept at 18˚C for 3-7 days before being transferred to 29˚C (permissive temperature) for 24 hours. For the Dam-Mef2 experiments in R16A06, a minimum of 90 brains were dissected per replicate, for the Dam-Mef2 experiments in R74G01 cells, 40 brains were dissected, and for the Dam-acj6 in atonal cells, a minimum of 30 brains. 2 biological replicates were performed for each experiment. The DamID protocol is based on (Marshall et al., 2016) with the following changes: After the overnight DpnI digestion , 0.5 µl of DpnI was added for an extra 1 hour incubation and MyTaq™ HS DNA Polymerase was used for the PCR amplification (instead of Advantage 2 cDNA Polymerase).
Targeted DamID

tag: tissue

value: Brain

tag: developmental stage

value: Adult

tag: age

value: 4-8 day

tag: genotype


title: ΔH3.3B; ΔH3.3A round 2 sample5

city: Umeå

first: Henrik

last: Lindehell

address: Umeå universitet

department: Department of Molecular Biology

country: Sweden

institute: Umeå University

library_source: transcriptomic

data_processing:
Adaptor sequence was trimmed from the sequenced reads, and masked for low-complexity or low-quality sequence, then mapped to BDGP6 whole genome using Star v2.5.3 (DOBIN et al. 2013) with default settings.
Read counts were obtained with featureCounts v1.5.1 with default settings
Genome_build: BDGP6
Supplementary_files_format_and_content: Raw count table in tab delimited .txt format

molecule: total RNA

source_name: Male 3rd Instar larvae brain

extract_protocol:
For each sample, five male third instar larvae brains were homogenized and RNA was purified using the Directzol microprep kit (Zymo research) and the standard protocol with on column DNase treatment was used.
Total-RNA libraries were synthesised using the Ovation RNA-Seq system for Drosophila (NuGEN). Standard protocol procedure with integrated DNase treatment was used to make the sequencing libraries. Fragmentation was performed using a Covaris E220 Focused-ultrasonicator with the recommended settings for 200 base pair target length.

value: 3rd instar larvae

value: brain

tag: Sex

value: male

value: delta-H3.3B; delta-H3.3A


title: primary skeletal myotubes, bOHB treatment, replicate 3

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

data_processing:
Sequencing reads that contained adapters and/or had low quality, aligned to rRNA were filtered off before mapping.
The tool Salmon (version 1.2.1) was used to map the cleaned reads to the GRCm38.p6 mouse genome assembly-based transcriptome sequences as annotated by the GENCODE consortium (release M25). Salmon parameters used: -i ./salmon_index_M25  --libType A --seqBias --numBiasSamples 10000000 --gcBias --biasSpeedSamp 5 --validateMappings --numGibbsSamples 100
The Salmon-obtained transcript abundance estimates and lengths were imported in R using the package tximport (version 1.16.1) to estimate gene level counts.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample (gene level counts were calculated from the Salmon-obtained transcript abundance estimates; TxImport.GeneLevel.counts.GEO.txt)
Supplementary_files_format_and_content: R-object (txi.counts.annotated.GEO.Rdata; exported tximport object) containing gene level counts estimated from the Salmon-obtained transcript abundance estimates. Note: count data was not transformed nor scaled (i.e. countsFromAbundance = "no"), and can be used for subsequent analysis in edgeR or DESeq2.
Supplementary_files_format_and_content: R object (txi.lengthScaledTPM.annotated.GEO.Rdata; exported tximport object) containing scaled gene level counts estimated from the Salmon-obtained transcript abundance estimates. Note: count data was scaled using library size and transcript gene length (i.e. countsFromAbundance = "lengthScaledTPM"), and these scaled counts can be used for subsequent analysis in limma (voom function).

organism: Mus musculus

source_name: primary mouse skeletal myotubes, treated with β-hydroxybutyric acid (bOHB; 5mM) for 6 hrs

growth_protocol: Primary mouse adipocytes (isolation and differentiation of stromal vascular fraction): Inguinal white adipose tissue from 3-4 C57Bl/6 male mice was collected and placed in Dulbecco’s modified eagle’s medium (DMEM; Lonza) supplemented with 1% Penicillin/Streptomycin (PS) and 1% bovine serum albumin (BSA; Sigma-Aldrich). Material was minced finely with scissors and digested in collagenase-containing medium (DMEM with 3.2 mM CaCl2, 1.5 mg/ml collagenase type II (C6885, Sigma-Aldrich), 10% FBS, 0.5% BSA, and 15 mM HEPES) for 1 h at 37°C, with occasional vortexing. Cells were filtered through a 100-μm cell strainer (Falcon). Subsequently, the cell suspension was centrifuged at 1600 rpm for 10 min and the pellet was resuspended in erythrocyte lysis buffer (155 mM NH4Cl, 12 mM NaHCO3, 0.1 mM EDTA). Upon incubation for 2 min at room temperature, cells were centrifuged at 1200 rpm for 5 min and the pelleted cells were resuspended in DMEM containing 10% fetal bovine serum (FBS) and 1% PS (DMEM/FBS/PS) and plated. Upon confluence, the cells were differentiated according to the protocol as described previously [PMID: 22569073 and 23150577]. Briefly, confluent SVFs were plated in 1:1 surface ratio, and differentiation was induced 2 days afterwards by switching to a differentiation induction cocktail (DMEM/FBS/PS, 0.5 mM isobutylmethylxanthine, 1 μM dexamethasone, 7 μg/ml insulin and 1 µM rosiglitazone) for 3 days. Subsequently, cells were maintained in DMEM/FBS/PS, and 7 μg/ml insulin for 3-6 days and switched to DMEM/FBS/PS for 3 days. Average rate of differentiation was at least 80% as determined by eye. Primary mouse macrophages (isolation and differentiation of bone marrow derived monocytes): Bone marrow cells were isolated from femurs of C57Bl/6 male mice following standard protocol and differentiated into macrophages (bone marrow-derived macrophages, BMDMs) in 6-8 days in DMEM/FBS/PS supplemented with 20% L929-conditioned medium (L929). After 6-8 days, non-adherent cells were removed, and adherent cells were washed and plated in 12-well plates in DMEM/FBS/PS + 10% L929. After 24 hours, medium was switched to 2% L929 in DMEM/FBS/PS overnight. Cells were treated the following day. Primary skeletal myotubes (isolation and differentiation of skeletal myocytes): Myoblasts from hindlimb muscle of WT-C57Bl/6 male mice were isolated as previously described [PMID: 29879622]. In brief, the muscles were excised, washed in 1× PBS, minced thoroughly, and digested using 1.5 mL collagenase digestion buffer (500 U/ml or 4 mg/mL collagenase type II (C6885, Sigma-Aldrich), 1.5 U/ml or 5 mg/mL Dispase II (D4693, Sigma-Aldrich), and 2.5 mM CaCl2 in 1× PBS) at 37°C water bath for 1 h in a 50 ml tube, agitating the tube every 5 min. After digestion, the cell suspension containing small pieces of muscle tissue was diluted in proliferation medium (PM: Ham's F-10 Nutrient Mix (#31550023, Thermo Fisher Scientific) supplemented with 20% fetal calf serum, 10% HS, 0.5% sterile filtered chicken embryo extract (#092850145, MP Biomedicals), 2.5 ng/ml basic fibroblast growth factor (#PHG0367, Thermo Fisher Scientific), 1% gentamycin, and 1% PS), and the suspension was seeded onto matrigel-coated (0.9 mg/ml, #354234, Corning) T150 flasks at 20% surface coverage. Cells were grown in 5% CO2 incubator at 37°C. Confluence was reached latest after 5 d in culture, upon which cells were trypsinized (0.25% trypsin), filtered with 70 µm filters, centrifuged at 300 g for 5 min, and then seeded on an uncoated T150 flask for 45 min to get rid of fibroblasts. Subsequently, myoblasts were seeded in PM at 150.000 cells/mL onto matrigel-coated 12-well plates cells. Upon reaching confluence, differentiation was induced by switching to differentiation medium (DM: Ham's F-10 Nutrient Mix supplemented with 5% horse serum (HS) and 1% PS). DM was replaced every other day. Myotubes fully differentiated by Day 5 of differentiation in DM. The medium was renewed every other day. Primary mouse hepatocytes (isolation and culturing of hepatocytes): Primary hepatocytes were isolated from C57BL/6NHsd male mice via collagenase perfusion. Cells were plated onto collagen (0.9 mg/ml) coated 24-well plates at 200,000 cells/well in Williams E medium (PAN Biotech), substituted with 10% FBS, 100 nM dexamethasone and penicillin/streptomycin and maintained at 37 °C in an atmosphere with 5% CO2. After four hours of attachment, cells were washed with phosphate buffer saline (PBS) and allowed to rest in dexamethasone-free medium overnight before treatment.

extract_protocol:
Total RNA from all cell culture samples was extracted using TRIzol reagent (Thermo Fisher Scientific) and purified using the Qiagen RNeasy Mini kit (Qiagen) according to manufacturer’s instructions. RNA concentration was measured with a Nanodrop 1000 spectrometer and RNA integrity was determined using an Agilent 2100 Bioanalyzer with RNA 6000 microchips (Agilent Technologies).
Library construction and RNA sequencing on BGISEQ-500 were conducted at Beijing Genomics Institute (BGI) for pair-end 150bp runs. At BGI, Genomic DNA was removed with two digestions using Amplification grade DNAse I (Invitrogen). The RNA was sheared and reverse transcribed using random primers to obtain cDNA, which was used for library construction. The library quality was determined by using Bioanalyzer 2100 (Agilent Technologies). Then, the library was used for sequencing with the sequencing platform BGISEQ-500 (BGI).

treatment_protocol: Primary cells were treated for 6h with 5 mM βOHB or Butyrate, with PBS as control. Adipocytes and Macrophages were treated in DMEM/FCS/PS. Myotubes were treated in DM. Hepatocytes were treated in Williams E medium. Cells were washed with PBS once and stored in -80 °C until RNA was isolated.

tag: strain

tag: cell type

value: primary skeletal myotubes

tag: treatment

value: 5 mM bOHB [(R)-(–)-3-Hydroxybutyric acid sodium salt]

tag: exposure time

value: 6 hrs


title: ΔH3.3B; ΔH3.3A round 2 sample3


title: Adult Brain, CUT TAG Dros Ey IgG Ab

description: CUT&TAG control


title: primary skeletal myotubes, butyric acid treatment, replicate 1

source_name: primary mouse skeletal myotubes, treated with butyric acid (bOHB; 5mM) for 6 hrs

value: 5 mM NaB [butyric acid sodium salt]


title: ΔH3.3B; ΔH3.3A round 2 sample1


title: Adult Brain, CUT Tag ey-GFP GFP Ab high salt


title: Adult Brain, TADA_UAS-Mef2-Dam_x_R16A06 sample2


title: Oregon-R round2 sample5

value: wildtype


title: primary skeletal myotubes, control treatment, replicate 3

source_name: primary mouse skeletal myotubes, treated with vehicle (PBS) for 6 hrs

value: control (PBS)


title: Oregon-R round2 sample6


title: Oregon-R round2 sample4


title: ΔH3.3B; ΔH3.3A round 2 sample2


title: Adult Brain, CUT TAG Dros Ey GFP Ab


title: primary skeletal myotubes, bOHB treatment, replicate 1


title: ΔHisC; 12xH3K36K  round1 sample 4

value: delta-HisC; 12xH3K36K


title: primary hepatocytes, control treatment, replicate 1

source_name: primary mouse hepatocytes, treated with vehicle (PBS) for 6 hrs

value: primary hepatocytes


title: Oregon-R round2 sample2


title: Oregon-R round2 sample1


title: primary skeletal myotubes, control treatment, replicate 2


title: Oregon-R round2 sample3


title: Adult Brain, CUT TAG Dros Ey H3K4Me3 Ab

description: CUT&TAG control


title: Adult Brain, CUT Tag ey-GFP GFP Ab pit stop high Tn5


title: primary skeletal myotubes, control treatment, replicate 1


title: ΔHisC; 12xH3K36R  round1 sample 4

value: delta-HisC; 12xH3K36R


title: ΔHisC; 12xH3K36K  round1 sample 3


title: ΔHisC; 12xH3K36R  round1 sample 5


title: ΔHisC; 12xH3K36K  round1 sample 1


title: primary macrophages, butyric acid treatment, replicate 3

source_name: primary mouse macrophages, treated with butyric acid (bOHB; 5mM) for 6 hrs

value: primary macrophages


title: ΔHisC; 12xH3K36R  round1 sample 3


title: Adult Brain, CUT Tag ey-GFP GFP Ab high Tn5

value: Brain

value: 3 day


title: ΔHisC; 12xH3K36R  round1 sample 2


title: primary macrophages, butyric acid treatment, replicate 2


title: Adult Brain, CUT TAG Dros Repo IgG Ab

description: CUT&TAG control

value: Adult


title: ΔHisC; 12xH3K36R  round1 sample 1

value: 3rd instar larvae


title: Ash1NSD round1 sample3

value: brain

value: ash122 NSDds46/ash19011 NSD ds46


title: ΔHisC; 12xH3K36K  round1 sample 2

value: male


title: Ash1NSD round1 sample5


title: Ash1NSD round1 sample2


title: primary macrophages, butyric acid treatment, replicate 1


title: primary macrophages, bOHB treatment, replicate 3

source_name: primary mouse macrophages, treated with β-hydroxybutyric acid (bOHB; 5mM) for 6 hrs


title: Ash1NSD round1 sample4


title: Adult Brain, CUT TAG Dros Repo GFP Ab


title: primary macrophages, bOHB treatment, replicate 2


title: Ash1 round1 sample5


title: Adult Brain, OmniATAC ato TfAP2 RNAi

data_processing:
The 10X samples were each processed (alignment, barcode assignment and UMI counting) with Cell Ranger ATAC (version 1.2.0) count pipeline.
For the ATAC samples the raw reads were first filtered and scanned for adapters using fastq‐mcf from the ea‐utils package. Read quality was then checked using FastQC. The reads were mapped to the Drosophila genome (dm6) using STAR. The outputted BAM file from STAR was then indexedand sorted using SAMtools. Using genomeCoverageBed from BedTools, the BAM file was converted to a BedGraph file. For fast, visualization in the IGV GenomeBrowser, the BedGraph file was further processed to a BigWig file using bedGraphtoBigWig.
Cut&Tag samples were processed similarly to ATAC-seq samples
TaDa sequencing data were mapped back to release 6.03 of the Drosophila genome using a previously described pipelines ( Marshall and Brand, 2015). Peaks were called and mapped to genes using a custom Perl program (available at https://github.com/tonysouthall/Peak_calling_DamID)
Genome_build: dm6 (dmel_r6.16_FB2017_03)
Supplementary_files_format_and_content: gff, narrowPeak, bigWig

extract_protocol:
100 GFP-expressing and 15 GFP negative fly brains were dissected in PBS on ice. The brains were then centrifuged at 800 xg for 5 min, after which the supernatant was replaced by 50 μL of dispase (3 mg/mL, Sigma-Aldrich_D4818-2mg), 75 μl collagenase I (100 mg/mL, Invitrogen_17100-017), and 125 μL trypsin-EDTA (0.05%, Invitrogen_25300054). Brains were dissociated at 25°C in a Thermoshaker (Grant Bio PCMT) for 15 min at 25°C at 1,000 rpm and the solution was mixed by pipette every 5 min. After, cell suspensions were passed through a 10 μM pluriStrainer (ImTec Diagnostics_435001050) and viability was assessed by the LUNA-FL Dual Fluorescence Cell Counter. Next, 4 aliquots were made containing GFP-brains cells with/without PI (10%) and GFP-positive brains with/without PI (10%). The GFP-negative brains were used to set the gates on the machine for cell size and viability (PI), the GFP-positive brains for the GFP fluorescence, after which the GFP positive cells with PI were sorted. Between 2.6 and 11k GFP positive cells were sorted and 50k cells per negative control. After sorting, regular omni-ATAC-seq was performed as described by Corces et al. (Corces et al., 2017).
omniATAC-seq

value: UAS-CD4tdGFP/CyO; ato-Gal4, UAS-Dcr2/TM2 x P{KK109052}VIE-260B


title: primary macrophages, bOHB treatment, replicate 1

value: 5 mM bOHB [(R)-(–)-3-Hydroxybutyric acid sodium salt]


title: Ash1 round1 sample3


title: Ash1 round1 sample4


title: primary macrophages, control treatment, replicate 3

source_name: primary mouse macrophages, treated with vehicle (PBS) for 6 hrs

value: 6 hrs


title: Adult Brain, OmniATAC ato Acj6 RNAi

value: UAS-CD4tdGFP/CyO; ato-Gal4, UAS-Dcr2/TM2 x y[1] v[1]; P{y[+t7.7] v[+t1.8]=TRiP.JF02497}attP2


title: Ash1 round1 sample1


title: Ash1 round1 sample2


title: Adult Brain, OmniATAC ato sample 2


title: primary macrophages, control treatment, replicate 2


title: Adult Brain, CUT TAG Dros Repo H3K4Me3 Ab

description: CUT&TAG control


title: NSD round1 sample4


title: NSD round1 sample5


title: Adult Brain, OmniATAC ato sample 1


title: Adult Brain, OmniATAC R16A06 Mef2 RNAi


title: primary macrophages, control treatment, replicate 1


title: Set2 round1 sample3


title: primary adipocytes, butyric acid treatment, replicate 2

source_name: primary mouse adipocytes, treated with butyric acid (bOHB; 5mM) for 6 hrs

value: primary adipocytes

value: 5 mM NaB [butyric acid sodium salt]


title: Set2 round1 sample2


title: Set2 round1 sample4


title: NSD round1 sample1


title: Oregon-R round1 sample4

value: wildtype


title: Ash1NSD round1 sample1


title: Oregon-R round1 sample2


title: WT_Wound_FA_1

city: Chicago

first: Irina

last: Budunova

state: IL

address: 303 E. Chicago Ave, WARD 9-015

department: Dermatology

country: USA

institute: Northwestern University

data_processing:
The processing was performed by LC Sciences (https://www.lcsciences.com). Firstly, Cutadapt (version 1.10) and perl scripts (in house) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases.
Then sequence quality was verified using FastQC (version 0.10.1, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
HISAT (version 2.0) was used to map reads to the genome of ftp://ftp.ensembl.org/pub/release-96/fasta/homo_sapiens/dna/.
The mapped reads of each sample (150 nucleotides, double-end readings) were assembled using StringTie (version 1.3). Then, all transcriptomes were merged to reconstruct a comprehensive transcriptome using perl scripts and gffcompare.
After the ﬁnal transcriptome was generated, StringTie and edgeR (version 2016.09.29) was used to estimate the expression levels of all transcripts.
Genome_build: ftp://ftp.ensembl.org/pub/release-96/fasta/homo_sapiens/dna/
Supplementary_files_format_and_content: tab-delimited text files include FPKM and Total Count

organism: Homo sapiens

source_name: HaCaT cells

growth_protocol: HaCat cells were grown to confluency/near confluency in DMEM medium supplemented with 10% FBS.

extract_protocol:
total RNA was isolated using Rneasy miRNA kit
The library was constructed by LC Sciences (https://www.lcsciences.com). Poly(A) RNA sequencing library was prepared following Illumina’s TruSeq-stranded-mRNA sample preparation protocol. RNA integrity was checked with Agilent Technologies 2100 Bioanalyzer. Poly(A) tail-containing mRNAs were purified using oligo-(dT) magnetic beads with two rounds of purification. After purification, poly(A) RNA was fragmented using divalent cation buffer in elevated temperature. Quality control analysis and quantification of the sequencing library were performed using Agilent Technologies 2100 Bioanalyzer High Sensitivity DNA Chip. Paired-ended sequencing was performed on Illumina’s NovaSeq 6000 sequencing system.

treatment_protocol: The grown cells were treated with either vehicle (WT or KO), 1uM glucocorticoid floocinolone acetonide (FA) (WT_FA or KO_FA), or wounded by scratching (WT_Wound or KO_Wound), or wounded and treated with FA (WT_Wound_FA or KO_Wound_FA), with all conditions incubated for 24 h before harvesting.

value: WT (Cas9 only)

value: wounded & treated with FA

tag: sample type


title: NSD round1 sample3


title: primary adipocytes, bOHB treatment, replicate 2

source_name: primary mouse adipocytes, treated with β-hydroxybutyric acid (bOHB; 5mM) for 6 hrs


title: primary adipocytes, butyric acid treatment, replicate 3


title: Oregon-R round1 sample1


title: primary adipocytes, bOHB treatment, replicate 1


title: AL80 - Hmr_Flag_deltaC_induced

city: Munich

first: Tamas

last: Schauer

address: Feodor-Lynen-Straße 21

department: Institute of Epigenetics and Stem Cells

country: Germany

institute: Helmholtz Zentrum München

data_processing:
Sequencing reads (50 bp, single end) were mapped to the Drosophila genome (version dm6) using bowtie2 (version 2.2.9) and filtered by mapping quality (-q 2) using samtools (version 1.3.1). Sequencing depth and input normalized coverages were generated by Homer (version 4.9). Enriched peaks were identified by Homer with the parameters -i input.dir -style factor -F 2 -size 200 for each replicate.
Genome_build: dm6
Supplementary_files_format_and_content: Peak list in bed format and input normalized tracks in bedgraph format

source_name: SL2 cells

growth_protocol: Drosophila SL2 cells stably transfected with FLAG-HA-HMR under a CuSO4 inducible promoter (pMT) were grown at 26˚C in Schneider Drosophila medium (Invitrogen) supplemented with 10% fetal calf serum and antibiotics (100 units/mL penicillin and 100 μg/mL streptomycin). Transfected cells were selected with 20 ug/mL Hygromycin B. Cells were grown to confluence in 550 mL flasks and induced for 20-24h with 250 uM CuSO4 before harvesting for chromatin immunoprecipitation.

extract_protocol:
Chromatin immunoprecipitation was essentially performed as in Gerland et al., PlosOne 2017. For each ChIP reaction, chromatin isolated from 1–2 x 10^6 cells was incubated either with 5 ug of mouse anti-FLAG (F1804, SIGMA-ALDRICH - RRID: AB262044) pre-coupled directly to Protein A/G Sepharose or with rat anti-HMR 2C10 (RRID: AB2569849) antibody pre-coupled to Protein A/G Sepharose through a rabbit IgG anti-rat.
Libraries for AL02-78 were prepared with Diagenode Microplex Library Prep Kit v2 (starting with 1ng of DNA), AL79-80 with "NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (starting with 2 ng of DNA)

tag: cell line

tag: ChIP

value: FLAG

tag: input id

tag: construct

value: pMT HMR-dC-FLAG-HA

value: induced (CuSO4 250 uM)


title: Oregon-R round1 sample5


title: Adult Brain, OmniATAC R16A06 Mamo-RNAi

value: Brain

value: Adult

value: 3 day


title: Oregon-R round1 sample3

value: 3rd instar larvae

value: brain


title: AL78 - Hmr_Flag_deltaC_induced


title: primary adipocytes, bOHB treatment, replicate 3


title: Set2 round1 sample1

value: male


title: AL75 - Hmr_Flag_deltaC_induced

value: Input


title: primary adipocytes, butyric acid treatment, replicate 1

value: 6 hrs


title: primary adipocytes, control treatment, replicate 2

source_name: primary mouse adipocytes, treated with vehicle (PBS) for 6 hrs

value: control (PBS)


title: WT_Wound_FA_2


title: NSD round1 sample2


title: AL79 - Hmr_Flag_FL_induced

value: pMT HMR-FL-FLAG-HA


title: primary adipocytes, control treatment, replicate 3

value: primary adipocytes


title: WT_2

value: untreated control (+ vehicle)

value: WT


title: AL63 - Hmr_Flag_FL_induced


title: MEC-1

city: Zhanjiang

first: Ping

last: Jiang

state: Guangdong

address: Mazhang district haida street

department: College of Coastal Agricultural Sciences, Guangdong Ocean University

country: China

data_processing:
Whole transcriptome libraries preparation and deep sequencing
The sequencing library of each RNA sample was pre- pared by using Ion Total RNA-Seq Kit v2
Firstly, Raw Data Treatment: Using high-throughput Life technologies Ion Proton Sequencer, the transcript with poly (A)+ RNA of Human were analyzed. Reads sequenced were filtered and mapped to Cattle genome (download from NCBI) using Mapsplice software. The mapped reads was counted to achieve the expression of each gene based on the gene annotation information from NCBI database.
Secondly, Data Filtering:In order to achieve the best quality of the RNA Sequencing, Novelbio applied the reads filtration to filter the reads with lower quality and short sequence under following criteria: read length > 50; over 30% base quality >13.
Thirdly, Identification of differentially expressed genes :The DE-Seq algorithm was  applied  to  filter  differentially expressed  genes. After  the  significance  analysis  and  FDR  (false discovery  rate)  analysis ,  we  selected  the  differentially expressed  genes  according  to  the FDR threshold set at p < 0.05 and FDR <0.05. And the fold changes of any two groups are more than 2.
All the predicted target genes were intersected with the DEGs obtained by RNA-seq, and then the DEGs and DERs were obtained by a combined analysis.
After filtering the low quality reads, the clean reads data were aligned to the Ensemble bovine reference genome (Bos taurus UMD_3.1.1) and the methylation of mC sites were detected using Bismark (version 0.12.5).
Genome_build: Bos_taurus_UMD_3.1.1
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample .

organism: Bos taurus

source_name: bovine mammalian epithelial cells

growth_protocol: The cells were cultured in a basal medium containing Dulbecco's modified Eagle's medium and Nutrient Mixture F-12 (DMEM/F12, HyClone, Logan, USA) containing 10% FBS (foetal bovine serum, Tian hang, Zhejiang, China), 25 µL hydrocortisone (25 g/ml, Abcam, Cambridge, UK), and 25 L insulin (0.25 EU/mg, Abcam, Cambridge (HyClone, Logan, USA).

extract_protocol:
Total RNA was extracted with standard chloroform extraction from ACADSB−/− and negative control cells. DNase I (NEB, Beijing, China) was used to treat total RNA and Trizol reagent to extract it (Invitrogen, USA). The RNA quality was checked using the Bioanalyzer 2200 (Aligent)and then stored at -80°C, and the cDNA libraries for each pooled RNA sample were created using the VAHTSTM Total RNA-seq (H/M/R) according to the manufacturer's instructions.
The sequencing library of each RNA sample was prepared by using Ion Total RNA-Seq Kit

treatment_protocol: The Zhang lab's pSpCas9(BB)-2A-GFP (PX458, addgene 48318) vector was chosen as the vector backbone because it expresses Cas9 Streptococcus pyogenes with an invariant sgRNA scaffold and cloning sites for inserting the guide sequence. Two complementary sgRNA oligo DNA were synthesized, annealed to form double-stranded DNA in the presence of 10×NEB annealing buffer, and cloned into the BbsI sites of the PX458 targeting vector, according to the location and specificity. Transient transfecting bMECs cells resulted in the knockout of the ACADSB gene fragment. After 24 hours, the cells were collected using trypsin without EDTA solution, and the cells were screened using flow cytometry to see if they could express a green fluorescent protein (FCM). The single positive cells were cultured in 96-well plates containing 20% serum and 1% antibiotics. Seven days later, under a microscope, a small pile of cell pellets can be seen. After digesting the cells and continuing culturing, a large population of cells can be observed under the microscope 15 days later.

tag: breed

value: chinese Holstein  dairy cow

tag: Stage

value: Lactation period

value: bovine mammary tissue

value: bovine mammalian epithelial cells (bMECs)

value: control


title: WT_Wound_2

value: WT (Cas9 only)

value: wounded + vehicle


title: AL67 - Hmr_Flag_FL_induced

value: FLAG

value: induced (CuSO4 250 uM)


title: MEC-2

institute: College of Coastal Agricultural Sciences, Guangdong Ocean University


title: KO_Wound_1

value: REDD1 KO


title: Adult Brain, OmniATAC R16A06 Onecut-RNAi

value: Brain

value: Adult

value: 3 day


title: ACKO Cell-3

source_name: ACADSB knock out bovine mammalian epithelial cells

value: ACADSB knock out


title: KO_Wound_FA_1

value: wounded & treated with FA


title: AL74 - Hmr_Flag_FL_induced

value: Input

value: pMT HMR-FL-FLAG-HA


title: primary adipocytes, control treatment, replicate 1

value: primary adipocytes

value: control (PBS)

value: 6 hrs


title: AL77 - Hmr_Flag_FL_induced


title: WT_FA_1

value: treated with FA


title: AL68 - Hmr_Flag_deltaC_induced

value: pMT HMR-dC-FLAG-HA


title: KO_Wound_2


title: MEC-3

value: chinese Holstein  dairy cow

value: Lactation period

value: bovine mammary tissue

value: bovine mammalian epithelial cells (bMECs)

value: control


title: AL65 - Hmr_Flag_FL_induced

value: HMR

value: induced (CuSO4 250 uM)


title: AL56 - Hmr_Flag_deltaC_induced


title: AL66 - Hmr_Flag_deltaC_induced


title: ACKO Cell-2


title: AL55 - Hmr_Flag_FL_induced


title: hippocampus, C-2

type: RNA

city: beijing

first: huihui

last: miao

address: 10th Tieyi road

institute: Capital medical university,Beijing Shijitan Hospital

description: circRNA

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 ℃ for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the lncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

scan_protocol: Agilent DNA Microarray Scanner (part number G2505C) was used to scan the arrays.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, lncRNAs and mRNAs that at least two out of two samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis.

source_name: Mouse brain

label_protocol: mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Total RNA was extracted according to the manufacturer’s instructions from the two groups using TRIzol reagent (Invitrogen, Carlsbad, CA, USA). The RNA integrity of each sample was estimated using standard denaturing agarose gel electrophoresis and quantified via a NanoDrop spectrophotometer (NanoDrop, Wilmington, DE, USA).

value: 18 months

value: male

value: hippocampus


title: KO_Wound_FA_2

value: REDD1 KO

value: wounded & treated with FA


title: KO_FA_2


title: WT_1

value: WT (Cas9 only)

value: untreated control (+ vehicle)

value: WT


title: ACKO Cell-1

value: ACADSB knock out


title: WT_FA_2

value: treated with FA


title: AL64 - Hmr_Flag_deltaC_induced

value: Input

value: pMT HMR-dC-FLAG-HA


title: hippocampus, C-1

description: circRNA


title: Spontaneous sputum of subject 118 in tube with stabilizer

city: Parma

first: Mirco

last: Govoni

address: Largo Francesco Belloli 11/A

country: Italy

institute: Chiesi Farmaceutici

data_processing:
Read alignment was performed using StarAlign (v2.6.1a, Dobin et al. 2013) to the human reference genome GRCh38.  Only uniquely mapped reads were output for downstream analysis and all other reads discarded.  Sequences with >=3 base mismatches (against reference) were also discarded. In addition, gene counts were output for downstream analysis
StringTie (v1.3.4d, Pertea et al. 2015) was used to generate gene expression data, represented as Fragments Per Kilobase per Million fragments mapped (FPKM), Transcripts per million (TPM), and per gene coverage for each gene present in the human (GRCh38) ENSEMBL annotation file. The flag “–B” specified to ensure results are output in a single tab separated file, and the option “--rf” was specified to ensure reads were treated as an fr-firststrand stranded library. To generate the gene level expression, all exons that can be a part of any of the transcripts for that gene were summed
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include TPM for every gene and every sample
Supplementary_files_format_and_content: tab-delimited text files include raw gene counts for every gene and every sample

source_name: spontaneous sputum

extract_protocol:
RNA-zol
Kapa Hyper Prep Total RNA Seq (Roche)

tag: disease state

value: COPD

value: Sputum


title: hippocampus, A/S-3

description: circRNA

value: surgery

tag: tissue


title: AL20 - Hmr_Flag_deltaC_induced


title: hippocampus, C-3

description: circRNA

value: control


title: Adult Brain, OmniATAC repoGal4 UAS_lolaN x tubGal80ts

description:
lolaN_repo_vs_elav_c3.0_common.bed
lolaN_repo_vs_elav_c3.0_cond1.bed
lolaN_repo_vs_elav_c3.0_cond2.bed

source_name: Adult Brain

extract_protocol:
Brains were dissected from one male and one female fly in PBS. Next, 50μl cold lysis buffer was added (10 mM Tris‐HCl pH  7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA‐630). After spinning down at 800g, supernatant was discarded and transposition mix was addded, followed by general omniATAC-seq
omniATAC-seq

value: Brain

tag: developmental stage

value: Adult

value: 5 day

value: repoGal4 UAS_lolaN x tubGal80ts


title: pupa72h_brain_DGRP-409-502_sample2

data_processing:
The 10X samples were each processed (alignment, barcode assignment and UMI counting) with Cell Ranger ATAC (version 1.2.0) count pipeline.
For the ATAC samples the raw reads were first filtered and scanned for adapters using fastq‐mcf from the ea‐utils package. Read quality was then checked using FastQC. The reads were mapped to the Drosophila genome (dm6) using STAR. The outputted BAM file from STAR was then indexedand sorted using SAMtools. Using genomeCoverageBed from BedTools, the BAM file was converted to a BedGraph file. For fast, visualization in the IGV GenomeBrowser, the BedGraph file was further processed to a BigWig file using bedGraphtoBigWig.
Genome_build: dm6 (dmel_r6.16_FB2017_03)
81 bigwigs are attached based on samples belonging to 10X_ADULT (adult brain) and to 10X_PUPA_72H
10X_ADULT and 10X_PUPA_72H samples were subset based on cell type and merged to acquire cell type specific bam files
bam files were then deduplicated, black listed regions removed and RPGC normalised to acquire bigwig files

source_name: Pupa Brain

extract_protocol:
D. melanogaster adult brains were dissected and transferred to a tube containing 100 µl ice cold DPBS solution. After centrifugation at 800 g for 5 min, the supernatant was replaced by 500 µl nuclei lysis buffer composed of 10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.1% Nonidet P40, 0.01% Digitonin, and 1% BSA, in Nuclease-free water. The following procedure was followed to extract the nuclei from the brain tissue: incubation in nuclei lysis buffer on ice for 5 min, transfer to a dounce tissue grinder tube (Merck), 25 strokes with pestle A, incubation on ice for 10 min, 25 strokes with pestle B. The lysis was stopped by adding 1 ml of wash buffer composed of 10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20 and 1% BSA, in Nuclease-free water. Nuclei were pelleted by centrifugation at 800 g for 5 min at 4°C and resuspended in 1x Nuclei Buffer (10x Genomics). Nuclei suspensions were passed through a 40 µM Flowmi filter (VWR Bel-Art SP Scienceware). Nuclei concentration was assessed by the LUNA-FL Dual Fluorescence Cell Counter.
10x Genomics CHROMIUM Single Cell ATAC Library & Gel Bead Kit v1

value: Pupa

tag: age

value: 72 hours


title: AL58 - Hmr_Flag_FL_induced

value: HMR

value: pMT HMR-FL-FLAG-HA

value: induced (CuSO4 250 uM)


title: KO_1

tag: genotype

value: REDD1 KO

value: untreated control (+ vehicle)

value: KO


title: AL59 - Hmr_Flag_deltaC_induced

value: pMT HMR-dC-FLAG-HA


title: AL24 - Hmr_Flag_deltaC_induced


title: KO_FA_1

value: treated with FA


title: Liver tissue_14 weeks_standard chow diet_rep3

city: Xi’an. China

first: ting

last: li

state: Shaanxi

address: NO.76 Yanta West Road, Health Science Center, Xi’an Jiaotong University, Xi’an. China

department: Health Science Center

institute: Xi’an Jiaotong University

description:
Gene expression data from  liver tissue of Normal rat
Zheng 4

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).1.Assemble the slides into an slide holder. 2.Place assembled slide holders into scanner carousel.3.Verify scan settings for one-color scans.4.Click Scan Slot m-n on the Scan Control main window where the letter m represents the Start slot where the first slide is located and the letter n represents the End slot where the last slide is located.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v11.5.1 software package (Agilent Technologies). After quantile normalization of the raw data, genes that all samples have flags in Detected (“All Targets Value”) were chosen for further data analysis. Differentially expressed genes with statistical significance were identified through Volcano Plot filtering. Hierarchical Clustering was performed using the Agilent GeneSpring GX software (version 11.5.1). GO analysis and Pathway analysis were performed in the standard enrichment computation method.

organism: Rattus norvegicus

source_name: Liver tissue, 14 weeks, standard chow diet

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology). Briefly, total RNA from each sample was linearly amplified and labeled with Cy3-UTP. The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000

growth_protocol: The two groups of rats were fed by14 weeks of high fat diet and normal chow diet seperatly

extract_protocol: Total RNA was isolated from the rat liver samples using TRIzol reagent (Invitrogen,Carlsbad,CA,USA) and purified using the RNeasy Mini Qiagen purification kit (QIAGEN,Valencia,CA) according to the manufacturer’s instructions. Integrity and concentration of RNA were assessed after RNA extraction and prior to sample labeling by NanoDrop ND-1000 (Thermo Fisher scientific,Waltham,MA). The integrity of RNA were assessed by Denaturing Agarose Gel Electrophoresis.

treatment_protocol: liver tissues were collected in RNase-free tubes and promptly frozen in liquid nitrogen.

tag: gender

value: male

value: liver


title: Adult Brain, OmniATAC elavGal4 UAS_lolaN x tubGal80ts

value: elavGal4 UAS_lolaN x tubGal80ts


title: KO_2


title: pupa48h_brain_DGRP-409-502_sample1

value: Brain

value: 48 hours


title: hippocampus, A/S-2

description: circRNA

tag: strain

value: 18 months

tag: Sex

value: surgery

value: hippocampus


title: AL28 - Hmr_Flag_deltaC_induced

value: FLAG

tag: treatment


title: AL18 - Hmr_Flag_FL_induced

value: Input


title: pupa72h_brain_DGRP-409-502_sample1

value: Pupa

value: 72 hours


title: pupa48h_brain_DGRP-409-502_sample2


title: Liver tissue_14 weeks_high fat diet_rep4

description:
Gene expression data from  liver tissue of NAFLD rat
N 3-3

source_name: Liver tissue, 14 weeks, high fat diet

value: NAFLD

value: high fat diet


title: AL07 - Hmr_Flag_FL_induced

value: pMT HMR-FL-FLAG-HA

value: induced (CuSO4 250 uM)


title: AL22 - Hmr_Flag_FL_induced

value: HMR


title: Spontaneous sputum of subject 111 in tube with stabilizer

value: COPD

value: Sputum


title: Spontaneous sputum of subject 115 in pot with stabilizer


title: Liver tissue_14 weeks_standard chow diet_rep1

description:
Gene expression data from  liver tissue of Normal rat
Zheng 2

value: control

value: male

value: liver


title: hippocampus, A/S-1

description: circRNA

value: 18 months


title: Liver tissue_14 weeks_standard chow diet_rep2

description:
Gene expression data from  liver tissue of Normal rat
Zheng 3


title: AL06 - Hmr_Flag_deltaC_induced

value: pMT HMR-dC-FLAG-HA


title: WT_Wound_1

value: WT (Cas9 only)

value: wounded + vehicle


title: ARID1A KO cells under tunicamycin treatment, replicate 3

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

data_processing:
RNA-Seq data analysis was done with rsem (ver. 1.2.3) and hg19 genome with ensemble transcriptome information
DESeq2 was used for differentail expression analysis
Genome_build: hg19
Supplementary_files_format_and_content: Prosessed files contains the raw counts for each gene

source_name: RMG1 cell line

extract_protocol:
RNA was extracted with Trizol (Invitrogen) for all RNA preparations, then subsequently cleaned and DNase treated using RNeasy columns (Qiagen)
Libraries for RNA-Seq were prepared with ScriptSeq complete Gold kit (Epicenter) and subjected to a 75 bp paired-end sequencing run on NextSeq 500, using Illumina’s NextSeq 500 high output sequencing kit following the manufacturer’s instructions

value: KO

value: TM

tag: replicate


title: Spontaneous sputum of subject 118 in pot with stabilizer


title: adult_centralbrain_DGRP-409-502_sample2

value: Brain

value: Adult

value: 1 day


title: AL26 - Hmr_Flag_FL_induced

value: FLAG

value: pMT HMR-FL-FLAG-HA


title: Spontaneous sputum of subject 110 in pot with stabilizer


title: Spontaneous sputum of subject 110 in tube with stabilizer


title: pupa24h_brain_DGRP-551_hyb_sample2

value: Pupa

value: 24 hours


title: AL08 - Hmr_Flag_deltaC_induced

value: induced (CuSO4 250 uM)


title: larval_brain_DGRP-551_hyb_sample2

source_name: Larva Brain

value: Larva


title: Liver tissue_14 weeks_high fat diet_rep5

description:
Gene expression data from  liver tissue of NAFLD rat
N 4-1

value: NAFLD

value: male

value: high fat diet


title: ARID1A KO cells under tunicamycin treatment, replicate 1


title: Spontaneous sputum of subject 115 in tube with stabilizer

value: COPD

value: Sputum


title: Spontaneous sputum of subject 111 in pot with stabilizer


title: ARID1A KO cells under control condition, replicate 3

value: ctr


title: adult_brain_DGRP-551_Hyb-409-502_639_sample4_6k


title: ARID1A KO cells under control condition, replicate 2

value: KO


title: Ribo-WT-1opt_3

city: Dallas

first: xueliang

last: lyu

state: Texas

address: 6001 Forest Park Road

department: Physiology

institute: UT Southwestern Medical Center

data_processing:
Sequenced reads were trimmed for adaptor sequence by our in-house scripts.
Clean reads were then mapped to reference sequences using bowtie2 and RPKM values were calculated by cufflinks with parameters --min-intron-length 4 --max-intron-length 5000 --library-type fr-firststrand --multi-read-correct --upper-quartile-norm
Genome_build: All of the ribosome profiling and accompanying mRNA-seq clean reads were mapped to coding sequence (CDS) regions of N. crassa genes.
Supplementary_files_format_and_content: For both of ribosome profiling and accompanying mRNA-seq, tab-delimited text files including RPKM values were generated by cufflinks for each sample.

organism: Neurospora crassa

source_name: mycelia

growth_protocol: For both of ribosome profiling and the accompanying mRNA-seq, fresh conidia (one week post inoculation on slants) of Δcpc-3 and wild-type strains were cultured in plates with 50 ml growth medium (1 × Vogel’s, 2% glucose) at room temperate for two days. The cultures were cut into small discs with a diameter of 1 cm and then were transferred into flasks with the same medium and grown with orbital shaking (200 rpm) under constant light for 12 h.

extract_protocol:
For both of ribosome profiling and the accompanying mRNA-seq, the ribosome protected fragments (RPFs) and total RNAs were extracted according to ARTseq Ribosome Profiling Kit(Catalog Number: RPYSC12116).
For both of ribosome profiling and the accompanying mRNA-seq, libraries were prepared for sequencing according to ARTseq Ribosome Profiling Kit(Catalog Number: RPYSC12116).

treatment_protocol: For both of ribosome profiling and the accompanying mRNA-seq, CHX (final concentration of 0.1 mg/ml) was only added into the cell lysis buffer.

tag: host strain

value: WT

tag: reporter expressed in host strain

value: mycelia

tag: molecule

value: ribosome protected fragments


title: adult_brain_DGRP-551_Hyb-409-502_639_sample5_8k

value: Brain

value: Adult

value: 1 day


title: Spontaneous sputum of subject 107 in pot with stabilizer


title: adult_brain_DGRP-551_Hyb-409-502_639_sample3_4k


title: Spontaneous sputum of subject 107 in tube with stabilizer


title: ARID1A KO cells under control condition, replicate 1


title: adult_brain_DGRP-551_Hyb-409-502_639_sample2_2k


title: Spontaneous sputum of subject 106 in pot with stabilizer


title: larval_brain_DGRP-551_hyb_sample1


title: ARID1A WT cells under tunicamycin treatment, replicate 2

value: TM


title: Liver tissue_14 weeks_high fat diet_rep1

description:
Gene expression data from  liver tissue of NAFLD rat
N 1-4

value: liver


title: adult_centralbrain_DGRP-409-502_sample1


title: Liver tissue_14 weeks_high fat diet_rep2

description:
Gene expression data from  liver tissue of NAFLD rat
N 1-5


title: AL03 - Hmr_Flag_FL_induced

tag: cell line

tag: ChIP

value: Input

tag: input id

value: pMT HMR-FL-FLAG-HA

value: induced (CuSO4 250 uM)


title: Liver tissue_14 weeks_high fat diet_rep3

description:
Gene expression data from  liver tissue of NAFLD rat
N 3-2

value: NAFLD

value: male


title: ARID1A WT cells under tunicamycin treatment, replicate 1


title: pupa24h_brain_DGRP-551_hyb_sample1

value: Pupa

value: 24 hours


title: Spontaneous sputum of subject 108 in pot with stabilizer

value: COPD

value: Sputum


title: ARID1A KO cells under tunicamycin treatment, replicate 2

value: KO


title: Term_EVT_patient_2701

city: La Jolla

first: Robert

middle: E

last: Morey

state: CA

address: 2880 Torrey Pines Scenic Dr

department: Pathology

institute: UCSD

data_processing:
Quality control was performed using FastQC (v. 0.11.8) and multiQC (v. 1.6).
Reads were mapped to GRCh38.p10 (GENCODE release 26) using STAR (v. 2.7.3a) (PMID: 23104886; Dobin, 2012) and annotated using featureCounts (subread v.1.6.3, GENCODE release 26 primary assembly annotation) (PMID:24227677; Liao, 2014). The STAR parameters used were: --runMode alignReads --outSAMmode Full --outSAMattributes Standard --genomeLoad LoadAndKeep --clip3pAdapterSeq AGATCGGAAGAGC --clip3pAdapterMMp 1 -- outFilterScoreMinOverLread 0.3 --outFilterMatchNminOverLread 0.3. The featureCounts parameters were: -s 2 -p -t exon -T 13 -g gene_id (PMID:24227677; Liao, 2014).
Ensembl genes without at least three samples with 5 or more reads were removed from analysis.
Normalization and differential expression analysis were performed using the R (v. 3.6.3) package DEseq2 (v. 1.28.1), (Love 2014). BiomaRt (v. 2.42.1) was used to convert Ensembl gene ID’s to HUGO gene names.
Sample sex was accounted for in the DESeq2 design.
Genome_build: GRCh38.p10 (GENCODE release 26)
Supplementary_files_format_and_content: Matrix table with normalized gene counts for every gene and every sample post filtering

molecule: polyA RNA

growth_protocol: First and term placentae tissues were collected under a UCSD Human Research Protections Program Committee Institutional Review Board-approved protocol; all patients provided informed consent for collection and use of these tissues. Term placentae was obtained immediately after C-section and placed on ice. For first trimester placentae, “normal” refers to elective termination of pregnancy in the absence of structural fetal abnormalities; for third trimester placentae (term), “normal” is defined by a non-hypertensive, non-diabetic singleton pregnancy, where the placenta is normally grown and shows no gross or histological abnormalities.

extract_protocol:
Total RNA was isolated using the mirVana miRNA isolation kit (Ambion). RNA concentration was measured by Qubit RNA BR assay kit (ThermoFisher) and the quality of isolated RNA was checked using a bioanalyzer (Agilent). All samples were found to have a RIN above 7.5.
RNA-seq libraries were prepared using the TruSeq Stranded mRNA sample preparation kit (Illumina) at the IGM Genomics Center at UC San Diego.

treatment_protocol: Isolation of cytotrophoblast (CTB) and extravillous trophoblast (EVT) from term placentae (37- to 41-weeks GA) was performed as previously described in (PMID: 24004950). Tissue from the basal plate (for EVT) and chorionic portion (for CTB) was dissected and minced, rinsed in 1X PBS (Corning), and digested for 20 minutes in 1X Ca/Mg-free HBSS (Gibco), 1X trypsin (Gibco), collagenase, and DNase (Roche) three times, discarding the supernatant after each digestion. A Percoll gradient (Sigma-Aldrich) centrifugation separation was then performed. Cells were then subjected to positive selection using magnetic activated cell sorting (MACS) (Miltenyi Biotec) and a PE-conjugated antibody against HLA-G (EXBIO MEM-G/9). The bound fraction was collected, tested for purity using flow cytometry. EVT preparations that contained greater than 90% HLA-G+ cells were considered as adequate and used in downstream experiments. The unbound fraction was collected and CTB were selected using APC-conjugated antibody against EGFR (Biolegend #352906;) and tested for purity using flow cytometry. CTB preparations yielding greater than 90% EGFR positivity were considered adequate and used in downstream experiments. Isolation of primary first trimester (9- to 14-week gestational age) trophoblast cells from placenta samples was performed as previously described in (PMID: 28167044, 29361559).  Briefly, chorionic villi were minced, washed in Hanks’ balanced salt solution (Gibco) and digested three times with DNase I (Roche) and trypsin (Gibco). The cells were then pelleted and separated on a Percoll gradient (Sigma-Aldrich) and subjected to sequential MACS selection similar to the term placental samples.

value: Male

value: extravillous trophoblast

tag: trimester

tag: gestational age (wksdays)


title: ARID1A WT cells under control condition, replicate 2

value: WT

value: ctr


title: Term_EVT_patient_2700

value: Female


title: ARID1A WT cells under control condition, replicate 3


title: AL05 - Hmr_Flag_FL_induced

value: HMR

tag: construct


title: IBPL1_J

city: Berkeley

first: Ida

last: Björkgren

address: 221A Weill Hall UC Berkeley

department: Department of Molecular and Cell Biology

institute: University of California, Berkeley

data_processing:
Basecalls performed using CASAVA. "Downstream analysis was performed using a combination of programs including STAR, HTseq,  Cufflink and our wrapped scripts. Alignments were parsed using Tophat program and  differential expressions were determined through DESeq2/edgeR. GO and KEGG enrichment  were implemented by the ClusterProfiler. Gene fusion and difference of alternative splicing event  were detected by Star-fusion and rMATS software" (Novogene)
Sequences were mapped to mm10 genome using STAR v2.5 with mismatch paramater=2. "Reference genome and gene model annotation files were downloaded from genome website  browser (NCBI/UCSC/Ensembl) directly. Indexes of the reference genome was built using STAR  and paired-end clean reads were aligned to the reference genome using STAR (v2.5). STAR used  the method of Maximal Mappable Prefix(MMP) which can generate a precise mapping result  for junction reads." (Novogene)
"HTSeq v0.6.1 was used to count the read numbers mapped of each gene. And then FPKM of each  gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM,  Reads Per Kilobase of exon model per Million mapped reads, considers the effect of sequencing  depth and gene length for the reads count at the same time, and is currently the most commonly  used method for estimating gene expression levels (Mortazavi et al., 2008)." (Novogene)
"(For DESeq2 with biological replicates) Differential expression analysis between two  conditions/groups (two biological replicates per condition) was performed using the DESeq2  R package (2_1.6.3). DESeq2 provide statistical routines for determining differential  expression in digital gene expression data using a model based on the negative binomial  distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s  approach for controlling the False Discovery Rate(FDR). Genes with an adjusted P-value <0.05  found by DESeq2 were assigned as differentially expressed.  (For edgeR without biological replicates) Prior to differential gene expression analysis, for  each sequenced library, the read counts were adjusted by edgeR program package through one  scaling normalized factor. Differential expression analysis of two conditions was performed  using the edgeR R package (3.16.5). The P values were adjusted using the Benjamini &  Hochberg method. Corrected P-value of 0.05 and absolute foldchange of 1 were set as the  threshold for significantly differential expression.  The Venn diagrams were prepared using the function vennDiagram in R based on the gene list  for different group." (Novogene)
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Choroid Plexus

growth_protocol: The C57Bl/6N (Charles River) mice and the Abhydrolase domain-containing protein 2 (Abhd2) knockout mice of similar background were kept at the Animal Facility of the University of California, Berkeley, in a room with controlled light (14 hours light, 10 hours darkness) and temperature (23±0.5°C). The mice were fed a standard chow diet (PicoLab Rodent diet 20, LabDiet, 5053) and hyper-chlorinated water ad libitum. All experiments were performed in accordance with NIH Guidelines for Animal Research and approved by UC Berkeley Animal Care and Use Committee (AUP 2015-07-7742), with every effort made to minimize suffering for the animals.

extract_protocol:
For gene expression analyses of the choroid plexus, the lateral choroid plexuses (LCPs) from adult mice were dissected out and snap frozen. The animals were euthanized by CO2 and cervical dislocation around 10 am when the females were in proestrus. mRNA isolation was performed using the Quick-RNA Microprep Kit (Zymo Research, R1050) according to the manufacturer’s instructions.
The mRNA samples were processed for sequencing at QB3 Vincent J. Coates Genomics Sequencing Laboratory, UC Berkeley. The LCP mRNA was enriched for using Oligo dT beads from the Invitrogen Dynabeads mRNA Direct kit (61011). Subsequent library preparation steps of fragmentation, adapter ligation, and cDNA synthesis were done on the enriched mRNA using the KAPA RNA HyperPrep kit (Roche, KK8540). Truncated universal stub adapters were used for ligation, and indexed primers were used during PCR amplification to complete the adapters and to enrich the libraries for adapter-ligated fragments. Samples were checked for quality on an AATI (now Agilent) Fragment Analyzer. Libraries were then quantified using qPCR on a BioRad CFX Connect to measure molarity of only sequence-able molecules using the Kapa Biosystems Universal Illumina quant kit, pooled equimolar, clustered at 3nM with 2% PhiX v3 control library spike-in, and sequenced as a 100bp paired end run on an Illumina HiSeq 4000. Bcl files were then converted to fastq format and demultiplexed using the innate bcl2fastq v1.19 software.

tag: tissue

value: Choroid Plexus

value: F

tag: abhd2 genotype

value: hoz


title: 3D_day35_2

city: Basel

first: Rosemarie

last: Ungricht

address: Fabrikstrasse 22

department: DAx

country: Switzerland

institute: Novartis Institute for BioMedical Research

data_processing:
Illumina's bcl2fastq2 version 2.17.1.14 was used for basecalling.
10x Genomics' cellranger mkfastq version 2.0.2 and 2.2.0 were used to demultiplex fastqs using default settings.
10x Genomics' cellranger count version 2.0.2 and 2.2.0 were used to generate mapped bam files using default settings.
Genome_build: GRCh38
Supplementary_files_format_and_content: Genes-by-cells matrix in Hierarchical Data Format 5 File (H5).

source_name: kidney organoid

growth_protocol: Kidney organoids were grown according to the protocol described by Morizane and Bonventre (2017).

extract_protocol:
Organoids were dissociated with a 1:1 mix of 0.25% Trypsin-EDTA and non-enzymatic cell dissociation solution (both Gibco) for 20 min at 37°C. After 10 and 20 min, organoids were broken up by pipetting (up and down 20x). Then cells were washed twice with 10% and 1% FBS in PBS and the cell suspension was passed through a 40 µm and a 20 µm filter.
scRNA-Seq libraries were prepared using a GemCode Single Cell 3′ Gel Bead Kit according to the manufacturer’s instructions (10× Genomics).

treatment_protocol: 12 3D suspension organoids were pooled per sample.

value: kidney organoid

tag: time after start of differentiation in days


title: Term_EVT_patient_2706

tag: gender


title: Ribo-WT-1wt_3

value: mycelia

value: ribosome protected fragments


title: Spontaneous sputum of subject 108 in tube with stabilizer

tag: disease state


title: Term_EVT_patient_2667


title: Spontaneous sputum of subject 106 in tube with stabilizer


title: ARID1A WT cells under tunicamycin treatment, replicate 3

value: TM


title: Ribo-WT-3wt_3


title: AL02 - Hmr_Flag_deltaC_induced

value: Input

value: pMT HMR-dC-FLAG-HA

value: induced (CuSO4 250 uM)


title: 3D_day28_3


title: IBPL1_H

tag: Sex

value: wt

tag: strain


title: 3D_day35_1

tag: replicate


title: Actinin-BirA* 2

city: Farmington

first: Travis

last: Hinson

state: Connecticut

address: 10 Discovery Dr

institute: JAX-GM

data_processing:
Trimmed reads were aligned using STAR
HTSeq was utilized to convert files to raw counts
Counts were analyzed tith DESeq2
Genome_build: h38
Supplementary_files_format_and_content: STAR alignment .bam files were converted to .counts using HTSeq (.counts files provided)

source_name: iPSC-CMs (cardiomyocytes)

extract_protocol:
Samples were trizoled and routine RNA extraction protocol was followed
Illumina TruSeq Stranded Total RNA library preparation with Ribo-Zero depletion for rRNA

tag: age

value: Day 25

tag: background

tag: cell type

value: iPSC-CMs (cardiomyocytes)


title: IBPL1_L


title: ARID1A WT cells under control condition, replicate 1

value: WT

tag: treatment


title: IBPL1_F

value: M


title: adult_brain_DGRP-551_Hyb-409-502_639_sample1

value: Brain

tag: developmental stage

value: Adult

value: 1 day

tag: genotype


title: IBPL1_E

value: Choroid Plexus


title: Term_EVT_patient_2656

value: Female

value: extravillous trophoblast

tag: trimester


title: IBPL1_I

value: F


title: STB_82

city: Oulu

first: Antti

last: Haapalainen

address: Aapistie 5A

department: CRC

country: Finland

institute: University of Oulu

description: sequencing was done in 1 lane

data_processing:
The base calling was done using bcl2fastq (v. 1.8.4)
Read alignment was done using TopHat version 2.0.10 to hg19 human genome reference
Genewise read counts were calculated using HTSeq2
Genome_build: Human hg19
Supplementary_files_format_and_content: files are tab delimited text files containing the genewise read counts for each sample

source_name: placenta

extract_protocol:
RNA isolation from frozen placenta specimens by using Qiagen Rneasy Micro Kit
Illumina Truseq stranded mRNA

tag: condition

value: spontaneous birth


title: Ribo-WT-3opt_3

tag: host strain

tag: reporter expressed in host strain

value: mycelia

tag: molecule

value: ribosome protected fragments


title: 3D_day28_1

tag: tissue

value: kidney organoid

tag: time after start of differentiation in days


title: 3D_day28_2


title: 3D_day21_2


title: 3D_day21_1


title: IBPL1_G

tag: abhd2 genotype


title: Actinin-BirA* 1


title: Control 3


title: Actinin-BirA* 3


title: First_Trimester_EVT_patient_951

tag: gender

tag: gestational age (wksdays)


title: STB_56

description: sequencing was done in 1 lane


title: IBPL1_K

tag: Sex

value: hoz

tag: strain


title: IBPL1_D


title: Term_EVT_patient_2342

value: Male


title: First_Trimester_EVT_patient_970


title: First_Trimester_EVT_patient_977


title: First_Trimester_EVT_patient_1099


title: STB_40

description: sequencing was done in 1 lane


title: Actinin-BirA* 4

tag: age

value: Day 25

tag: background


title: Control 4

tag: cell type

value: iPSC-CMs (cardiomyocytes)


title: STB_34

description: sequencing was done in 1 lane


title: IBPL1_A

value: wt


title: First_Trimester_EVT_patient_1096


title: 14-07w-JFJ_rep6

city: Schlieren

first: Lynn

middle: Jenny Alix

last: Ebner

state: Zürich

address: Wagistrasse 14

department: Department of Ophthalmology

institute: Universität Zürich

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRC38p5 whole genome using STAR
Genome_build: GRC38p5
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: Retina

extract_protocol:
Retinas were isolated through a slit in the cornea and snap-frozen in liquid nitrogen. RNA was isolated using an RNA isolation kit (Nucleo Spin RNA, Macherey-Nagel GmbH & Co.KG, Düren, Germany) with an additional, on-column DNase I treatment according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For all experiments performed in Zurich (ZH), mice were placed in their homecage in isobaric hypoxia chambers and exposed to hypoxia for 6 h, 48 h, or 11 weeks. Briefly, oxygen concentration was decreased gradually by 2% every 10 min by altering the oxygen:nitrogen ratio until either 14% or 7% O2 was reached. For hypobaric experiments performed at high altitude (JFJ), mice were exposed to the environmental air pressure of approximately 64.65 kPa (slightly fluctuating depending on weather and time of the year), which decreases the ambient partial pressure of oxygen from 21.2 kPa (sea level) to 13.7 kPa

value: Retina

value: hypoxia

tag: time point

tag: location

value: Jungfraujoch (3450masl)


title: IBPL1_C

value: M


title: IBPL1_B

value: Choroid Plexus


title: TK- BMDM M2

city: Cincinnati

first: Susan

last: Waltz

state: Ohio

address: 3125 Eden Ave

department: Cancer Biology

institute: University of Cincinnati

description: run1581_lane12_read1_indexD702-D503=TK-_BMDM_M2

data_processing:
Following removal of primers and barcodes, raw reads were aligned to the mm10 genome using UCSC annotations in GeneSpring NGS software (Agilent)
Data were quantified, log2 transformed, and normalized using the DESeq algorithm.
Data were baselined to the median of all samples.
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited with Gene ID, Gene Symbol, and RPKM

source_name: Bone marrow derived macrophages from FVB RON TK-/- mice

growth_protocol: Maintained in regular DMEM high glucose with 10% serum, sodium pyruvate, 6 mM Gln

extract_protocol:
Total RNA was extracted using the TRIZOL method
Libraries prepared using the Illumina TruSeq RNA preparation kit
Single end 50-bp reads

treatment_protocol: Treated with 10 ng/mL rIL-4 for 72 hours

tag: strain background

value: FVB

tag: genotype/variation

value: RON TK-/-; RON deficient

tag: treatment

value: Bone marrow derived macrophages (BMDM)


title: First_Trimester_EVT_patient_1097

value: Female

value: extravillous trophoblast

tag: trimester


title: STB_32

description: sequencing was done in 1 lane

tag: condition

value: spontaneous birth


title: WT BMDM M2

description: run1581_lane12_read1_indexD701-D504=WT_BMDM_M2

source_name: Bone marrow derived macrophages from FVB WT mice

value: WT; RON proficient

value: Treated with 10 ng/mL rIL-4 for 72 hours


title: 14-07w-JFJ_rep5

tag: tissue


title: SPTB_48

description: sequencing was done in 1 lane

value: spontaneous preterm birth


title: Control 1

value: Day 25


title: 14-07w-JFJ_rep4


title: First_Trimester_EVT_patient_1094

value: Male


title: SPTB_86

description: sequencing was done in 1 lane


title: First_Trimester_EVT_patient_1089


title: Control 2

value: iPSC-CMs (cardiomyocytes)


title: SPTB_9

description: sequencing was done in 1 lane


title: primary non-MCL p53/Mb1Cre lymphoma oTP10

city: Ghent

first: Wouter

last: Van Loocke

state: East Flanders

address: C. Heymanslaan 10

department: Biomolecular Medicine

institute: Ghent University

data_processing:
FastQC was used for QC on fastq files
Fastq files were aligned to human reference genome GRCm38 using STARv2.42 and gencode v15 as guide gtf
Counts were generated on the fly by STAR
Genome_build: GRCm38
Supplementary_files_format_and_content: tsv raw count matrix

source_name: primary lymphoma

growth_protocol: not applicable

extract_protocol:
Fresh primary lymphoma cells (5x10exp6) were frozen in 700 µl of QIAZOL and stored in -80°C. RNA was prepared using a miRNeasy mini kit (Qiagen).
QuantSeq 3ʹ mRNA-seq reverse Library Prep Kit (Lexogen) was used according to manufacturer’s instruction to generate compatible library for Illumina sequencing.

treatment_protocol: not applicable

tag: genotype

tag: immunophenotype

value: non-MCL

tag: mouse id

tag: tumor type

value: lymphoma


title: SPTB_13

description: sequencing was done in 1 lane


title: 14-07w-JFJ_rep3

value: Retina

value: hypoxia

value: Jungfraujoch (3450masl)


title: primary non-MCL p53/Mb1Cre lymphoma oTP17


title: primary non-MCL p53/Mb1Cre lymphoma oTP11

value: thymoma


title: First_Trimester_EVT_patient_1087

tag: gender

tag: gestational age (wksdays)


title: SPTB_4

description: sequencing was done in 1 lane


title: primary non-MCL p53/Mb1Cre lymphoma TP21

tag: strain

value: Spleen


title: First_Trimester_EVT_patient_1026


title: ETB_55

description: sequencing was done in 1 lane

value: elective term birth (caesarean section)


title: 14-48h-JFJ_rep5


title: 14-48h-JFJ_rep4


title: Term_CTB_patient_2567

value: Female

value: cytotrophoblast


title: 14-07w-JFJ_rep2


title: primary non-MCL Ccnd2/p53/Mb1Cre transplant TP33

source_name: primary transplant

value: MCL-like

value: primary:45080607 spleen; NSG #3


title: Term_CTB_patient_2504


title: Term_CTB_patient_2536


title: Term_CTB_patient_2538


title: 14-48h-JFJ_rep6


title: primary non-MCL p53/Mb1Cre lymphoma TP25


title: STB_44

description: sequencing was done in 1 lane

value: spontaneous birth


title: SPTB_14

description: sequencing was done in 1 lane

value: spontaneous preterm birth


title: 14-48h-JFJ_rep1


title: 14-07w-JFJ_rep1


title: Term_CTB_patient_2430


title: primary non-MCL p53/Mb1Cre lymphoma TP5


title: primary non-MCL p53/Mb1Cre lymphoma oTP9

value: Mediastinal lymphoma


title: Term_CTB_patient_2418


title: Term_CTB_patient_2554


title: 14-48h-JFJ_rep3


title: primary non-MCL Ccnd2/p53/Mb1Cre transplant TP31

value: primary:12201130 spleen; NSG 35


title: ETB_22

description: sequencing was done in 1 lane


title: primary non-MCL Ccnd2/p53/Mb1Cre transplant TP29

value: primary:12201131 spleen; NSG 62


title: Term_CTB_patient_2453

value: Male


title: 14-48h-JFJ_rep2


title: primary non-MCL Ccnd2/p53/Mb1Cre transplant TP27

value: primary:319300747 Mesentric lymphoma GI; NSG 21


title: ETB_28

description: sequencing was done in 1 lane


title: Term_CTB_patient_2256


title: 14-11w-ZH_rep6

value: Retina

value: Zurich (400masl)


title: Term_CTB_patient_2239


title: ETB_49

description: sequencing was done in 1 lane


title: ETB_33

description: sequencing was done in 1 lane


title: First_Trimester_CTB_patient_832


title: primary non-MCL Ccnd2/p53/Mb1Cre transplant TP28

value: primary:12201131 spleen; NSG 5/19


title: 14-11w-ZH_rep1

value: hypoxia


title: 14-11w-ZH_rep2


title: First_Trimester_CTB_patient_830


title: First_Trimester_CTB_patient_831


title: primary MCL-like Ccnd2/p53/Mb1Cre lymphoma TP19

value: Spleen


title: primary non-MCL Ccnd2/p53/Mb1Cre transplant TP26

value: primary:319300747 Mesentric lymphoma GI; NSG 18


title: 14-11w-ZH_rep5


title: ShLSD1 #2_07

city: Bunkyo-Ku

first: Ken

last: Tajima

state: Tokyo

address: 2-1-1 Hongo

department: Department of Respiratory Medicine

country: Japan

institute: Juntendo University

hyb_protocol: Following fragmentation, 2 μg of Single-Stranded cDNA was hybridized for 16 hr at 45˚C on Clariom S Array, Human. Arrays was washed and stained in the GeneChip Fluidics Station 450 (Thermo Fisher Scientific).

scan_protocol: Clariom S array was scanned using GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Expression Console Software 1.4 offered SST-RMA for gene level analysis using Thermo Fisher Scientific default analysis settings.

label: biotin

label_protocol: Biotinylated cDNA was prepared from 100 ng total RNA using GeneChip WT PLUS Reagent Kit (Thermo Fisher Scientific) following the manufacturer's instructions.

growth_protocol: ACC-MESO-1 cells were maintained in RPMI-1640 medium (Wako, Osaka, Japan) supplemented with 10% fetal bovine serum (FBS), penicillin (100 U/mL), and streptomycin (100 μg/mL) at 37C in 5 % CO2.

extract_protocol: RNA was isolated using an RNeasy Mini kit (Qiagen).

tag: cell line

value: mesothelioma

tag: shRNA

value: ShLSD1 #2


title: ShLSD1 #2_09

tag: cell type


title: ETB_19

description: sequencing was done in 1 lane

value: elective term birth (caesarean section)


title: primary MCL-like Ccnd2/p53/Mb1Cre lymphoma TP20

value: MCL-like


title: ShLSD1 #1_05

value: ShLSD1 #1


title: ShLSD1 #2_08


title: 14-11w-ZH_rep4

tag: time point

tag: location


title: First_Trimester_CTB_patient_825

value: cytotrophoblast


title: First_Trimester_CTB_patient_805

value: Female


title: primary MCL-like Ccnd2/p53/Mb1Cre lymphoma TP13


title: 14-48h-ZH_rep6


title: 14-11w-ZH_rep3


title: primary MCL-like Ccnd2/p53/Mb1Cre lymphoma TP7

value: Mesentric lymphoma


title: primary non-MCL Ccnd2/p53/Mb1Cre transplant TP35

value: non-MCL


title: First_Trimester_CTB_patient_804


title: 14-48h-ZH_rep1


title: GROseq DC3000_rep2

city: Beiing

first: Yijun

last: Qi

address: NO.1 Qinghuayuan

department: School of Life Sciences

institute: Tsinghua University

data_processing:
Library strategy: GRO-seq
GRO-seq: Raw reads from each library were de-duplicated and barcode sequences were removed using FASTX-Toolkit (v0.0.13). All processed read mates were aligned to TAIR10 using Bowtie2 (version 2.3.5) with default parameters. Nascent RNA levels were calculated as FPKM values using Homer (version 4.11.1). Differential gene transcription analysis was done using edgeR (version 3.26.5) with default parameters.The RNAs that have absolute log2 fold change value > 1 and P-value < 0.05 in two biological replicates were retained as reliable differentially transcribed RNAs.
Genome_build: Arabidopsis TAIR10

organism: Arabidopsis thaliana

source_name: 24-day-old leaves

growth_protocol: Arabidopsis seeds were sterilized with 5% NaClO containing 0.05% Tween-20 for 15 min and then stratified for 2 days at 4°C in dark. After that, the seeds were plated on half-strength MS medium with the supplementation of 1% sucrose, 0.4% agar and grown for 12 days at 22°C with a 16 h light/8 h dark photoperiod. For 24-day-old seedlings, the plate-grown seedlings were transferred to soil and grown in greenhouse under a 16h light/8h dark photoperiod for additional 12 days.

extract_protocol:
GRO-seq libraries were constructed as previously described with minor modifications (Wang et al, 2011). Briefly, nuclei were resuspended by nuclear run-on buffer and were incubated for 5 min at 30°C in water bath, followed by proteinase K digestion and acidic phenol/ chloroform purification. After fragmentation, nascent RNAs with 5’-bromo-UTP were immuno-precipitated twice by using beads conjugated with an anti-BrdU antibody (Santa Cruz, sc-32323 AC). After poly-A tail addition and reverse transcription, the resulting first-strand cDNA was separated in a 10% TBE-urea polyacrylamide gel. cDNA that is 100–400 nt long was gel-recovered and self-ligated using CircLigase (Epicentre). The circularized single-stranded cDNA was relinearized with APE 1 (NEB) and then PCR-amplified using Phusion™ High-Fidelity DNA Polymerase (Thermo Scientific) at optimal cycle numbers. The PCR products were separated in a 10% native TBE polyacrylamide gel and the 140–225 bp products were recovered. All libraries were sequenced on Illumina NovaSeq 6000 platform (SE 75 bp reads).
Total RNA was extracted using RNeazy Plant Mini Kit (QIAGEN, 74904). The RNA sequencing (RNA-seq) libraries were generated using NEXTFLEX ®Rapid Directional qRNA-SeqTM Kit (Bioo Scientific, NOVA-5130-01D) according to the manufacturer’s instructions.

treatment_protocol: For heat treatment, 12-day-old wild-type Col-0 seedlings were transferred to a growth chamber set at 37°C and incubated for 30 min. For mock treatment, the seedlings were kept at the growth chamber set at 22°C and incubated for 30 min. For DC3000 treatment, whole leaves of 24-day-old soil-grown plants were syringe-infiltrated with suspensions of DC3000 at OD600 = 0.001. For mock treatment, the leaves were syringe-infiltrated with 10 mM MgSO4. The treated leaves were harvested 24 h after infiltration.

value: Columbia

value: 24 hour post DC3000 (OD=0.001) treatment


title: First_Trimester_CTB_patient_788


title: GROseq Mock_for_DC3000_rep2

value: 24 hour post 10 mM MgSO4 treatment


title: 14-48h-ZH_rep2

value: Retina

value: Zurich (400masl)


title: primary non-MCL Ccnd2/p53/Mb1Cre lymphoma oTP14b


title: 14-48h-ZH_rep5

value: hypoxia


title: primary non-MCL Ccnd2/p53/Mb1Cre transplant TP36

value: Spleen


title: ShLSD1 #1_06


title: 14-48h-ZH_rep3


title: primary non-MCL Ccnd2/p53/Mb1Cre lymphoma TP8

value: Mediastinal lymphoma


title: 14-48h-ZH_rep4


title: primary non-MCL Ccnd2/p53/Mb1Cre lymphoma TP15


title: GROseq DC3000_rep1


title: First_Trimester_CTB_patient_822

value: Male


title: WTC11 iPSCs - RNA-seq_rep2

city: SAN FRANCISCO

first: Yin

last: Shen

state: CALIFORNIA

address: 513 Parnassus Ave

department: Department of Neurology

institute: UCSF

data_processing:
Reads were trimmed to 51bp before aligning to hg38 genome assembly using STAR (v2.7.2b) with ENCODE recommended parameters
Gene expression levels (FPKM) were calculated using RSEM rsem-calculate-expression (v1.3.1) with gencode.v32 as annotation
TMM normaliztion of FPKM was performed by edgeR v3.24.3
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files of averaged FPKM values across samples

source_name: human iPSCs

growth_protocol: WTC11 iPS cells were cultured on Matrigel-coated (Corning, 354277) plates with Essential 8™ Medium (Life Technologies, A1517001). WTC11 iPSCs were passaged using Accutase (STEMCELL Technologies, 07922) and 10 μM ROCK inhibitor Y-27632 (STEMCELL Technologies, 72302).

extract_protocol:
RNA was extracted from fresh cells using the RNeasy Plus Mini Kit (Qiagen, 74134).
Approximately 1000 ng of extracted RNA was used to prepare libraries for sequencing using the TruSeq Stranded mRNA Library Prep Kit (Illumina, 20020594).

value: WTC11 iPSCs


title: Adult Brain, OmniATAC R16A06

city: LEUVEN

first: Stein

last: Aerts

address: Herestraat 49, bus 602

department: Center for Brain & Disease Research

institute: KULeuven/VIB

data_processing:
The 10X samples were each processed (alignment, barcode assignment and UMI counting) with Cell Ranger ATAC (version 1.2.0) count pipeline.
For the ATAC samples the raw reads were first filtered and scanned for adapters using fastq‐mcf from the ea‐utils package. Read quality was then checked using FastQC. The reads were mapped to the Drosophila genome (dm6) using STAR. The outputted BAM file from STAR was then indexedand sorted using SAMtools. Using genomeCoverageBed from BedTools, the BAM file was converted to a BedGraph file. For fast, visualization in the IGV GenomeBrowser, the BedGraph file was further processed to a BigWig file using bedGraphtoBigWig.
Cut&Tag samples were processed similarly to ATAC-seq samples
TaDa sequencing data were mapped back to release 6.03 of the Drosophila genome using a previously described pipelines ( Marshall and Brand, 2015). Peaks were called and mapped to genes using a custom Perl program (available at https://github.com/tonysouthall/Peak_calling_DamID)
Genome_build: dm6 (dmel_r6.16_FB2017_03)
Supplementary_files_format_and_content: gff, narrowPeak, bigWig

source_name: Adult Brain

extract_protocol:
100 GFP-expressing and 15 GFP negative fly brains were dissected in PBS on ice. The brains were then centrifuged at 800 xg for 5 min, after which the supernatant was replaced by 50 μL of dispase (3 mg/mL, Sigma-Aldrich_D4818-2mg), 75 μl collagenase I (100 mg/mL, Invitrogen_17100-017), and 125 μL trypsin-EDTA (0.05%, Invitrogen_25300054). Brains were dissociated at 25°C in a Thermoshaker (Grant Bio PCMT) for 15 min at 25°C at 1,000 rpm and the solution was mixed by pipette every 5 min. After, cell suspensions were passed through a 10 μM pluriStrainer (ImTec Diagnostics_435001050) and viability was assessed by the LUNA-FL Dual Fluorescence Cell Counter. Next, 4 aliquots were made containing GFP-brains cells with/without PI (10%) and GFP-positive brains with/without PI (10%). The GFP-negative brains were used to set the gates on the machine for cell size and viability (PI), the GFP-positive brains for the GFP fluorescence, after which the GFP positive cells with PI were sorted. Between 2.6 and 11k GFP positive cells were sorted and 50k cells per negative control. After sorting, regular omni-ATAC-seq was performed as described by Corces et al. (Corces et al., 2017).
omniATAC-seq

value: Brain

tag: developmental stage

value: Adult

tag: age

value: 3 day


title: First_Trimester_CTB_patient_793

value: cytotrophoblast

tag: trimester


title: GROseq Mock_for_DC3000_rep1

tag: treatment


title: ShLSD1 #1_04

value: mesothelioma

value: ShLSD1 #1


title: 14-06h-ZH_rep6

tag: tissue

tag: condition


title: Control_03

value: Control


title: Control_02


title: First_Trimester_CTB_patient_716

value: Female


title: Control_01


title: WTC11 iPSCs - RNA-seq_rep1


title: 14-06h-ZH_rep5


title: GROseq Heat_rep2

source_name: 12-day-old seedling

tag: genotype

value: Columbia

value: 0.5 hour post heat (37℃) treatment


title: OmniATAC_GFP_pos_MB419B

value: 1 day


title: OmniATAC_GFP_pos_MB418B


title: Cut&Tag_WTC11 iPSCs - CTCF_rep2

data_processing:
Library strategy: CUT&Tag
Sequencing reads were mapped to hg38 using bowtie2 with the following options: --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700
Picard Tools was used to remove blacklisted regions and duplicate reads
SEACR (Meers et al. 2019) was used to call peaks on merged replicates.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig file was generated with bamCoverage --binSize=1
Supplementary_files_format_and_content: Peaks called by MACS2

extract_protocol:
Cells were washed with PBS and nuclei were extracted prior to library construction.
CUT&Tag libraries were prepaed according to the published protocol (Kaya-Okur, H.S. et al. 2019).

tag: antibody


title: Cut&Tag_WTC11 iPSCs - CTCF_rep1


title: GROseq Wt_rep2


title: OmniATAC_GFP_pos_MB371B

data_processing:
The 10X samples were each processed (alignment, barcode assignment and UMI counting) with Cell Ranger ATAC (version 1.2.0) count pipeline.
For the ATAC samples the raw reads were first filtered and scanned for adapters using fastq‐mcf from the ea‐utils package. Read quality was then checked using FastQC. The reads were mapped to the Drosophila genome (dm6) using STAR. The outputted BAM file from STAR was then indexedand sorted using SAMtools. Using genomeCoverageBed from BedTools, the BAM file was converted to a BedGraph file. For fast, visualization in the IGV GenomeBrowser, the BedGraph file was further processed to a BigWig file using bedGraphtoBigWig.
Genome_build: dm6 (dmel_r6.16_FB2017_03)
81 bigwigs are attached based on samples belonging to 10X_ADULT (adult brain) and to 10X_PUPA_72H
10X_ADULT and 10X_PUPA_72H samples were subset based on cell type and merged to acquire cell type specific bam files
bam files were then deduplicated, black listed regions removed and RPGC normalised to acquire bigwig files


title: 14-06h-ZH_rep2

value: Retina

value: Zurich (400masl)


title: GROseq Heat_rep1


title: OmniATAC_GFP_neg_MB419B


title: 14-06h-ZH_rep4

value: hypoxia


title: 14-06h-ZH_rep1


title: 07-06h-ZH_rep6


title: OmniATAC_GFP_neg_MB371B


title: WTC11 iPSCs - H3K27ac_input_rep2

data_processing:
Sequencing reads were trimmed to 50 bp and mapped to hg38 using bowtie2 with the following options:--local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700.
Picard Tools was used to remove blacklisted regions and duplicate reads
MACS2 was used to call peaks on merged replicates at an FDR cutoff of 1%.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig file was generated with bamCoverage --binSize=1
Supplementary_files_format_and_content: Peaks called by MACS2

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared using Tru-seq adapters and size-selected using SPRIselect beads prior to amplification and paired-end sequencing.


title: WTC11 iPSCs - H3K27ac_rep1


title: GROseq Wt_rep1


title: Patient2834_MSC_cntrl

type: genomic

description: Genomic DNA was extracted from placental tissue or MSCs and hybridized to the Illumina InfiniumOmni2-5-8v1-4 BeadChip

hyb_protocol: Standard Illumina Protocol

scan_protocol: Arrays were imaged using Illumina's HiScan System using standard recommended Illumina scanner setting

data_processing: Samples were called in GenomeStudio (Illumina) with an average overall call rate of 99.4%. The CTB sample from one patient (1391) was removed from the analysis due to a low call rate (91.3%). CNVs were identified using the cnvPartition Plug-in (v. 3.2.0) in GenomeStudio. The cnvPartition confidence threshold was set at 100, with a minimum number of SNPs per CNV region of 10. The R (v. 3.6.1) package, allele-specific copy number analysis of tumors (ASCAT) (v. 2.5.2) (Van Loo, 2010 PMC2947907), was used to estimate the ploidy of EVT samples. LogR ratios and BAF values were exported from GenomeStudio and no GC wave correction was performed. EVT samples were considered “tumor” samples and matched UC-MSCs were used as “reference” samples.

label: Cy5 and Cy3

source_name: umbilical cord mesenchymal stem cells

label_protocol: Standard Illumina Protocol

growth_protocol: First and term placentae tissues were collected under a UCSD Human Research Protections Program Committee Institutional Review Board-approved protocol; all patients provided informed consent for collection and use of these tissues. Term placentae was obtained immediately after C-section and placed on ice. For first trimester placentae, “normal” refers to elective termination of pregnancy in the absence of structural fetal abnormalities; for third trimester placentae (term), “normal” is defined by a non-hypertensive, non-diabetic singleton pregnancy, where the placenta is normally grown and shows no gross or histological abnormalities. Human umbilical cord (UC) was collected aseptically under a protocol approved by the Human Research Protections Program Committee of the UCSD Institutional Review Board (IRB number: 181917X). All patients provided informed consent for collection and use of these tissues, and all experiments were performed within guidelines and regulations set forth by the IRB. Umbilical cord mesenchymal stem cells (UC-MSCs) were derived from minced umbilical cord tissue per a published protocol (PMID: 19657615, 25058409) from umbilical cord (UC) samples that were collected and processed within 24 hours of delivery.

extract_protocol: DNA was isolated from placental cell pellets from two first trimester and three term placentae (Qiagen DNeasy Blood and Tissue kit) and quantified (Qubit dsDNA BR Assay Kits, Thermo Fisher Scientific) according to the manufacturer’s protocol. DNA from matched UC-MSCs from the three term placental patients were isolated in the same manner.

treatment_protocol: UC’s were minced and washed to remove blood and then cultured in basal medium (aMEM with nucleotide (ThermoFisher), containing 10% MSC-qualified FBS (OmegaScientific)). Cultures were maintained in a humidified atmosphere with 5% CO2 at 37°C. Approximately three weeks after plating, adherent fibroblast-like cells were detached using TrypLE Express for 5 minutes at 37oC (ThermoFisher) and filtered to remove any tissue fragments. The collected cells were then reseeded and maintained in growth medium containing b-FGF.   After two weeks of growth with medium replacement every three days, the cells were checked for purity by flow cytometry analysis (BD FACSCanto 2 HTS). Cells were assessed for the expression of CD73 (FITC Mouse Anti-Human CD73 – BD #561254) and the absence of CD31 (APC-Cy™7 Mouse Anti-Human CD31 BD #563653) and CD45 (APC Mouse Anti-Human CD45 – BD #560973). UC-MSCs samples displayed CD73 expression in over 90% of cells and 0% expression of CD31 and CD45. Sex of first trimester cell samples was determined based on PCR for SRY. Isolation of cytotrophoblast (CTB) and extravillous trophoblast (EVT) from term placentae (37- to 41-weeks GA) was performed as previously described in (PMID: 24004950). Tissue from the basal plate (for EVT) and chorionic portion (for CTB) was dissected and minced, rinsed in 1X PBS (Corning), and digested for 20 minutes in 1X Ca/Mg-free HBSS (Gibco), 1X trypsin (Gibco), collagenase, and DNase (Roche) three times, discarding the supernatant after each digestion. A Percoll gradient (Sigma-Aldrich) centrifugation separation was then performed. Cells were then subjected to positive selection using magnetic activated cell sorting (MACS) (Miltenyi Biotec) and a PE-conjugated antibody against HLA-G (EXBIO MEM-G/9). The bound fraction was collected, tested for purity using flow cytometry. EVT preparations that contained greater than 90% HLA-G+ cells were considered as adequate and used in downstream experiments. The unbound fraction was collected and CTB were selected using APC-conjugated antibody against EGFR (Biolegend #352906;) and tested for purity using flow cytometry. CTB preparations yielding greater than 90% EGFR positivity were considered adequate and used in downstream experiments. Isolation of primary first trimester (9- to 14-week gestational age) trophoblast cells from placenta samples was performed as previously described in (PMID: 28167044, 29361559).  Briefly, chorionic villi were minced, washed in Hanks’ balanced salt solution (Gibco) and digested three times with DNase I (Roche) and trypsin (Gibco). The cells were then pelleted and separated on a Percoll gradient (Sigma-Aldrich) and subjected to sequential MACS selection similar to the term placental samples.

value: MSC

tag: ga (gestational age wks)


title: pupa12h_brain_DGRP_mix_DGRP-551_Hyb-409-502-639_sample2_seq1

source_name: Pupa Brain

extract_protocol:
D. melanogaster adult brains were dissected and transferred to a tube containing 100 µl ice cold DPBS solution. After centrifugation at 800 g for 5 min, the supernatant was replaced by 500 µl nuclei lysis buffer composed of 10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.1% Nonidet P40, 0.01% Digitonin, and 1% BSA, in Nuclease-free water. The following procedure was followed to extract the nuclei from the brain tissue: incubation in nuclei lysis buffer on ice for 5 min, transfer to a dounce tissue grinder tube (Merck), 25 strokes with pestle A, incubation on ice for 10 min, 25 strokes with pestle B. The lysis was stopped by adding 1 ml of wash buffer composed of 10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20 and 1% BSA, in Nuclease-free water. Nuclei were pelleted by centrifugation at 800 g for 5 min at 4°C and resuspended in 1x Nuclei Buffer (10x Genomics). Nuclei suspensions were passed through a 40 µM Flowmi filter (VWR Bel-Art SP Scienceware). Nuclei concentration was assessed by the LUNA-FL Dual Fluorescence Cell Counter.
10x Genomics CHROMIUM Single Cell ATAC Library & Gel Bead Kit v1

value: Pupa

value: 12 hours


title: WTC11 iPSCs - H3K27ac_input_rep1

value: WTC11 iPSCs


title: 07-06h-ZH_rep5


title: Patient2834_HLAG_EVT

source_name: term placental tissue

tag: gender

value: EVT


title: pupa12h_brain_DGRP_mix_DGRP-551_Hyb-409-502-639_sample1_seq1

value: Brain


title: Patient2834_EGFR_CTB

value: CTB


title: pupa6h_brain_DGRP_mix_DGRP-551_Hyb-409-502-639_sample2_seq1

value: 6 hours


title: 07-06h-ZH_rep4


title: 14-06h-ZH_rep3


title: Patient2771_MSC_cntrl

value: Male


title: WTC11 iPSCs - H3K27ac_rep2


title: pupa6h_brain_DGRP_mix_DGRP-551_Hyb-409-502-639_sample1_seq1


title: Patient2771_EGFR_CTB


title: subpallium of gestational week 11

city: XiaMen

first: yuan

last: yu

state: FuJian

address: JiMei Street, 668

department: Center for precision medicine

institute: HuaQiao university

data_processing:
Aligned and quantified using the Cell Ranger Single-Cell Software Suite (v.3.0.1, 10x Genomics).
Genome_build: GRCh38
Supplementary_files_format_and_content: mtx
Supplementary_files_format_and_content: tsv

source_name: human fetal tissue

extract_protocol:
Dissect human fetal subpallium tissue and digestion to prepare a single-cell suspension.
Using chromium next GEM single cell 3’ GEM protocol (Library &Gel Bead Kit v3.1, 16 rxns PN-1000121)

value: geatational week 11

value: Subpallium of fetal brain


title: 07-06h-ZH_rep2


title: 07-06h-ZH_rep1


title: pupa3h_brain_DGRP_mix_DGRP-551_Hyb-409-502-639_sample2_seq1

value: 3 hours


title: Patient2754_MSC_cntrl

value: Female


title: subpallium of gestational week 9

value: geatational week 9


title: subpallium of gestational week 12

value: geatational week 12


title: Patient2754_EGFR_CTB


title: pupa3h_brain_DGRP_mix_DGRP-551_Hyb-409-502-639_sample1_seq1


title: Human monocytes RNA-seq VACV replicate 2

city: Beijing

first: Guoqiang

last: Zhang

address: 1 Beichen West Road, Chaoyang District

institute: INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES

description: VACV treatment

data_processing:
The original data was filtered through the quality control software fastp, and the Hista2 software was used to compare with the reference gene sequence. The reference genome is Hg38. The gene information is downloaded from the NCBI database.
The featureCounts software is used to calculate the gene expression between samples. Perform gene differential expression analysis on the two sets of samples through the R package DESeq2 software.
Genome_build: Hg38
Supplementary_files_format_and_content: Txt files for the DESeq2 results of RNA-seq

source_name: Human monocytes(THP-1)

extract_protocol:
Total RNAs were isolated from embryos at the indicated stages using TRIzol reagent (TIAN GEN).
To RNA-seq,  Illumina Truseq libraries were constructed according to the manufacturer’s instructions and sequenced using NovaSeq platform. with paired end read length of 150 bp. RNA-seq library generation with NEBNext® Ultra II Directional RNA Library Prep Kit (New England Biolabs, Inc., USA).

value: monocytes (THP-1)


title: subpallium of gestational week 10

value: geatational week 10