title: ZF zygote IP 1cell Rep5

city: Ann Arbor

first: Kin Fai

last: Au

state: MI

address: 100 Washtenaw Avenue

department: Department of Computational Medicine and Bioinformatics

institute: University of Michigan

data_processing:
Quality of raw reads was assessed using FastQC (v0.11.8) and sequencing adapters were trimmed using Cutadapt (v1.8.1) if clear adapter signal was detected at the 3'end of the reads. There is no adapter removal for zebrafish zygote samples (GSM5599713, GSM5599714, GSM5599715, GSM5599716, GSM5599717, GSM5599718, GSM5599719, GSM5599720, GSM5599721, GSM5599722, GSM5599723, GSM5599724, GSM5599725), mouse polyA-selected RNA samples (GSM5599726, GSM5599727, GSM5599728, GSM5599729, GSM5599730, GSM5599731, GSM5599732, GSM5599733), and mouse MII oocyte Input sample (GSM5599734).
Trimmed reads were aligned to the reference genome (mm10 for mouse, danRer11 for zebrafish) using HISAT2 (v2.1.0) with the parameter “-5 8 --no-mixed --no-discordant”. Multiply-aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools (v1.9). The read pairs that overlapped with ribosomal RNAs were removed using BEDTools (v2.28.0).
Genome coverage bigWig files (bin size = 10 bp, normalized by RPKM) were generated by deepTools (v3.2.0) bamCoverage with the parameter “-bs 10 --normalizeUsing RPKM”.
Genome_build: mm10 for mouse, danRer11 for zebrafish
Supplementary_files_format_and_content: The bigWig files are generated by deepTools (v3.2.0) bamCoverage with the bin size=10bp and normalized by RPKM.

organism: Danio rerio

source_name: ZF zygote IP 1cell

extract_protocol:
For zebrafish bulk-zygote samples, total RNA was extracted from 100 zebrafish zygotes using TRIzol™ Reagent and eluated in 100 μl of RNase-free water. Then, 10 μl and 5 μl samples were taken for 10-zygote and 5-zygote samples, respectively, and volumes were adjusted to 12 μl with nuclease-free water. For zebrafish single-zygote samples, single zygote was manually picked and distributed into 12 μl of 1X Lysis buffer (Takara).
For the polyA-selected RNA samples of mouse liver and embryonic stem cell (WT and Mettl3 KO), total RNA was extracted using TRIzol™ Reagent (Thermo Fisher Scientific) and PolyA+ RNA was selected twice by Dynabeads™ mRNA Purification Kit (Thermo Fisher Scientific).
For mouse embryonic stem cell samples, the cells were sorted into 12 μl 1X Lysis buffer using BD FACSMelody™ Cell Sorter (BD Biosciences).
For mouse oocyte and embryo samples, after three washes in M2 medium, oocytes and embryos were manually picked and put into 12 μl 1X Lysis buffer.
For picoMeRIP-seq experiment, NEBNext® rRNA Depletion Kit (NEB) was used to delete DNA and rRNA; RNA samples were sheared by sonication, incubated with the anti-m6A antibody from Millipore (ABE572), and precipitated using ethanol.
SMART-Seq® Stranded Kit (Takara, Cat. # 634442) was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits (Roche) and the size distribution was checked using TapeStation D1000 ScreenTape (Agilent Technologies).

treatment_protocol:
For mouse GV oocyte collection, 8-week-old C57BL6/N females were injected with 5 units (U) of pregnant mare serum gonadotropin (PMSG). After 48 hours, ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium (Sigma) supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3-Isobutyl-1-methylxanthine (IBMX, Sigma) to prevent the oocytes from further progress to germinal vesicle breakdown (GVBD). The cumulus cells were gently removed by pipetting, and the oocytes were briefly exposed to acidic Tyrode's solution (Sigma) to remove the zona pellucida, followed by three washes in M2 medium.
For mouse MII oocyte collection, 4-5-week-old C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin (hCG) 45 hours later. The oviducts were dissected 20-22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells, and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida, followed by three washes in M2 medium.
For mouse early embryo collection, 8-week-old C57BL/6N females were superovulated by hormone injection (5 U PMSG followed by 5 U hCG 45 hours later) and transferred to cages with 8-week-old C57BL/6N males for mating. At 27-28 hours (zygote), 39-43 hours (2-cell), 68-70 hours (8-cell), and 92-94 hours (blastocyst) after hCG administration, the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES-buffered CZB medium, then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida, followed by three washes in M2 medium.

tag: developmental stage

value: Zygote

tag: molecule subtype

value: rRNA-free RNA


title: ZF zygote IP 1cell Rep4

status: Public on May 05 2023

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA


title: RNA_SOX9neg_rep1

city: New York

first: Yihao

last: Yang

state: NY

address: 1230 York Ave

institute: The Rockefeller University

description:
Salmon (v 1.4.0)
Tximport (v 1.12.3)
Biological replicate 1
DEG_SOX9pos_vs_SOX9neg.txt

data_processing:
FASTQ files were trimmed of barcodes using Skewer (version 0.2.2) and transcript abundance quantified using Salmon with a modified Gencode transcript index (version GRCm38 release M24) to include TRE-MYC-SOX9. Gene level counts and TPMs were calculated using the tximport package in R.
To generate gene signiture of SOX9 positive and negative placodes, DESeq2 was used to generate differentially expressed gene (DEG) list.
Assembly: mm10 (UCSC release)
Supplementary files format and content: tab-delineated text file contain calculated TPM or tab-delineated text file contain DEG results from DESeq2

organism: Mus musculus

source_name: mouse back skin

extract_protocol:
FACS-sorted EdpSCs were directly sorted into TRI Reagent, and total RNA was purified using the Direct-zol RNA kit (Zymo Research) according to the kit protocol. RNA quality was determined by Agilent 2100 Bioanalyzer.
RNA libraries were generated using SMARTer RNA kit for low input RNA-seq and sequenced on NextSeq or NovaSeq SP 50PE.

treatment_protocol: mouse was injected with doxycycline at P21 and maintained on dox feed for indicated period of time

tag: mouse strain

tag: mouse age

tag: genotype

tag: mouse sex

value: mixed

tag: sorting scheme

value: CD31/45/117/140a-neg CD49f-high PCAD-lo eGFPneg


title: ATAC_PTC_ctrl_2

city: Aachen

first: René

last: Krüger

address: Pauwelsstraße 20

department: Institute for Stem Cell Biology

country: Germany

institute: RWTH Aachen University Medical School

library_source: genomic

data_processing:
RAW reads were trimmed for Illumina adapter sequences using cutadapt version 1.18 and aligned to the GRCh38 genome using Bowtie2 version 2.3.4.1.
Reads aligned to mtDNA, low quality reads (MAPQ <30), ENCODE blacklisted regions and duplicates were removed using samtools version 1.8 and Picard version 2.25.2.
Bigwig files were generated using deeptools bamCoverage version 3.5.0, command –normalizeUsing RPGC --binsize 1.
Assembly: GRCh38
Supplementary files format and content: bigWig

molecule: genomic DNA

organism: Homo sapiens

source_name: Primary renal tubular cells

growth_protocol: Primary human tubular cells were isolated from tumor nephrectomy specimens and grown in Dulbecco’s modified Eagle’s medium/Ham’s F-12 supplemented with 2.5% (day 1) or 0% (day 2 onwards) fetal calf serum, 2 mM L-glutamine, 100 U/ml penicillin and 100 μg/ml streptomycin, 5 μg/ml insulin, 5 μg/ml transferrin, and 5ng/ml selenium (Sigma), triiodothyronine (T3, Sigma) 10 ng/ml, hydrocortisone 1 mg/ml, epidermal growth factor 100 µg/ml (Peprotech). Epithelial origin was confirmed by immunocytochemistry for N- and E-Cadherin.

extract_protocol:
The Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) was performed according to the Omni-ATAC protocol published by Corces et al. (Corces, M., Trevino, A., Hamilton, E. et al. An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat Methods 14, 959–962 (2017). https://doi.org/10.1038/nmeth.4396). In short, libraries were prepared using the Illumina Tagment DNA TDE1 Enzyme and Buffer Kit (Illumina, San Diego, CA, USA) and purified using the DNA Clean and Concentrator-5 Kit (Zymo Research, Freiburg, Germany) according to the manufacturer’s protocol. Following purification, library fragments were amplified by using the NEB Next® High-Fidelity 2X PCR Master Mix (New England Biolabs, Ipswich, UK) and custom-made indexed Nextera PCR primers (Sigma Aldrich, St. Louis, MO, USA). Libraries were amplified for a total of 8 – 12 cycles. Library clean-up and double-sided size selection was performed using AMPure XP beads (Beckman Coulter GmbH, Krefeld, Germany) according to the manufacturer’s recommendations.
ATAC-seq library preparation was carried out using the Omni-ATAC protocol. Libraries were sequenced on IlluminaNovaseq 6000 platforms following the manufacturer's protocols.

treatment_protocol: Sub-confluent cell cultures were exposed to 1 mM dimethyloxalylglycine (DMOG, Cayman) for 16h to induce HIF stabilization.

tag: cell type

value: Primary renal tubular cells

tag: treatment

value: control


title: ZF zygote IP 1cell Rep3


title: RNA_W12_rep2

description:
Salmon (v 1.4.0)
Tximport (v 1.12.3)
Biological replicate 2
D0-W12_TPM.txt

value: grafted W12

value: K14rtTA; TRE-myc-Sox9

value: male

value: CD31/45/117/140a-neg CD49f-high CD34-neg Ly6A-high


title: ATAC_PTC_ctrl_1


title: W1_H3K27ac_rep1_rep2_high_Mnase

description:
SOX9_D7_IFE_High_Low_POOL_H3K27ac_MERGE_sorted_RIP.bw
W1_barcode_high.txt

data_processing:
MINT-ChIP reads were processed with appropriate modifications made for the T7 barcode adaptor in read2 instead read 1 (van Galen et al). Reads were first demultiplexed by Illumina’s bcl2fastq2 and further demultiplexed using the additional the T7 barcode in read2 with FASTX-Toolkit.
The demultiplexed reads were aligned with Bowtie2 (v 2.2.9) to the mm10 reference genome The aligned reads were deduplicated with Picard for both PCR and IVT duplicates (v. 2.3.0). Bamfiles from biological replicates are combined with Samtools (1.9). H3K27ac peaks are called with MACS2 (v2.1.1), and H3K4me1 peaks are called with epic2 peak caller based on SICER (0.0.36).
bigwig files were generated on the combined bamfiles using deeptools (2.5.4) bamcoverage with (1,000,000/total reads in peaks) as the scale factor. For totalH3, RPKM is used for normalization.
Assembly: mm10 (UCSC release)
Supplementary files format and content: BIGWIG file generated from combined bamfiles

extract_protocol:
FACS sorted cells were used for MINT-ChIP according to van Galen et al (doi::10.1016/j.molcel.2015.11.003).
libraries are prepared according to van Galen et al (doi::10.1016/j.molcel.2015.11.003).
All libraries were sequenced on Illumina NextSeq using 40-bp paired-end reads.

treatment_protocol: Mouse was injected with doxycycline at P21 and maintained on dox feed for indicated period of time.

tag: Sex


title: RNA_W12_rep1

description:
Salmon (v 1.4.0)
Tximport (v 1.12.3)
Biological replicate 1
D0-W12_TPM.txt


title: ZF zygote IP 1cell Rep2


title: ZF zygote IP 1cell Rep1


title: nChIP U2OS WTcells H3K4me3 Rep1

first: Benjamin

middle: H

last: Weekley

address: 1470 Madison Ave

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Raw reads were trimmed to remove any adapters using Trim Galore (0.6.0)
Samples were aligned to the hg19 genome using bowtie2 (2.3.5.1) in paired end mode with the options –no-mixed and –no-discordant
Low quality reads were filtered out using Samtools (1.9) with a cutoff MAPQ of 30, and duplicated reads removed using the Picard toolkit
Unique read files were used for peak calling using MACS2 (3.0.0a6) using the callpeaks function with the options -f BAMPE -q 0.05 –min-length 147 –nomodel, using the corresponding input or control IP as -c. Narrow and broad peak calling modes were both utilized and then merged to capture all peaks.
For visualization, each sample was normalized using RPKM and genome coverage tracks (bigwig files) were produced using deepTools (3.5.1) bamCoverage function with the options –binSize 10 –smoothLength 30 and using an ENCODE hg19 blacklist file (https://doi.org/10.1038/s41598-019-45839-z) to discard regions with consistent non-specific signal
Assembly: GRCh37/hg19
Supplementary files format and content: Bigwig files for visualization (including merged MMP2-HA)
Supplementary files format and content: MACS2 called peaks (Some narrow mode only, others narrow mode and broad mode merged together)

growth_protocol: DMEM, 10% fetal bovine serum, 1X glutaMAX, 1X antibiotic-antimycotic, 1X NEAAs. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Mononucleosomes were liberated from nuclei using MNase. S1 and S2 fractions were pooled for ChIPs using the respective antibodies.
ChIP-seq liibraries were made using the NEBNext Ultra II kit from NEB, along with their multiplex primers. The manufactureres protocol followed and number of cycles determined by spike-in of SYBR for quantification

treatment_protocol: Grown to 2 days over-confluence

tag: cell line

value: Human osteosarcoma

value: WT

tag: chip antibody

value: H3K4me3 (Epicypher, 13-0041)

tag: time

value: Overconfluent


title: ZF zygote IP 5cell Rep3

source_name: ZF zygote IP 5cell


title: cultured_noHMG_dox_rep1

description:
Biological replicate 1
ATAC_KC_noHMG_D3_rep1_RPKM.bw

data_processing:
The raw sequencing reads were trimmed with skewer (v0.2.2) and aligned with Bowtie2 (v 2.2.9) to the mm10 reference genome.
The aligned reads were deduplicated with Picard (v. 2.3.0) and shifted to correct for Tn5 insertion bias.
Bamfiles from biological replicates are combined with Samtools (1.9)
Peaks were called on replicate-pooled bamfiles with MACS2 (v. 2.1.1) with default settings.
bigwig files were generated on the combinded bamfiles using deeptools (2.5.4) bamcoverage with reads in peaks as the scale factor. For cultured cell data, RPKM is used for normalization.
Assembly: GRCm38 (mm10)
Supplementary files format and content: BIGWIG files generated from combined bamfiles

source_name: keratinocytes extracted from mouse back skin

extract_protocol:
Cells were isolated by FACS into FACS sorting buffer. Cells were pelleted and lysed using 0.01% IGEPAL CA-630. ATAC libraries were prepared on these solubilized nuclei, according to Buenrostro et al. 2015.
Illumina Nextera, Buenrostro et al., 2015

treatment_protocol: Mouse was injected with doxycycline at P21 and maintained on dox feed for indicated period of time. Cells in culture are treated with 1ug/ml dox for indicated period of time

value: K14rtTA; TRE-myc-Sox9noHMG


title: RNA_W6_rep1


title: cultured_WT_nodox_rep1

description:
Biological replicate 1
ATAC_KC_WTSOX9_D0_rep1_RPKM.bw


title: cultured_WT_dox_rep1

description:
Biological replicate 1
ATAC_KC_WTSOX9_D3_rep1_RPKM.bw


title: nChIP U2OS WTcells HA Rep1


title: ATAC_PTC_DMOG_2

value: DMOG


title: RNA_SOX9neg_rep2

description:
Salmon (v 1.4.0)
Tximport (v 1.12.3)
Biological replicate 2
DEG_SOX9pos_vs_SOX9neg.txt


title: ZF zygote IP 5cell Rep2


title: nChIP Pro-MMP2-3XHA H3K4me3 Rep1

value: Pro-MMP2-3XHA stable


title: RNA_W2_rep2


title: D0_H3K4me1_rep1_rep2_high_MNase

description:
SOX9_D0_IFE_High_Low_POOL_H3K4me1_MERGE_sorted_RIP.bw
D0_barcode_high.txt


title: ZF zygote IP 5cell Rep1

value: Zygote


title: RNA_W1_rep2


title: W12_ATAC_rep1

description:
Biological replicate 1
SOX9_M3_Rep1_Rep2_dedup_sorted_PEPATAC_normalized_RIP.bw


title: RNA_W2_rep1


title: cultured_noTA_dox_rep1

description:
Biological replicate 1
ATAC_KC_noTA_D3_rep1_RPKM.bw

value: K14rtTA; TRE-myc-Sox9noTA


title: nChIP Pro-MMP2-3XHA HA Rep2

description:
nChIP_Pro-MMP2-3XHA_HA_Merged.RPKM.bs10.sl30.bw
nChIP_Pro-MMP2-3XHA_HA_Merged_MACS2_NarrowandBroadmerged.bed


title: ZF zygote IP 10cell Rep3

source_name: ZF zygote IP 10cell

value: rRNA-free RNA


title: nChIP Pro-MMP2-3XHA HA Rep3


title: ZF zygote IP 10cell Rep2


title: W6_ATAC_rep2

description:
Biological replicate 2
SOX9_W6_Rep1_Rep2_dedup_sorted_PEPATAC_normalized_RIP.bw


title: nChIP Pro-MMP2-3XHA HA Rep1


title: ZF zygote IP 10cell Rep1


title: RNA_W1_rep1


title: RNA_D0_rep2


title: W6_ATAC_rep1

description:
Biological replicate 1
SOX9_W6_Rep1_Rep2_dedup_sorted_PEPATAC_normalized_RIP.bw


title: RNA_D0_rep1


title: ZF zygote Input 10cell Rep2

source_name: ZF zygote Input 10cell


title: U2OS MMP2KD_26 OverConfluent Replicate 2 [U226_Over_Rep2]

data_processing:
Raw reads were trimmed to remove any adapters using Trim Galore (0.6.0)
Samples were aligned to the hg19 genome using STAR (2.7.3a)
Htseq(2.0.0) was used to generate raw transcript counts
Assembly: hg19
Supplementary files format and content: Tab delimited files containing gene names and HTseq counts

molecule: polyA RNA

source_name: cell line

extract_protocol:
RNA was harvested using TRIzol reagent. 1 ug of total RNA was used for PolyA selection and subsequent library prep
Libraries were constructed using the NEBNext Ultra II RNA Library Prep Kit for Illumina following the manufacturers protocol

treatment_protocol: Cells were plated at 30 % confluence (Day -2) and grown to reach confluence (2 days later, day 0) or allowed to continue to grow to become over-confluent (2 additional days, day +2). WT cells contained a blank pLKO.1 vector, while MMP-2 sh1 (23) and MMP-2 sh2 (26) cells contained shRNAs that succesfully tageted and knocked down MMP-2.

tag: tissue

value: cell line

value: OverConfluent


title: W2_ATAC_rep2

description:
Biological replicate 2
SOX9_D14_Rep1_Rep2_dedup_sorted_PEPATAC_normalized_RIP.bw


title: ZF zygote Input 10cell Rep1


title: W12_ATAC_rep2

description:
Biological replicate 2
SOX9_M3_Rep1_Rep2_dedup_sorted_PEPATAC_normalized_RIP.bw


title: U2OS MMP2KD_26 OverConfluent Replicate 1 [U226_Over_Rep1]


title: W2_ATAC_rep1

description:
Biological replicate 1
SOX9_D14_Rep1_Rep2_dedup_sorted_PEPATAC_normalized_RIP.bw


title: MS blastocyst Input 9blastocyst

source_name: MS blastocyst Input 9blastocyst

value: Blastocyst

tag: strain


title: monocyte derived macrophages from mouse ascites, ovarian tumour-bearing, bio rep4 [AeMM-4]

city: Shanghai

first: Xipeng

last: Wang

state: Shanghai

address: No. 1665, Kongjiang Road, Yangpu District, Shanghai

country: China

institute: Xinhua Hospital Affiliated to Shanghai Jiaotong University School of Medicine

description: AeMM4 in matrix of processed data

data_processing:
STAR(2.7.2a)
Data quality control was conducted by Fastp.
Trimmed sequence reads were mapped to mm10 using STAR(2.7.2a) (parameter:  --quantMode GeneCounts \--twopassMode Basic \ --outSAMtype BAM SortedByCoordinate \       --outReadsUnmapped None \ --chimSegmentMin 12 \ --chimJunctionOverhangMin 12 \--alignSJDBoverhangMin 10 \--alignMatesGapMax 100000 \--alignIntronMax 100000 \--chimSegmentReadGapMax 3 \--alignSJstitchMismatchNmax 5 -1 5 5 \ --outSAMstrandField intronMotif \ --chimOutJunctionFormat 1)
Read count extraction and normalization were performed using subread featureCounts.
Assembly: mm10
Supplementary files format and content: comma-delimited csv. files include batch-removed tpm values for each Sample

source_name: ascites

extract_protocol:
RNA was harvested using cell lysis buffer, followed by reverse transcription.The cDNA obtained by reverse transcription was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Smart-seq2 method.

value: ascites

value: monocyte derived macrophages

tag: strain  background


title: W1_ATAC_rep1

description:
Biological replicate 1
SOX9_D7_Rep1_Rep2_dedup_sorted_PEPATAC_normalized_RIP.bw

value: K14rtTA; TRE-myc-Sox9

value: male


title: monocyte derived macrophages from mouse ascites, ovarian tumour-bearing, bio rep2 [AeMM-2]

description: AeMM2 in matrix of processed data


title: MS MII oocyte Input 100cell

source_name: MS MII oocyte Input 100cell

value: MII oocyte


title: MS liver IP 100pg Rep2

source_name: MS liver IP 100pg

value: Liver


title: monocyte derived macrophages from mouse ascites, ovarian tumour-bearing, bio rep3 [AeMM-3]

description: AeMM3 in matrix of processed data


title: MS liver IP 100pg Rep1


title: U2OS MMP2KD_26 Confluent Replicate 1 [U226_Conf_Rep1]

value: Human osteosarcoma

value: Confluent


title: D0_ATAC_rep2

description:
Biological replicate 2
SOX9_D0_Rep1_Rep2_sort_dedup_sorted_PEPATAC_normalized_RIP.bw

value: CD31/45/117/140a-neg CD49f-high CD34-neg Ly6A-high


title: U2OS MMP2KD_26 Confluent Replicate 3 [U226_Conf_Rep3]


title: MS liver IP 1ng Rep2

source_name: MS liver IP 1ng


title: U2OS MMP2KD_26 Confluent Replicate 2 [U226_Conf_Rep2]


title: D0_ATAC_rep1

description:
Biological replicate 1
SOX9_D0_Rep1_Rep2_sort_dedup_sorted_PEPATAC_normalized_RIP.bw


title: embryonic derived macrophages from mouse ascites, ovarian tumour-bearing, bio rep4 [AeEM-4]

description: AeEM4 in matrix of processed data

value: embryonic derived macrophages


title: U2OS MMP2KD_26 OverConfluent Replicate 3 [U226_Over_Rep3]


title: U2OS MMP2KD_26 Proliferating Replicate 3 [U226_Prol_Rep3]

value: Proliferating


title: MS liver IP 1ng Rep1


title: embryonic derived macrophages from mouse ascites, ovarian tumour-bearing, bio rep3 [AeEM-3]

description: AeEM3 in matrix of processed data


title: W1_ATAC_rep2

description:
Biological replicate 2
SOX9_D7_Rep1_Rep2_dedup_sorted_PEPATAC_normalized_RIP.bw


title: MS liver IP 10ng Rep2

source_name: MS liver IP 10ng


title: embryonic derived macrophages from mouse ascites, ovarian tumour-bearing, bio rep2 [AeEM-2]

description: AeEM2 in matrix of processed data


title: MS liver IP 10ng Rep1


title: HeLa CENP-A TAP, siCHAF1B, Ms CENP-A

city: Chicago

first: Daniel

last: Foltz

state: IL

address: 303 E Superior St

institute: Northwestern University

data_processing:
Raw BCL output files were processed and demultiplexed using Illumina BaseSpace application Generate FASTQ version 1.0.0. Reads were trimmed from 150bp to 50bp using Illumina BaseSpace application FASTQ Toolkit v2.2.0.
Reads were trimmed for adaptor sequences using trimmomatic v0.33 with option –phred33 and then aligned to hg38 (https://www.ncbi.nlm.nih.gov/data-hub/genome/GCF_000001405.40/), CHM13v2 (https://www.ncbi.nlm.nih.gov/data-hub/genome/GCF_009914755.1/) and E.coli K12 (https://www.ncbi.nlm.nih.gov/data-hub/genome/GCF_000005845.2/) genomes, using bowtie2 v1.1.2 with options –v 2.
PCR duplicates were removed with picard MarkDuplicates v1.131.
CUT&RUN profiles were then calibrated by spike-in normalization using E. coli DNA as the internal reference or spike-in, analogous to that done for ChIP-seq (Meers et al. Elife. (2019). PMID: 31232687) to determine the normalization coefficient (NC). Spike-in normalized BigWig files were generated with deepTools bamCoverage -scaleFactor (NC) with defaults values.
Assembly: T2T-CHM13v2 and hg38
Supplementary files format and content: bigWig
Library strategy: CUT&RUN

source_name: HeLa

growth_protocol: cells were grown in DMEM supplemented with 10% fetal bovine serum and 1% pen/strep at 37°C incubator with 5% CO2

extract_protocol:
For each CUT&RUN sequencing experiment, 4 x 10^5 siRNA treated HeLaCENP-A-TAP cells were harvested at RT and resuspended in Wash Buffer (20mM HEPES-NaOH pH 7.5, 150mM NaCl, 0.5mM spermidine, 1X Roche protease inhibitor cocktail). HeLaCENP-A-TAP cells were incubated with 10uL Concanavalin A-coated magnetic beads (BioMag) in Binding Buffer (20mM HEPES-KOH pH 7.9, 10mM KCl, 1mM CaCl2, 1mM MnCl2 for 7m with rotation. The bead-cell slurry was permeabilized in Antibody buffer (20 mM HEPES-NaOH pH 7.5, 150 mM NaCl, 0.5 mM spermidine, 0.0025% digitonin, 2 mM EDTA, 0.1% BSA, 100 nM TSA, 0.1 unit/ml citrate synthase, 1 mM Oxaloacetic acid, 1x Roche protease inhibitor cocktail) and incubated with anti-CENP-A antibody (Antibody 1 = Millipore 07-574, Antibody 2 = Invitrogen MA1-20832) or IgG as a control in Antibody Buffer overnight at 4℃. Following two washes in Digitonin Buffer, beads were incubated in 50uL Digitonin Buffer (20mM HEPES-NaOH pH 7.5, 150mM NaCl, 05mM spermidine, 0.0025% digitonin, 1X protease inhibitor cocktail ) with 1x CUTANA pAG-MNase (EpiCypher 15-1016) for 1h at 4℃. The beads were washed twice in Digitonin Buffer followed by a wash in Low-Salt Wash Buffer (20mM HEPES-NaOH pH 7.5, 0.5mM spermidine, 0.0025% digitonin, 1X protease inhibitor cocktail). The beads were then incubated with ice-cold Calcium Incubation Buffer (3.5 mM HEPES-NaOH pH 7.5, 10 mM CaCl2, 0.0025% digitonin) for 30 min at  0℃. Beads were resuspended with EGTA-Stop Buffer (170 mM NaCl, 20 mM EGTA, 0.0025% digitonin, 50 μg/ml RNase A, 50pg/ml CUTANA E. coli Spike-in DNA – EpiCypher 18-1401) and incubated for 30 min at 37℃. To extract the DNA, 200ul of Oligo Binding Buffer (Zymo) was added to each sample and the total volume was then added to a Zymo-Spin DCC-5 column and centrifuged. The column was washed twice with DNA Wash buffer from the DNA Clean & Concentrator-5 Kit (Zymo). The DNA was eluted from the column in 15ul of DNA Elution Buffer and sample concentration was measured using a Qubit 3.0 fluorometer.
CUT&RUN libraries were prepared using an NEBNext Ultra II Library Kit for Illumina and NEBNext Multiplex Oligos for Illumina (Dual Index Primer Set 1) with modifications to manufacturer's protocol. Modifications: End Prep heat inactivation step was conducted at 50°C for 60 min. TheNEBNext Adaptor was diluted 1:25 in 10 mM Tris–HCl, pH 8.0 with 10 mM NaCl. After Adaptor Ligation, a DNA cleanup using 1.75× volumes of Sera-Mag Select beads was conducted. The PCR cycle conditions were programmed as following: 1 cycle: 98°C for 30s, 12cycles: 98°C for 10s, 65°C for 30s, 1 cycle: 65°C for 5m, Hold:4°C. After PCR amplification, DNA cleanup was conducted twice with 1.2× volumes of Sera-Mag Select (Cytiva) beads. Quality control was conducted on the resulting 15uL elution using Agilent 4200 TapeStation D1000 ScreenTape to determine sample concentration and sample quality.

treatment_protocol: siRNA transfections were performed using Lipofectamine RNAiMax reagent according to manufacturer's instructions and cells were collected 72h post siRNA transfection

value: HeLa

value: epithelial cells

value: TAP tagged CENP-A OE

value: hCHAF1B siRNA (Dharmacon J-019937-08-0005)

tag: cut&run antibody

value: CENP-A (mouse, Invitrogen #MA1-20832)


title: U2OS MMP2KD_26 Proliferating Replicate 1 [U226_Prol_Rep1]

value: cell line


title: embryonic derived macrophages from mouse ascites, ovarian tumour-bearing, bio rep1 [AeEM-1]

description: AeEM1 in matrix of processed data

value: ascites


title: HeLa CENP-A TAP, siCHAF1B, Rb CENP-A

value: CENP-A (rabbit, Millipore #07-574)


title: HeLa CENP-A TAP, siNT, Ms CENP-A

value: NT control siRNA (Dharmacon D-001810-10-05)


title: U2OS MMP2KD_23 OverConfluent Replicate 3 [U223_Over_Rep3]

value: OverConfluent


title: monocyte derived macrophages from mouse ascites, ovarian tumour-bearing, bio rep1 [AeMM-1]

description: AeMM1 in matrix of processed data

value: monocyte derived macrophages


title: MS liver Input 100pg

source_name: MS liver Input 100pg

value: Liver


title: U2OS MMP2KD_23 OverConfluent Replicate 2 [U223_Over_Rep2]

value: Human osteosarcoma


title: HeLa CENP-A TAP, siNT, Rb CENP-A


title: MS liver Input 10ng

source_name: MS liver Input 10ng


title: U2OS MMP2KD_23 OverConfluent Replicate 1 [U223_Over_Rep1]


title: RNA_W6_rep2

description:
Salmon (v 1.4.0)
Tximport (v 1.12.3)
Biological replicate 2
D0-W12_TPM.txt

value: K14rtTA; TRE-myc-Sox9

value: male


title: RNA-seq of K562 cells, Day 0, wild-type replicate 3

city: Cambridge

first: Richard

last: She

state: Massachusetts

address: 455 Main St Rm 639, Whitehead Institute

institute: Whitehead Institute

description:
K562_RNAseq_Table2.txt
K562_WT_rep3

data_processing:
RNA-seq sequencing reads were aligned to the human genome via STAR aligner, run with default parameters.
Counts for each transcript were then quantified by featureCounts
Assembly: hg19/GRCh37
Supplementary files format and content: tab-delimited text files include log2 fold-change between wild-type and sgRNA depleted cells

source_name: bone marrow

growth_protocol: K562 cells and Jurkat cells were grown in RPMI + 10% FBS + 1% penicillin-streptomycin-glutamine. HeLa cells were grown in DMEM + 10% FBS + 1% penicillin-streptomycin-glutamine.

extract_protocol:
Cell pellets were lysed with Trizol and RNA was extracted with the Zymo direct-zol RNA miniprep kit
RNA-seq libraries were constructed with the Illumina TruSeq Stranded Total RNA kit.

value: bone marrow

value: K562 cell line

value: chronic myelogenous leukemia (CML)

value: WT

value: Day 0


title: CHO_LAC_rep3

first: Nissim

last: Hay

address: 900 South Ashland Ave

department: BMG

institute: University of Illinois Chicago

data_processing:
Quality check was done using FastQC v0.11.8
Sequenced reads were trimmed using cutadapt v1.18, then mapped to CHOK1GS (Ensembl) using STAR v2.7.0a
Read counts were quantified by featureCount v2.0.1 and normalized to counts per million reads (CPM) using edgeR v3.8
Assembly: CHOK1GS
Supplementary files format and content: tab delimited-text file including CPM values from each sample

organism: Cricetulus griseus

source_name: MI5-4 (CHO)

growth_protocol: MI5-4 CHO cells were cultured in Minimum Essential Medium alpha containing 1,000 mg/L glucose supplemented with 10% fetal bovine serum and 1% penicillin‒streptomycin at 37 °C in a humidified atmosphere with 5% CO2.

extract_protocol:
Total RNA was extracted from MI5-4 CHO cells using a Direct-zol RNA MicroPrep Kit. The RNA purity, concentration, and integrity were evaluated with an Agilent TapeStation 4200.
RNA libraries were prepared using a Nugen Universal Plus mRNA-seq library preparation kit.

treatment_protocol: EV cells were treated 10 mM sodium lactate for 24 h.

value: MI5-4 (CHO)


title: RNA-seq of K562 cells, Day 5, eIF3D sgRNA, replicate 3

description:
K562_RNAseq_Table2.txt
K562_sgEIF3D_rep3

value: eIF3D sgRNA

value: Day 5 post lentivirus infection


title: CHO_LAC_rep2


title: U2OS MMP2KD_23 Confluent Replicate 3 [U223_Conf_Rep3]

value: cell line

value: Confluent


title: U2OS MMP2KD_23 Confluent Replicate 2 [U223_Conf_Rep2]


title: Ob_1h_after_MMTT_7

city: Moscow

first: Pavel

last: Makhnovsky

address: 76A Khoroshevskoye shosse

country: Russia

institute: Institute of Biomedical Problems of the Russian Academy of Sciences

data_processing:
Adapter sequences and low quality reads were trimmed using the Timmomatic tool (v0.36) (options:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:35)
High-quality reads were aligned to the reference human GRCh38.p13 primary assembly genome using HISAT v2.1.0
Uniqe reads were counted for known exons of each gene using Rsubread package (R) and Ensembl annotation (GRCh38.101)
TPM values calculated using kallisto v0.44.0
Assembly: GRCh38.p13 primary genome assembly
Supplementary files format and content: tab-delimited text files: Read_counts.txt — uniquely aligned read counts for genes

source_name: musculus vastus lateralis

extract_protocol:
A frozen muscle sample (~10-15 mg) was lysed by the RLT buffer (Qiagen, Germany) using a drill homogenizer and total RNA was extracted by a silica spin column (CleanRNA Standard, Evrogen, Russia). RNA concentration and integrity were evaluated by a fluorimetric assay (Qubit 4, ThermoScientific, USA) and capillary electrophoresis (TapeStation, Agilent, Germany), respectively.
Strand-specific libraries were prepared by the NEBNext Ultra II Directional RNA Library Preparation kit (NEB, USA)

treatment_protocol: Seven healthy subjects, 7 obese patients, and 7 obese patients with T2D were involved in the study.  Subjects arrived at the laboratory at 09:00 after 12 h overnight fast. The venous blood was drawn from the v. intermedia cubiti using catheter prior to, and at 30, and 60 min after the mixed meal tolerant test (MMTT; nutritional drink Resource 2.0 [Nestle Health Science, France], 3 ml/kg of body mass, protein:lipid:carbohydrate 9:9:21, 840 kJ/100 ml). The plasma concentration of glucose and glycated hemoglobin was evaluated using an automatic analyzer Architect c8000 (Abbott Diagnostics, USA) and by HPLC (analyzer D10, BioRad, USA); the serum concentration of insulin and C-peptide was evaluated using an automatic analyzer Cobas 6000 (Roche, Switzerland). Biopsy samples were taken under local anesthesia (2 ml 2% lidocaine) using a modified Bergström needle with manual suction from the left vastus lateralis muscle prior to and after the MMTT.

value: musculus vastus lateralis

tag: individual

value: MMTT

tag: time point

value: 1 hour after treatment

tag: age

tag: diagnosis

value: Obesity

tag: bmi

tag: fasting glucose,_mm

tag: fasting insulin,_miu/l

tag: fasting c-peptid,_ng/ml

tag: hba1c, %

tag: homa ir


title: Ob_before_MMTT_7

tag: Sex

tag: treatment

value: No treatment

value: before treatment


title: U2OS MMP2KD_26 Proliferating Replicate 2 [U226_Prol_Rep2]

tag: cell line

tag: cell type

value: Human osteosarcoma

tag: time

value: Proliferating


title: Ob_1h_after_MMTT_6

tag: tissue

value: female


title: RNA-seq of K562 cells, Day 5, eIF1A sgRNA

description:
K562_RNAseq_Table1.txt
K562_sgEIF1A

value: bone marrow

value: K562 cell line

value: chronic myelogenous leukemia (CML)

tag: genotype

value: eIF1A sgRNA


title: Ob_before_MMTT_6

tag: individual


title: RNA-seq of K562 cells, Day 5, ZNF324 sgRNA

description:
K562_RNAseq_Table1.txt
K562_sgZNF324

value: ZNF324 sgRNA


title: U2OS MMP2KD_23 Confluent Replicate 1 [U223_Conf_Rep1]


title: RNA_PTC_DMOG_1

data_processing:
RAW reads were trimmed for Illumina adapter sequences using cutadapt version 1.18 and then aligned to the GRCh38 genome using STAR version 2.6.1c.
Bigwig files were generated using deeptools bamCoverage version v3.5.0, command –normalizeUsing BPM--binsize 1.
Assembly: GRCh38
Supplementary files format and content: bigWig

source_name: Primary renal tubular cells

extract_protocol:
RNA was isolated using the peqGold total RNA kit (VWR Peqlab, Erlangen, Germany) according to the manufacturer´s protocol.
Novogene NGS DNA Library Prep Set (Cat No.PT004). Libraries were sequenced on IlluminaNovaseq 6000  (Illumina).

value: Primary renal tubular cells

value: DMOG


title: CHO_WTHK2_rep3

value: MI5-4 (CHO)


title: Ob_1h_after_MMTT_5

value: musculus vastus lateralis

tag: time point


title: CHO_WTHK2_rep2


title: U2OS MMP2KD_23 Proliferating Replicate 3 [U223_Prol_Rep3]

value: cell line


title: Ob_before_MMTT_5

tag: age


title: U2OS MMP2KD_23 Proliferating Replicate 2 [U223_Prol_Rep2]


title: RNA-seq of Jurkat cells, Day 5, eIF3D sgRNA

description:
K562_RNAseq_Table2.txt
Jurkat_sgEIF3D

source_name: peripheral blood

value: peripheral blood

value: Jurkat cell line

value: immortalized T lymphocytes

value: eIF3D sgRNA

value: Day 5 post lentivirus infection


title: RNA-seq of HeLa cells, Day 0, WT

description:
K562_RNAseq_Table2.txt
HeLa_WT

source_name: cervical tissue

value: cervical tissue

value: HeLa cell line

value: cervical cancer cell

value: WT

value: Day 0


title: Ob_1h_after_MMTT_4

value: female

value: MMTT

value: 1 hour after treatment

tag: diagnosis

value: Obesity


title: CHO_WTHK2_rep1

value: MI5-4 (CHO)


title: Ob_before_MMTT_4

value: musculus vastus lateralis

value: No treatment

value: before treatment

tag: bmi


title: U2OS MMP2KD_23 Proliferating Replicate 1 [U223_Prol_Rep1]

value: cell line

value: Human osteosarcoma

value: Proliferating


title: CHO_EV_rep2


title: CHO_LAC_rep1


title: RNA-seq of HeLa cells, Day 5, eIF3D sgRNA

description:
K562_RNAseq_Table2.txt
HeLa_sgEIF3D

value: eIF3D sgRNA

value: Day 5 post lentivirus infection


title: Ob_1h_after_MMTT_3

value: male

tag: fasting glucose,_mm


title: U2OS WT OverConfluent Replicate 2 [U2WT_Over_Rep2]

value: OverConfluent


title: Ob_before_MMTT_3

tag: fasting insulin,_miu/l


title: CHO_EV_rep1


title: Pre-kill_Daudi-Cas9

city: San Francisco

first: Alexander

last: Marson

state: CA

address: 1650 Owens St

institute: Gladstone-UCSF Institute of Genomic Immunology

data_processing:
Library strategy: CRISPR screen
A table of individual guide abundance in each sample was generated using the count command in MAGeCK (version 0.5.8).
Genome_build: None
Supplementary_files_format_and_content: Count of guide RNAs.

organism: synthetic construct

source_name: Daudi-Cas9 cells

growth_protocol: Daudi-Cas9 cells (gift from Benjamin Gewurz) were cultured in RPMI 1640 (Gibco) supplemented with 10% FBS, 2 mM L-glutamine (Lonza), and 100 U/mL Penicillin-Streptomycin. Cells were confirmed to be negative for mycoplasma with a PCR method. For two weeks prior to lentiviral gRNA delivery, Daudi-Cas9 cells were cultured in complete RPMI supplemented with 5 μg/ml blasticidin (Thermo Fisher) (cRPMI+Blast). On the day of lentiviral transduction, 250 million Daudi-Cas9 cells were resuspended in cRPMI+Blast at 3 million cells/mL, supplemented with 4 μg/mL Polybrene (Sigma-Aldrich), and aliquoted into 6-well plates (2.5 mL per well). Each well of cells received 6.25 µL of lentiviral genome-wide KO CRISPR library, and the plates were centrifuged at 300xg for 2 hours at 25°C. After the centrifugation, the cells were rested at 37°C for 6 hours, the media was replaced with cRPMI+Blast with cells seeded at 0.3 million/mL, and the cells were cultured at 37°C for 3 days. Three days after transduction, Daudi-Cas9 cells were diluted to 0.3x106 cells/mL and treated with 5 ug/mL puromycin (Thermo Fisher). At this time point, the infection rate was determined to be 21% by staining cells with the 7-AAD viability dye (BioLegend) in FACS buffer (PBS, 0.5% bovine serum albumin [Sigma], 0.02% sodium azide) and assessing levels of BFP+ cells on the Attune NxT flow cytometer (Thermo Fisher). After four days of antibiotic selection, Daudi-Cas9 cells were placed in complete RPMI without blasticidin or puromycin. Puromycin-selected cells were >90% BFP+, as measured by flow cytometry following a viability stain. From this point onwards, Daudi-Cas9 cells were passaged every 2 to 3 days, maintaining at least 45x106 cells at each passage to retain sufficient knockout library diversity (>495X coverage per gRNA in the genome-wide knockout library).4 For 24 hours prior to the co-culture with expanded gd T cells, genome-wide knockout library Daudi-Cas9 cells were treated with 50 µM of zoledronate (Sigma-Aldrich). Residual cells in leukoreduction chambers of Trima Apheresis from de-identified donors (Vitalant, San Francisco, CA) were used as the source of primary cells for the co-culture screen. Primary human peripheral blood mononuclear cells (PBMCs) were isolated using Lymphoprep (STEMCELL) and SepMate-50 PBMC Isolation Tubes (STEMCELL). To expand Vg9Vd2 T cells, PBMCs were resuspended in cRPMI with 100 U/mL human IL-2 and 5 µM zoledronate. PBMC cultures were supplemented with 100 U/mL IL-2 at 2, 4, and 6 days after seeding the cultures. After 8 days of Vg9Vd2 T cell expansion, gd T cells were isolated following the manufacturer’s instructions using a custom human gd T cell negative isolation kit without CD16 and CD25 depletion (STEMCELL).

extract_protocol:
Cell pellets were lysed overnight at 66°C in 400 µL of cell lysis buffer (1% SDS, 50 mM Tris, pH 8, 10 mM EDTA) and 16 µL of sodium chloride (5 M), with 2.5 million cells per 416-µL lysis reaction. 8 µL of RNase A (10 mg/mL, Qiagen) was added to the cell lysis solution and incubated at 37°C for 1 hour. 8 µL of Proteinase K (20 mg/mL, Ambion) was then added and incubated at 55°C for 1 hour. 5PRIME Phase Lock Gel – Light tubes (Quantabio) were prepared by spinning the gel at 17,000xg for 1 minute. Equal volumes of the cell lysis solution and Phenol:Chloroform:Isoamyl alcohol (25:24:1, saturated with 10 mM Tris, pH 8.0, 1 mM EDTA, Sigma) were added to a 5PRIME Phase Lock Gel – Light tube. The tubes were vigorously inverted and centrifuged (17,000xg, 5 min, room temperature). The aqueous layer containing the genomic DNA above the gel was poured into DNA LoBind tubes (Eppendorf). 40 µL of sodium acetate (3 M), 1 µL of GenElute-LPA (Sigma-Aldrich), and 600 µL of isopropanol were added, and the solution was vortexed and frozen at -80°C. Once thawed, the solution was centrifuged at 17,000xg for 30 minutes at 4°C. After discarding the supernatant, the DNA pellet was washed with fresh room temperature ethanol (70%) and mixed by inverting the tube. The solution was then centrifuged at 17,000xg for 5 minutes at 4°C. The supernatant was removed and the DNA pellet was left to air dry for 15 minutes. The DNA Elution Buffer (Zymo Research) was added to the DNA pellet and incubated for 15 minutes at 65°C to resuspend the genomic DNA.
A two-step PCR method was used to amplify and index the genomic DNA samples for Next Generation Sequencing (NGS). For the first PCR reaction, 10 µg of genomic DNA was used per 100-µL reaction (0.75 µL of Ex Taq polymerase, 10 µL of 10x ExTaq buffer, 8 µL of dNTPs, 0.5 µL of primer #1 (100uM), and 0.5 µL of primer #2 (100uM)) to amplify the integrated gRNA. The PCR #1 program was 5 min at 95°C; 28 cycles of 30 sec at 95°C, 30 sec at 53°C, 20 sec at 72°C; 10 min at 72°C. The PCR product solution was treated with SPRI purification (1.0X), and the DNA was eluted in 100 µL of water. To index the samples, 2 µL of purified PCR product (1:20 dilution) was used in a 50-µL PCR reaction containing 25 µL of Q5 Ultra II 2X MasterMix (NEB), 1.25 µL of Nextera i5 indexing primer (10 µM), and 1.25 µL of Nextera i7 indexing primer (10uM). The PCR #2 program was 3 min at 98°C; 10 cycles of 10 sec at 98°C, 10 sec at 62°C, 25 sec at 72°C; 2 min at 72°C. The final PCR product was treated with SPRI purification (0.7X), including two washes in 80% ethanol. DNA was eluted in 15 µL of water. The concentration was determined using a Qubit fluorometer (Thermo Fisher), and the library size was confirmed by gel electrophoresis and Bioanalyzer (Agilent). All indexed samples were pooled in equimolar amounts and analyzed by NGS.

treatment_protocol: Both Daudi-Cas9 cells and isolated gd T cells were resuspended at 2 million cells/mL in cRPMI. For each donor, T cells and Daudi-Cas9 cells were mixed at effector-to-target (E:T) ratios of 1:2 and 1:4. Cultures were supplemented with 5 µM zoledronate and 100 U/mL IL-2. Surviving Daudi-Cas9 cells were harvested after 24 hours of co-culturing with gd T cells. Using the manufacturer’s depletion protocol, the cell mixture was treated with the EasySep Human CD3 Positive Isolation Kit II (STEMCELL). Daudi-Cas9 cells were cultured in cRPMI+Blast for 4 days after isolation from the T cell co-culture and frozen down as cell pellets, which were used to generate sequencing libraries.

value: Daudi-Cas9 cells


title: RNA-seq of Jurkat cells, Day 0, WT

description:
K562_RNAseq_Table2.txt
Jurkat_WT

value: peripheral blood

value: Jurkat cell line

value: immortalized T lymphocytes

value: WT

value: Day 0


title: CRISPR_Donor3_E:T_1:2


title: U2OS WT OverConfluent Replicate 1 [U2WT_Over_Rep1]

source_name: cell line


title: Ob_1h_after_MMTT_2

value: female

value: MMTT

value: 1 hour after treatment

value: Obesity

tag: fasting c-peptid,_ng/ml


title: CHO_SAHK2_IgG

data_processing:
Quality check was done using FastQC v0.11.8
Sequenced reads were mapped to CHOK1GS (Ensembl) using Bowtie2 v2.4.2
Mapped reads with a MAPQ lower than 2 were filtered and sorted by samtools v1.10
Conversion of sorted bam files into bedgraph files was done using bedtools v2.30
Peaks were called using SEACR v1.3
Bigwig files were generated using deepTools v2.0
Assembly: CHOK1GS
Supplementary files format and content: bigwig files RPKM normalized by deepTools

extract_protocol:
MI5-4 CHO cells were incubated with NE1 buffer on ice for 10 min. After collecting nuclear pellets, concanavalin A-coated magnetic beads were mixed and incubated for 10 min at RT. Next, the unbound supernatant was removed, and the bead-bound cells were resuspended in antibody buffer. Anti-H3K18la (PTM-1406, PTM Biolabs), anti-H3K18ac (ab1191, Abcam), and anti-IgG negative control (13-0042, EpiCypher) antibodies were added, and incubated on a nutator overnight at 4 °C. The primary antibodies were removed, and incubation with 0.5 ug of secondary antibody was performed on a nutator for 1 h at RT followed by incubation with pAG-Tn5 in 300-wash buffer for 1 h at RT. The bead/nucleus pellet was resuspended in tagmentation buffer, and the mixture was incubated for 1 h at 37 °C. Next, the bead/nucleus pellet was resuspended in TAPS buffer. The bead/nucleus pellet was then resuspended in SDS release buffer and incubated for 1 h at 58 °C. Next, SDS quenching buffer was added.
To amplify the libraries, 2 ul of a universal i5 and a uniquely barcoded i7 primer (10 uM stocks) were added. A volume of 25 ul of NEBNext High-Fidelity 2x PCR Master mix was added and mixed. The samples were placed in athermocycler with aheated lid using the following cycling conditions: 58 °C for 5 min; 72 °C for 5 min; 98 °C for 45 sec; 14 cycles of 98 °C for 15 sec and 60 °C for 10 sec; final extension at 72 °C for 1 min; and hold at 8 °C. Post-PCR clean-up was performed by adding 1.3x AMPure XP beads, and the libraries were incubated with the beads for 10 min at RT, washed twice gently in 80% ethanol, and eluted in 15 ul of 10 mM Tris pH 8.0. The tubes were placed on a magnetic stand, and the liquid was withdrawn into a fresh tube.

value: MI5-4 (CHO)

tag: antibody

value: IgG


title: U2OS WT Confluent Replicate 3 [U2WT_Conf_Rep3]

value: cell line

value: Human osteosarcoma

value: Confluent


title: Ob_before_MMTT_2

value: musculus vastus lateralis

value: No treatment

value: before treatment

tag: hba1c, %

tag: homa ir


title: U2OS WT Confluent Replicate 2 [U2WT_Conf_Rep2]


title: CHO_EV_IgG


title: CHO_EV_rep3


title: CRISPR_Donor1_E:T_1:4

value: Daudi-Cas9 cells


title: CRISPR_Donor2_E:T_1:4


title: CHO_WTHK2_IgG


title: Ob_1h_after_MMTT_1

tag: Sex

value: male

tag: treatment


title: CRISPR_Daudi_3_BTN3A_High

growth_protocol: Daudi-Cas9 cells (gift from Benjamin Gewurz) were cultured in RPMI 1640 (Gibco) supplemented with 10% FBS, 2 mM L-glutamine (Lonza), and 100 U/mL Penicillin-Streptomycin. Cells were confirmed to be negative for mycoplasma with a PCR method. For two weeks prior to lentiviral gRNA delivery, Daudi-Cas9 cells were cultured in complete RPMI supplemented with 5 μg/ml blasticidin (Thermo Fisher) (cRPMI+Blast). On the day of lentiviral transduction, 250 million Daudi-Cas9 cells were resuspended in cRPMI+Blast at 3 million cells/mL, supplemented with 4 μg/mL Polybrene (Sigma-Aldrich), and aliquoted into 6-well plates (2.5 mL per well). Each well of cells received 6.25 µL of lentiviral genome-wide KO CRISPR library, and the plates were centrifuged at 300xg for 2 hours at 25°C. After the centrifugation, the cells were rested at 37°C for 6 hours, the media was replaced with cRPMI+Blast with cells seeded at 0.3 million/mL, and the cells were cultured at 37°C for 3 days. Three days after transduction, Daudi-Cas9 cells were diluted to 0.3x106 cells/mL and treated with 5 ug/mL puromycin (Thermo Fisher). At this time point, the infection rate was determined to be 21% by staining cells with the 7-AAD viability dye (BioLegend) in FACS buffer (PBS, 0.5% bovine serum albumin [Sigma], 0.02% sodium azide) and assessing levels of BFP+ cells on the Attune NxT flow cytometer (Thermo Fisher). After four days of antibiotic selection, Daudi-Cas9 cells were placed in complete RPMI without blasticidin or puromycin. Puromycin-selected cells were >90% BFP+, as measured by flow cytometry following a viability stain. From this point onwards, Daudi-Cas9 cells were passaged every 2 to 3 days, maintaining at least 45x106 cells at each passage to retain sufficient knockout library diversity (>495X coverage per gRNA in the genome-wide knockout library). Cells were sorted 14 days after transduction.

treatment_protocol: The screen was performed with 3 replicates of Daudi-Cas9 cell pools, each starting with 250 million cells, that were kept entirely separate starting with the lentiviral transduction step. All the replicates had an infection rate of 23-25%. Per replicate, 180 million Daudi-Cas9 cells were stained with the 7-AAD (Tonbo) viability dye and the anti-BTN3A1-Alexa Fluor 647 antibody (clone BT3.1, 1:40 dilution) (Novus Biologicals) 14 days after lentiviral transduction. Live BTN3A-high (top ~25%) and BTN3A-low (bottom ~25%) Daudi-Cas9 cells were sorted using FACSAria II, FACSAria III, and FACSAria Fusion (BD Biosciences) cell sorters. Each sorted population had between 12 and 23 million cells. Cell pellets were frozen and used to generate sequencing libraries. The final library was sequenced using a NovaSeq 6000 S4 PE150 kit (Illumina).

tag: cell type

tag: phenotype

value: high BTN3A


title: U2OS WT OverConfluent Replicate 3 [U2WT_Over_Rep3]

tag: tissue

tag: cell line

tag: time

value: OverConfluent


title: CHO_SAHK2_H3K18ac_rep2


title: U2OS WT Proliferating Replicate 3 [U2WT_Prol_Rep3]

value: Proliferating


title: U2OS WT Confluent Replicate 1 [U2WT_Conf_Rep1]


title: CRISPR_Daudi_3_BTN3A_Low

value: low BTN3A


title: Ob_before_MMTT_1

tag: individual

tag: time point


title: CHO_SAHK2_H3K18ac_rep1


title: U2OS WT Proliferating Replicate 2 [U2WT_Prol_Rep2]


title: H_1h_after_MMTT_7

value: female

value: MMTT

tag: age

tag: diagnosis

value: Metabolically healthy


title: CRISPR_Daudi_2_BTN3A_High


title: CHO_SAHK2_H3K18la_rep2

value: MI5-4 (CHO)


title: H_before_MMTT_7

tag: bmi

tag: fasting glucose,_mm


title: U2OS WT Proliferating Replicate 1 [U2WT_Prol_Rep1]


title: H_1h_after_MMTT_6

value: 1 hour after treatment

tag: fasting insulin,_miu/l

tag: fasting c-peptid,_ng/ml


title: CHO_SAHK2_H3K18la_rep1

tag: antibody


title: CRISPR_Daudi_2_BTN3A_Low


title: CRISPR_Daudi_1_BTN3A_High


title: SLC25A1 Guide 6 treateded with FSK

city: Minneapolis

first: Micah

last: Gearhart

state: MN

address: 6-160 Jackson Hall, 321 Church St.

department: Genetics, Cell Biology and Development

institute: University of Minnesota

data_processing:
Primary analysis and de-multiplexing was performed using Illumina’s bcl2gastq v2.20. 2x150bp FastQ paired-end reads for 12 samples (n=54.6 Million average per sample) were trimmed using Trimmomatic (v0.33) enabled with the optional “-q” option; 3bp sliding-window trimming from 3’ end requiring minimum Q30.
Read mapping was performed via Hisat2 (v2.1.0) using the human genome (GRCh38) as reference
Gene quantification of Ensembl v97 annotations was completed using Subread.
Counts were normalized using the median ratio method and differentially expressed genes were identified using the Wald test in DeSeq2
Assembly: GRCh38
Supplementary files format and content: Tab-separated table of integer counts

growth_protocol: BeWo cells were purchased from ATCC and maintained in culture with equal parts F12K (ATCC) (supplemented with 10% Fetal Bovine Serum (FBS, Atlantic Biologics), Penicillin-Streptomycin (Life Technologies)) and DMEM Complete (4.5 g/L glucose, Life Technologies) (supplemented with glutamine (LifeTechnologies), sodium pyruvate (LifeTechnologies), 10% fetal bovine serum (Atlantic Biologics), and Penicillin-Streptomycin (Life Technologies)).

extract_protocol:
RNA was harvested using Quick-RNA MiniPrep (Zymo).
Libraries were created using Illimunia TruSeq RNA sample preparation (Cat. # RS-122-2101) kit following manufacturer’s instructions.

treatment_protocol: To induce syncytialization, BeWo cells were cultured for 24 hours on tissue culture treated plates and DMSO (vehicle control, 0.4%) or 40 uM forskolin (Sigma) was added. Media and treatment were replaced at 24 hours during syncytialization and cells were harvested for analysis 48 hours after treatment.

value: cell line

value: BeWo (ATCC CCL-98)

value: choriocarcinoma

tag: genotype

value: SLC25A1 KO

value: 40 uM forskolin for 48 hours


title: H_before_MMTT_6

value: musculus vastus lateralis

tag: Sex

value: No treatment

value: before treatment

tag: hba1c, %

tag: homa ir


title: CHO_WTHK2_H3K18ac_rep2


title: SLC25A1 Guide 6 treateded with DMSO

tag: cell type

tag: treatment

value: DMSO (vehicle) for 48 hours


title: CRISPR_Daudi_1_BTN3A_Low

value: Daudi-Cas9 cells

tag: phenotype


title: H_1h_after_MMTT_5

tag: tissue


title: CHO_WTHK2_H3K18ac_rep1

tag: cell line


title: SLC25A1 Guide 4 treateded with FSK


title: SLC25A1 Guide 4 treateded with DMSO


title: H_1h_after_MMTT_4

value: male

tag: individual

tag: time point


title: CHO_WTHK2_H3K18la_rep1


title: CHO_WTHK2_H3K18la_rep2


title: SLC25A1 Guide 3 treateded with FSK


title: H_before_MMTT_4

tag: age

tag: diagnosis


title: SLC25A1 Guide 3 treateded with DMSO


title: H_1h_after_MMTT_3

tag: bmi

tag: fasting glucose,_mm


title: CHO_EV_H3K18ac_rep1


title: Non-Targeting Guide 4 treated with FSK

value: wild type


title: H_before_MMTT_3

tag: fasting insulin,_miu/l

tag: fasting c-peptid,_ng/ml


title: CHO_EV_H3K18ac_rep2

tag: antibody


title: Non-Targeting Guide 4 treated with DMSO

tag: genotype


title: CHO_EV_H3K18la_rep1


title: H_1h_after_MMTT_2

tag: Sex

tag: hba1c, %


title: Non-Targeting Guide 1 treated with FSK

tag: cell type


title: Non-Targeting Guide 1 treated with DMSO

tag: treatment


title: H_before_MMTT_5

value: female

tag: homa ir


title: H_1h_after_MMTT_1

tag: tissue

value: MMTT


title: H_before_MMTT_2

value: Metabolically healthy


title: Control Cells treated with FSK

tag: cell line


title: LexA shRNA day 30 biol rep 3

city: West Lafayette

first: Sarah

last: McGovern

state: IN

address: Department of Biochemistry

department: Biochemistry

institute: Purdue University

data_processing:
Trimming using Trimmomatic v0.39 to remove low-quality reads >36bp
HISAT2 used to align reads to Drosophila genome (Drosophila_melanogaster.BDGP6.28)
count.txts obtained using Htseq
RUVSeq v1.24.0 used to account.txt for variation between RNAi lines and batch effects, k=4
Assembly: Drosophila_melanogaster.BDGP6.28
Supplementary files format and content: tab-delimited text files with FBgn and CPM

molecule: nuclear RNA

organism: Drosophila melanogaster

source_name: male outer photoreceptors

growth_protocol: 25C 30 days post-eclosion raised 12h light: 12h dark cycle.

extract_protocol:
RNA was extracted using the Direct-zol RNA MicroPrep kit (Zymo, Irvine, CA, USA, Cat # R2050) with DNase I treatment
RNA-seq libraries were constructed using the Universal RNA-Seq Library Preparation Kit with Drosophila specific rRNA depletion (Tecan Genomics, Zurich, CH, Cat# 0520-A01) using 10 ng of RNA to generate each library

treatment_protocol: Nuclei were extracted from outer photoreceptors using nuclei immunoenrichment (https://www.protocols.io/view/in-vivo-tissue-specific-chromatin-profiling-in-dro-kxygxp1d4l8j/v1)

value: outer photoreceptor neurons

value: Rh1-GFPKASH, Rh1-Gal4>sh-LexA

value: day 30


title: H_before_MMTT_1

tag: individual


title: LexA shRNA day 30 biol rep 2


title: Control Cells treated with DMSO

value: cell line

value: BeWo (ATCC CCL-98)


title: LexA shRNA day 30 biol rep 1


title: T2D_1h_after_MMTT_7

tag: time point

value: 1 hour after treatment

value: T2D, Obesity


title: Cdk12 shRNA day 30 biol rep 3

value: Rh1-GFPKASH, Rh1-Gal4>sh-Cdk14

tag: age


title: WAPL_KD_Hi-C_r2

city: Philadelphia

middle: Sungjoo

last: Park

state: PA

address: 415 Curie Blvd

department: Genetics

institute: University of Pennsylvania

description: JoyceLab_E71_WAPL_MERGED_hic2cool_5kb_KR_allChr.cool

data_processing:
ChIP-seq:Sequencing quality was examined using FastQC (v0.11.9) to ensure that the library GC% and duplication rate were within expected range and adapters were effectively trimmed. Trimming was performed with Trimmomatic (v0.38) using a sliding window of four bases and a minimum average quality score of 20; reads shorter than 20 base pairs were discarded. Remaining reads were aligned against the GRCh38 reference genome using Bowtie2 (v2.4.1) allowing soft clipping ("--local") with the "sensitive local" preset options. Alignments were then filtered for duplicates using the Picard (v2.27.1) "MarkDuplicates" tool. Alignments that mapped to ENCODE blacklisted regions were also removed for downstream analysis using BEDtools v2.30.0.
ChIP-seq:Visualization tracks were generated using the deepTools (v3.3.1) "bamCompare" utility, in which  corresponding input controls were subtracted from IP and reads with a MAPQ score lower than 20 were discarded. Peaks were called for IP libraries against their corresponding input controls using MACS2 (v2.1.1), with default parameters and a 0.01 q-value cutoff. Lost, retained, and gained sites in GSK3A KD were determined with DiffBind v3.6.2 using the DESeq2 analysis method, a false-discovery cutoff of 0.1, and only reads with a minimum MAPQ score of 20. Example ChIP-seq tracks were generated in PyGenomeTracks v3.6.
Hi-C:Raw reads for each Hi-C sample were processed with HiC-Pro (version 2.11.1) to obtain putative interactions with default parameters except LIGATION_SITE = GATCGATC and GENOME_FRAGMENT generated for MboI restriction enzyme. For downstream analyses, ValidPairs were converted to hic files using the “hicpro2juicebox.sh” in utils of HiC-Pro. We recovered the following number of contacts in each condition: Control (507359205), GSK3A KD (445835605).
Assembly: hg38
Supplementary files format and content: ChIP-seq: Bigwig files were generated using BEDtools (v2.27.1) on each biological replicate; bed files of peaks for each biological replicate were called with MACS2 (v2.1.1), with default parameters and a 0.01 q-value cutoff
Supplementary files format and content: Hi-C: .hic files for each condition were generated using HiC-Pro (version 2.11.1) and converted to .cool files using Cooltools

growth_protocol: We obtained the HCT-116 cell line from ATCC (RRID:CVCL_0291). All cells were cultured in McCoy’s 5A medium supplemented with 10% fetal bovine serum, 2 mM l-glutamine, 100 U ml−1 penicillin, and 100 μg ml−1 streptomycin at 37 °C with 5% CO2.

extract_protocol:
ChIP-seq: ChIP was performed based on (Shah et al., Dev Cell 2021). HCT-116 cells were cross-linked in culture medium by addition of methanol-free formaldehyde (ThermoFisher, final 1% v/v) and incubated at room temperature for 10 minutes with gentle nutation. Crosslinking was quenched by addition of glycine (final 125 mM) and incubated at room temperature for 5 minutes with gentle nutation. Media was aspirated and replaced with cold DPBS. Cells were scraped and transferred to conical tubes, then pelleted by centrifugation (1500 rpm, 3 minutes, room temperature). Pellets were flash frozen on liquid nitrogen and stored at -80C.  For ChIP, 30 uL protein G magnetic beads (per sample; ThermoFisher) were washed three times in blocking solution (0.5% BSA in DPBS). Beads were then resuspended in 250 uL blocking solution and 2 ug antibody (RAD21, Abcam ab992; CTCF, Cell Signaling Technology 3418) was added. Beads and antibody were rotated at 4C for at least six hours. Nuclei were isolated from frozen cell pellets as follows: pellet was resuspended in 10 mL cold lysis buffer 1 (50mM HEPES-KOH pH7.5, 140mM NaCl, 1mM EDTA, 10% Glycerol, 0.5% NP-40,  0.25% Triton X-100, and protease inhibitors) and rotated at 4C for 10 minutes, followed by centrifugation (1500 rpm, 3 minutes, 4C). Supernatant was aspirated and the pellet was resuspended in 10 mL cold lysis buffer 2 (10mM Tris-HCl pH 8.0, 200mM NaCl, 1mM EDTA, 0.5mM EGTA, and protease inhibitors) and rotated at room temperature for 10 minutes, followed by centrifugation (1500 rpm, 3 minutes, 4C). Supernatant was discarded and nuclei were resuspended in 1 mL cold lysis buffer 3 (10mM Tris-HCl, pH 8.0, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Na-Deoxycholate, and protease inhibitors) and transferred to pre-chilled 1mL Covaris AFA tubes (Covaris). Nuclei were sonicated using a Covaris S220 sonicator (high cell chromatin shearing for 15 minutes; Covaris). Sonicated chromatin was transferred to 1.5mL microcentrifuge tubes and Triton-X 100 was added (1% final v/v) followed by centrifugation (top speed, 10 minutes, 4C). Supernatant was transferred to a new tube. Antibody-conjugated protein G beads were washed three times in blocking solution, resuspended in 50 ul blocking buffer, and added to 500 ug sonicated chromatin. Chromatin was rotated overnight at 4C. 50 ug lysate was reserved in a separate tube at -20C for input.   On day 2, beads were washed five times in 1 mL RIPA buffer (50mM HEPES-KOH pH 7.5, 500mM LiCl, 1mM EDTA, 1% NP-40, 0.7% Na-Deoxycholate). Beads were then washed in 1 mL final wash buffer (1xTE, 50mM NaCl) for 2 minutes. Beads were finally resuspended in 210 uL elution buffer (50mM Tris-HCl pH 8.0, 10mM EDTA, 1% SDS), and chromatin was eluted from beads by agitation at 65 °C for 30 minutes. 200 uL eluate was transferred to a new tube, and all samples (ChIP and input) were reverse cross-linked overnight at 65 °C with agitation for between 12 and 18 hours. 200 uL 1xTE was added to all samples, and samples were treated with RNase A (final 0.2mg/mL RNase; 37 °C for 2 hours) and proteinase K (final 0.2mg/mL Proteinase K; 55C for 2 hours). DNA was purified using phenol:chloroform extraction and resuspension in 10mM Tris-HCl pH 8.0.  In situ Hi-C: Hi-C libraries were generated from 10e6 cells using the Arima-HiC+ kit (Arima Genomics) according to manufacturer's instructions
ChIP-seq: ChIP and input DNA were quantified by Qubit (ThermoFisher) before library preparation using the NEBNext Ultra II DNA library prep kit (NEB). Samples were indexed for either single or dual-index sequencing. Library quality was assessed on Bioanalyzer (Agilent) and quantified by qPCR (Kapa Biosystems).   In situ Hi-C: Libraries were prepared using the Kapa Hyper Prep Kit with KAPA Library Amplification Primer Mix (KK8502), according to manufacturer’s recommendations. Libraries were validated for quality and size distribution using the Qubit dsDNA HS Assay Kit (Invitrogen, cat# Q32851), KAPA Library Quantification kit (Roche, Cat# KK4824) and TapeStation 2200 (Agilent).
ChIP-seq: Quantified libraries were sequenced via Illumina sequencing using the NextSeq500 (single end, 75bp) and NovaSeq6000 (paired-end, 100bp) platforms. Data from the same libraries were merged for final analysis.  In situ Hi-C: Paired-end sequenced (61bp+61bp) on a NovaSeq 6000 (Illumina).

treatment_protocol: RNAiMAX transfection reagent (Thermo Fisher Scientific) was diluted in Opti-MEM reduced serum medium (Thermo Fisher Scientific), and pipetted onto siRNA. Plates were incubated at room temperature for 20 minutes. HCT-116 cells were trypsinized and resuspended in antibiotic-free medium, then plated on siRNA duplexes to obtain a final siRNA concentration of 25 nM. After 72 h of RNAi treatment, cells were collected for experiments.

value: WAPL siRNA


title: CHO_EV_H3K18la_rep2

value: MI5-4 (CHO)


title: Cdk12 shRNA day 30 biol rep 2

value: Rh1-GFPKASH, Rh1-Gal4>sh-Cdk13


title: T2D_before_MMTT_7

value: musculus vastus lateralis

value: No treatment

value: before treatment

tag: diagnosis


title: WAPL_KD_Hi-C_r1

value: wild type


title: Cdk12 shRNA day 30 biol rep 1

value: Rh1-GFPKASH, Rh1-Gal4>sh-Cdk12

value: male


title: T2D_1h_after_MMTT_6

value: female

value: MMTT

tag: bmi


title: PDS5A_KD_Hi-C_r2

description: JoyceLab_E71_PDS5A_MERGED_hic2cool_5kb_KR_allChr.cool

value: PDS5A siRNA


title: PDS5A_KD_Hi-C_r1


title: cnc shRNA day 30 biol rep 2

value: outer photoreceptor neurons

value: Rh1-GFPKASH, Rh1-Gal4>sh-cnc

value: day 30


title: GSK3A_KD_Hi-C_r2

value: GSK3A siRNA


title: 6690_saline

type: genomic

city: Albany

first: Ramon

last: Bossardi Ramos

state: Ny

address: 43 New Scotland Avenue

department: Department of Molecular and Cellular Physiology

institute: Albany Medical College

hyb_protocol: standard protocol

scan_protocol: standard protocol

data_processing: Mouse data, probe, and intensity data for each sample were imported into R using the package RnBeads (version 2.10.0), followed by preprocessing to filter probes outside the CpG context, SNP probes, sex chromosome probes, probes without intensity value, and probes with a low standard deviation. The RnBeads.mm10 package was used to annotate the location of each probe. Downstream data analysis was performed using β values. The β value is the ratio of the methylated probe intensity to the overall intensity (the sum of the methylated and unmethylated probe intensities). βvalues range from 0 to 1, in which 0 is no methylation and 1 is complete methylation and were used to derive heatmaps and further analysis. Differential methylation between groups was defined as β value difference and adjusted p-value (Benjamini-Hochberg method, FDR <0.05).

label: cy3, cy5

label_protocol: standard protocol

extract_protocol: DNeasy Blood & Tissue Kit (Qiagen, USA)

value: Saline

tag: strain


title: T2D_before_MMTT_6

value: T2D, Obesity

tag: fasting glucose,_mm

tag: fasting insulin,_miu/l


title: T2D_before_MMTT_5

tag: fasting c-peptid,_ng/ml


title: 6658_saline


title: cnc shRNA day 30 biol rep 1

tag: genotype


title: 6629_lps_wild


title: 6657_lps_wild


title: 6659_lps_wild


title: 6626_saline


title: 6686_lps_socs3ikeo


title: dom shRNA day 30 biol rep 3

value: Rh1-GFPKASH, Rh1-Gal4>sh-dom

tag: Sex


title: T2D_1h_after_MMTT_4

value: 1 hour after treatment

tag: hba1c, %


title: 6628_saline


title: Control_Hi-C_r2

value: control siRNA


title: T2D_before_MMTT_4

value: musculus vastus lateralis

value: No treatment


title: 6610_lps_socs3ikeo


title: GSK3A2-Input

description:
GSK3A2-RAD21.subtract.bw
GSK3A2-RAD21.bed
RAD21_GSK3A.bw

value: wild type


title: dom shRNA day 30 biol rep 2

tag: cell type


title: 6607_lps_socs3ikeo

tag: treatment


title: Spt5 shRNA day 30 biol rep 3

value: Rh1-GFPKASH, Rh1-Gal4>sh-Spt7


title: Control_Hi-C_r1

description: re-analysis of GSM6696866


title: Muller's larva of Prostheceraeus crozieri repeat 4

city: London

first: Laura

last: Piovani

address: Room B02, Anatomy Building, Gower Street

department: GEE

country: United Kingdom

institute: UCL

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing and gene counting were made using the Cell Ranger software v4 and v6.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: for details see "Single-cell atlases of two lophotrochozoan larvae highlight their complex evolutionary histories" Piovani et al 2023
Supplementary files format and content: Tab-separated values files and matrix files

organism: Prostheceraeus crozeri

extract_protocol:
for protocol see "Single-cell atlases of two lophotrochozoan larvae highlight their complex evolutionary histories" Piovani et al 2023
for library contruction details see "Single-cell atlases of two lophotrochozoan larvae highlight their complex evolutionary histories" Piovani et al 2024

value: Muller's larvae

value: 1 day


title: Muller's larva of Prostheceraeus crozieri repeat 3

description: 10x Genomics


title: 62632_lps_socs3ikeo


title: Spt5 shRNA day 30 biol rep 2

value: Rh1-GFPKASH, Rh1-Gal4>sh-Spt6

value: male


title: GSK3A2-RAD21


title: 62631_lps_socs3ikeo


title: T2D_1h_after_MMTT_3

value: MMTT

tag: homa ir


title: 6623_lps_socs3_het

tag: tissue


title: 6609_lps_socs3_het


title: T2D_1h_after_MMTT_2


title: T2D_before_MMTT_2

value: before treatment


title: cic-TALEN rep 3

city: York

first: harry

middle: victor

last: isaacs

state: North Yorkshire

address: wentworth way

department: biology

institute: university of york

data_processing:
Cutadapt was used to remove adapter sequences and primers
Salmon was used to map reads to the NCBI Xenopus tropicalis reference transcriptome v9.1
Differential gene expression was determined using Sleuth and the counts aggregation method. The reduced model was defined as ‘~batch’, and the full model ‘~batch + treatment’ to mitigate variation accounted for by embryo batch.
Assembly: NCBI Xenopus tropicalis reference transcriptome v9.1
Supplementary files format and content: Tab delimited file with gene counts in transcripts per million (TPM)

organism: Xenopus tropicalis

source_name: whole embryo

growth_protocol: embryos were cultured in MRS/20 at 23 degrees

extract_protocol:
Total RNA was extracted from embryos with Trizol reagent (Invitrogen) as per manufacturer's instructions. RNA was further purified by LiCl precipitation and RNA integrity was checked using an Agilent 2100 Bioanalyzer.
NEBNext Poly(A) mRNA Magnetic Isolation Module was used to isolate Poly(A) mRNA from total RNA. NEBNext RNA Ultra II Directional RNA Library Prep Kit was used generate the cDNA  libraries

treatment_protocol: Embryos were injected with water, 5 pg Cska-Fgf4 plasmid or 1 ng of Cic-TALEN forward and reverse mRNAs

tag: Stage

value: Nigerian

value: whole embryo

value: cic knockdown

value: cic-TALEN pair mRNA injection


title: Spt5 shRNA day 30 biol rep 1

value: outer photoreceptor neurons

value: Rh1-GFPKASH, Rh1-Gal4>sh-Spt5

value: day 30


title: 6261_lps_socs3_het


title: cic-TALEN rep 2


title: cnc shRNA day 30 biol rep 3

value: Rh1-GFPKASH, Rh1-Gal4>sh-cnc


title: 6260_saline

value: Saline


title: T2D_1h_after_MMTT_1

value: musculus vastus lateralis

tag: individual

value: 1 hour after treatment

value: T2D, Obesity


title: dom shRNA day 30 biol rep 1

value: Rh1-GFPKASH, Rh1-Gal4>sh-dom


title: Spt6 shRNA day 30 biol rep 2

value: Rh1-GFPKASH, Rh1-Gal4>sh-Spt7


title: cska-fgf4 rep 3

value: Fgf4 overexpressing

value: cska-fgf4 plasmid injection


title: Scr1-Input

description:
Scr1-RAD21.subtract.bw
Scr1-CTCF.subtract.bw
Scr1-RAD21.bed
Scr1-CTCF.bed
RAD21_Scr.bw
CTCF_Scr.bw

tag: cell line

value: wild type

value: control siRNA


title: T2D_before_MMTT_1

value: male

value: No treatment

tag: time point

value: before treatment

tag: age


title: SC_high_passage

first: Faranak

last: Fattahi

state: California

department: Cellular and Molecular Pharmacology

institute: University of California San Francisco

data_processing:
Transcript Quantification: FASTA (fasta.gz) files were quantified using CellRanger. The specific command was 'cellranger count' with  parameters '--include-introns --nosecondary' all other paramters were default.
Preprocessing: filtered count matrices fromCellRanger were read into R and processed using Seurat (v4.0.4). The reminaing cells were filtered for total genes, total umis and mitochondrial percentage.
Analysis: Sample were analysed using Seurat's standard workflow.
Genome_build: GRCh38
Supplementary_files_format_and_content: Processed data is provided as (.csv) files and contain a gene count matrix of cell IDs post CellRanger filtering pre Seurat filtration.

growth_protocol: Low and high passage Schwann cells were differentiated from hPSC-derived neural crest cells and grown in Schwann Cell Medium (Sciencell, 1701).

extract_protocol:
Cells were washed with PBS and detached using trypsin. The enzyme was quenched with media containing 2% FBS and washed away by extra media followed by PBS. Cells were passed through a 37μm reversible cell strainer and put on ice. Before submission for library prep.
snRNA-seq libraries were prepared with Chromium Next GEM Single Cell 3′ Kit v3.1 (10x Genomics). The libraries were sequenced at UCSF GenomicsCoLab.

value: hPSC-derived Schwann Cell culture

tag: cell line source

tag: plating

value: attached


title: Scr1-RAD21

description:
Scr1-RAD21.subtract.bw
Scr1-RAD21.bed
RAD21_Scr.bw


title: cic-TALEN rep 1

tag: strain

value: Nigerian

value: whole embryo

value: cic knockdown

value: cic-TALEN pair mRNA injection


title: Taf1 shRNA day 30 biol rep 3

value: outer photoreceptor neurons

value: Rh1-GFPKASH, Rh1-Gal4>sh-Taf3

value: day 30


title: cska-fgf4 rep 2


title: SC_low_passage


title: Spt6 shRNA day 30 biol rep 1

value: Rh1-GFPKASH, Rh1-Gal4>sh-Spt6


title: 6259_lps_wild


title: Foxp1_knockdown_replicate3_RNA-seq

city: Jammu

first: Santhilal

last: Subhash

state: Jammu and Kashmir

address: Jagti, NH-44, PO Nagrota

department: Biosciences and Bioengineering

country: India

institute: Indian Institite of Technology Jammu

data_processing:
Obtained raw reads were aligned using HISAT2 v2.1.0 aligner against mm10 as reference genome with parameters, --dta --time --rna-strandness RF  --avoid-pseudogene --known-splicesite-infile --qc-filter
Quantification for transcripts from GENCODE vM10 was done using featureCounts from Subread v1.5.3 package with parameters -p -s 2 -B -C -F GTF -t exon -g gene_id --minOverlap 10 -Q 30 --ignoreDup -J
Quantified reads are RPKM normalized
Genome_build: mm10
Supplementary_files_format_and_content: Matrix containing tab-delimited data includes RPKM values for genes in each Sample.

source_name: 3T3-L1 adipocytes

growth_protocol: 3T3-L1 cells were growth and differentiated into adipocytes using standard protocol. Differentiation medium contained 1 µM dexamethasone, 0.5 mM isobutyl methylxanthine, 5 µg/ml insulin, 10 µM troglitazone. Cells were cultured in medium containing only 5 µg/ml insulin from day 4. From day 6 the cells were kept in growth medium

extract_protocol:
Total RNA from cells was extracted using TRI reagent and isolated using RNeasy mini kit (Quagen) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Ectopic overexpression or downregulation of Foxp1 in 3T3-L1 adipocytes

value: 3T3-L1 cells

value: adipocytes

value: Swiss mouse

tag: expression construct

value: Foxp1 shRNA


title: FACS sorted GFP-RBM3 Low, day 19 [N9_3_low]

first: Emmanouil

last: Metzakopian

address: Addrenbookes Campus

institute: UK Dementia Research Institute

library_source: other

data_processing:
bcl2fastq to assemble short reads
count gRNAs according to gRNA library for each sample
merge count vectors
Assembly: N/A gRNA target genomic regions according to GRCh38
Supplementary files format and content: rbm3-tun-library.csv contains the gRNA vectors for the experiment

molecule: other

source_name: BOB Cas9 clone 2

growth_protocol: iPSCs were enzymatically detached and dissociated into single cells using Accutase and plated into GelTrex (1:100 dilution)-coated culture plates in TeSR-E8 medium supplemented with 10 µM Rho-associated protein kinase (ROCK) inhibitor. After 24 hours (day 1), TeSR-E8 medium was changed to DMEM/F12 medium with GlutaMAX, supplemented with 1x N-2 supplement, 1x Non-Essential Amino Acids, 50 nM 2-Mercaptoethanol, 100 U/mL Penicillin-Streptomycin, and 1 µg/mL Doxycycline Hyclate (Dox) (iN-1 medium). After 24 hours (day 2), the medium was replaced with the same medium as the previous day. From day 3 to day 6, the culture was fed daily with Neurobasal medium supplemented with 1x B-27 supplement (minus vitamin A), 1x GlutaMAX, 50 nM 2-Mercaptoethanol, 100 U/mL Penicillin-Streptomycin, and 1 µg/mL Dox, 10 ng/mL Neurotrophin-3 (NT-3), and 10 ng/mL Brain-derived neurotrophic factor (BDNF) (iN-2 medium). After day 6, the medium was changed every other day.

extract_protocol:
Both clones of GFP-RBM3 iPSCs (N8, N9) were differentiated in GelTrex-coated T75 flasks. The total number of i-neurons used for each clone in each replicate was approximately 60,000,000 to ensure sufficient copies of individual sgRNAs could be obtained from the pool. 4 days post differentiation, the cultures were transduced with a whole-genome sgRNA lentiviral library (399 non-targeting sgRNAs and 91138 sgRNAs targeting 18466 genes across the human genome), co-expressing a BFP fluorescent reporter to indicate successfully transduced cells. The viral titer was determined in pilot experiments, resulting in 20% of the i-neurons becoming BFP-positive on day 18 to minimise multiple sgRNA entries into a single cell. I-neurons at 14, 15 or 16 days post differentiation (or 11, 12, 13 days post-transduction) were cooled at 32°C for 72h before dissociation with 20 min Accutase and 10 min Trypsin-EDTA incubation, followed by fluorescence-activated cell sorting (FACS). GFP intensity of all BFP-positive cells was manually separated into 4 quartiles, and only cells with the GFP intensity falling in the top or the bottom quartile were collected in separate tubes and their genomic DNA was extracted (see Genomic DNA extraction) immediately after. Around 3,000,000 i-neurons were collected in the low GFP or high GFP tube for each clone in each replicate.
The sequencing library was created in a two-stage PCR reaction. The first stage amplifies the enriched gRNA cassettes: 2 μg DNA, 1.5 μL Forward Primer (10 μM), 1.5 μL Reverse Primer (10 μM), 25 μL NEB Q5 High-Fidelity 2x Master Mix in a 50 μL reaction. The PCR condition was: 98C for 30 sec, 25 cycles of (98C for 10 sec, 62C for 30 sec, 72C for 15 sec), and 72C for 2 min. PCR product was purified using Ampure XP Beckman magnetic beads and diluted to 200 pg/μL. The second PCR attached the Illumina adaptors and barcodes: 1 μL PCR product from the first reaction, 0.75 μL Forwards Primer (20 uM), 0.75 μL Reverse Primer (20 uM), 10 μL Roche 2X KAPA HiFi ReadyMix in a 20 μL reaction. The PCR condition was: 95C for 3 min, 9 cycles of (98C for 20 sec, 66C for 15 sec, 72C for 20 sec), and 72C for 1 min. PCR products were purified using Ampure XP Beckman magnetic beads and eluted in 35 μL TE buffer. PCR products were quantified with NEBNext Library Quant Kit for Illumina. The library was run on an Illumina NextSeq 550, using an Illumina 75 cycle, high output kit at 1.4 pM.

treatment_protocol: Incubation at 32°C for 72h

value: BOB Cas9 clone 2

value: induced NGN2 Neurons

value: Tunicamycin


title: FACS sorted GFP-RBM3 High, day 19 [N9_3_high]


title: Spt6 shRNA day 30 biol rep 3

value: Rh1-GFPKASH, Rh1-Gal4>sh-Spt8

value: male


title: T2D_before_MMTT_3

value: musculus vastus lateralis

value: No treatment

value: before treatment

tag: diagnosis

value: T2D, Obesity

tag: bmi

tag: fasting glucose,_mm

tag: fasting insulin,_miu/l

tag: fasting c-peptid,_ng/ml


title: Taf1 shRNA day 30 biol rep 2

tag: cell type

value: outer photoreceptor neurons

tag: genotype

value: Rh1-GFPKASH, Rh1-Gal4>sh-Taf2

tag: Sex


title: FACS sorted GFP-RBM3 Low, day 18 [N9_2_low]

tag: treatment


title: water control rep 3

tag: Stage

value: Nigerian

tag: tissue

value: whole embryo

value: control

value: water injection


title: FACS sorted GFP-RBM3 High, day 18 [N9_2_high]

tag: cell line


title: Taf1 shRNA day 30 biol rep 1

value: Rh1-GFPKASH, Rh1-Gal4>sh-Taf1

tag: age

value: day 30


title: Foxp1_knockdown_replicate1_RNA-seq

value: 3T3-L1 cells

value: adipocytes

value: Swiss mouse

value: Foxp1 shRNA


title: TH1 shRNA day 30 biol rep 3

value: Rh1-GFPKASH, Rh1-Gal4>sh-TH3

value: male


title: water control rep 2


title: Foxp1_Control_replicate3_knockdown_RNA-seq

value: scrambled shRNA control


title: TH1 shRNA day 30 biol rep 2

value: Rh1-GFPKASH, Rh1-Gal4>sh-TH2


title: TH1 shRNA day 30 biol rep 1

value: Rh1-GFPKASH, Rh1-Gal4>sh-TH1


title: 7037 kid

data_processing:
Differentially expressed genes (DEGs) were identified by using the Transcriptome Analysis Console (TAC) software (version 4.0.2) with the ampliSeqRNA plugin (Thermofisher Scientific)
Assembly: mm10
Supplementary files format and content: tab-delimited text files read counts values for each Sample
Supplementary files format and content: File containing log-fold change, p-value, FDR and read counts for DEGs

source_name: endothelial

extract_protocol:
Mice kidney after LPS treatment was minced and lysed with Trizol reagent (Thermo Fisher). RNA quantity was determined using a Qubit Flex Fluorometer (Thermo Fisher Scientific, San Jose, CA).
Library preparation was performed using an Ion Chef System (Thermo Fisher Scientific, San Jose, CA)
RNA-seq - protocols for the Ion AmpliSeq Transcriptome Mouse Gene Expression Kit

treatment_protocol: We used mice carrying a TRAP transgene for translating ribosome affinity purification assays and -mediated RNA isolation from the endothelium of septic mice. Transgenic mouse in which a ribosomal subunit can be replaced by a floxed GFP-tagged version (EGFP/Rpl10a), rendering the ribosome amenable to immunoprecipitation via two specific monoclonal antibodies. Using this system under the endothelial-specific, tamoxifen-inducible cdh5-CreERT2 driver we isolated mRNAs that are actively translated in the endothelium of the kidneys. Severe, acute inflammation was induced by a single IP injection of a bolus of 250 μg/250 μl LPS. Control mice were given 250 μl of sterile saline via IP injection. Disease severity was scored 14 hours after the LPS challenge. Immediately after scoring, body weight and temperature were measured. Mice were then euthanized with an overdose of pentobarbital.

value: endothelial

value: kidney

value: Endothelium

value: WT

value: LPS


title: water control rep 1

value: Nigerian

value: whole embryo

value: control

value: water injection


title: FACS sorted GFP-RBM3 Low, day 17  [N9_1_low]

value: BOB Cas9 clone 2

value: induced NGN2 Neurons

value: Tunicamycin


title: FACS sorted GFP-RBM3 High, day 17  [N9_1_high]


title: Foxp1_Control_replicate2_knockdown_RNA-seq

value: 3T3-L1 cells

value: adipocytes

value: Swiss mouse


title: 7038 kid

value: Saline


title: Top1 shRNA day 30 biol rep 3

value: outer photoreceptor neurons

value: Rh1-GFPKASH, Rh1-Gal4>sh-Top3

value: male

value: day 30


title: cska-fgf4 rep 1

value: Fgf4 overexpressing

value: cska-fgf4 plasmid injection


title: T2D_1h_after_MMTT_5

value: musculus vastus lateralis

value: female

tag: individual

value: MMTT

tag: time point

value: 1 hour after treatment

value: T2D, Obesity

tag: hba1c, %

tag: homa ir


title: Foxp1_overexpression_replicate3_RNA-seq

tag: strain

tag: expression construct

value: constituent overexpression of FOXP1


title: Foxp1_knockdown_replicate2_RNA-seq

value: Foxp1 shRNA


title: 6262_saline


title: 7035 kid

value: endothelial

value: kidney

value: Endothelium

value: WT

value: LPS


title: Top1 shRNA day 30 biol rep 2

value: outer photoreceptor neurons

value: Rh1-GFPKASH, Rh1-Gal4>sh-Top2


title: FACS sorted GFP-RBM3 High, day 19 [N8_3_high]

source_name: BOB Cas9 clone 1

value: BOB Cas9 clone 1

value: induced NGN2 Neurons

value: Tunicamycin


title: FACS sorted GFP-RBM3 Low, day 18 [N8_2_low]


title: 7032 kid


title: FACS sorted GFP-RBM3 Low, day 19 [N8_3_low]


title: Foxp1_overexpression_replicate2_RNA-seq

value: 3T3-L1 cells

value: adipocytes

value: Swiss mouse


title: FACS sorted GFP-RBM3 High, day 18 [N8_2_high]


title: Foxp1_Control_replicate1_knockdown_RNA-seq

value: scrambled shRNA control


title: Foxp1_overexpression_replicate1_RNA-seq


title: 6998 kid


title: Trl shRNA day 30 biol rep 3

value: Rh1-GFPKASH, Rh1-Gal4>sh-Trl

value: male

value: day 30


title: FACS sorted GFP-RBM3 Low, day 17  [N8_1_low]


title: 6995 kid

value: endothelial

value: Saline


title: 6997 kid

value: kidney

value: Endothelium


title: FACS sorted GFP-RBM3 High, day 17  [N8_1_high]


title: Foxp1_Control_replicate2_overexpression_RNA-seq

value: empty vector control


title: Paraganglioma sample carrying the DLST-p.Y422C mutation

city: Madrid

first: Alberto

last: Cascón

address: Melchor Fernández Almagro 3

department: Human Cancer Genetics Program

country: Spain

institute: Spanish National Cancer Research Centre (CNIO)

data_processing:
HTSeq-Counts from CNIO series were generated with BlueBee® Genomics Platform (Lexogen, 090-094), from FASTQ files obtained from QuantSeq platform
STAR v2.5.2a algorithms were used to map the reads respectively to the reference genome GRCh38
The sample was integrated with previous samples, and batch effects due to the different platforms were corrected using ComBat from R/Bioconductor package sva v3.26.0
DESeq2 normalization and log2 transformation was performed.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include DESeq2 values for the sample

source_name: Paraganglioma

extract_protocol:
Total RNA extraction was performed from the FFPE specimen using Maxwell RSC RNA FFPE Kit (Promega), following manufacturers’ protocol. 500 ng of total RNA was used as starting material
Libraries were prepared using QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen, 015) with a UMI Second Strand Synthesis Module for QuantSeq FWD (Lexogen, 081), according to vendor’s protocol

value: Paraganglioma

value: Primary tumor


title: aging-2

status: Public on May 04 2023

city: Zhengzhou

first: zhenglong

last: guo

state: Henan

address: NO.7, Weiwu road

institute: Henan Provincial People's Hospital

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2)by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The clean reads were mapped to the reference genome using HISAT2 (v2.0.4). Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set then expression level of gene was calculated by RSEM (v1.2.12)
The heatmap was drawn by pheatmap (v1.0.8) (https://cran.r-project.org/web/packages/pheatmap/index.html)according to the gene expression in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5) (http://www.bioconductor.org/packages/release/bioc/html/ DESeq2.html)with Q value ≤ 0.05.
To take insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expressed gene was performed by Phyper (https://en.wikipedia.org/wiki/Hypergeometric_distribution) based on Hypergeometric test . The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05)
Assembly: mm10
Supplementary files format and content: xls file include FPKM values for each Sample

source_name: heart ventricle

extract_protocol:
Total RNA was extracted from 3 separate samples of adult and aged C57BL6 mouse heart ventricle using Trizol(Life science)and DNA-free kit(Ambion).
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform (BGI-Shenzhen, China).

value: heart ventricle

value: 24-26 month


title: 6992 kid

value: WT


title: young-3

value: 6-8 week


title: aging-1


title: young-2


title: Top1 shRNA day 30 biol rep 1

value: outer photoreceptor neurons

value: Rh1-GFPKASH, Rh1-Gal4>sh-Top1


title: Foxp1_Control_replicate3_overexpression_RNA-seq

value: 3T3-L1 cells

value: adipocytes

value: Swiss mouse


title: Trl shRNA day 30 biol rep 2

value: Rh1-GFPKASH, Rh1-Gal4>sh-Trl

value: male

value: day 30


title: GSK3A_KD_Hi-C_r1

value: wild type

value: GSK3A siRNA


title: young-1


title: Low level organic minerals, male 5

type: RNA

city: Ås

first: Aleksei

last: Krasnov

state: Viken

address: Øreveien, 47B

country: Norway

institute: Nofima AS

hyb_protocol: Hybridized according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol

scan_protocol: Arrays were scanned with Agilent G2565BA DNA microarray scanner at a resolution of 5 microns

data_processing: Images were processed using the standard procedures of the Agilent Feature Extraction (FE) Software version 9.5.1. After removal of flagged spots lowess normalization was performed

organism: Salmo salar

source_name: Low level organic minerals, male

label_protocol: Amplified and labeled with Low Input Quick Amp Labeling Kit (Agilent).

growth_protocol: Salmon post smolts were kept in tanks with sea water

extract_protocol: Total RNA was extracted using the RNeasy® Mini Kit (Qiagen)

treatment_protocol: A 2x4 factorial design (dietary trace mineral type organic vs inorganic x 4 dietary mineral levels) with 3 replications for each dietary treatment was applied. The tanks were equipped with continuous light and flow-through water systems using UV-treated filtrated sea water from 40 m depth (flow approximately 20 L/min). Oxygen levels were monitored daily, and water flow adjusted, when necessary, to achieve   oxygen saturation levels between 70 - 80%. The mean water temperature during the trial was 8.73 oC. Samples were collected after 12 weeks.

tag: condition

value: Low level organic minerals


title: Foxp1_Control_replicate1_overexpression_RNA-seq

value: empty vector control


title: Low level organic minerals, male 2


title: Low level organic minerals, female 6

source_name: Low level organic minerals, female

value: female


title: aging-3

value: heart ventricle


title: Low level organic minerals, male 4


title: Low level organic minerals, female 4


title: Trl shRNA day 30 biol rep 1


title: Low level organic minerals, female 3


title: Low level organic minerals, male 3


title: Low level organic minerals, male 6


title: Low level organic minerals, female 2


title: Low level organic minerals, female 5


title: Low level organic minerals, female 1


title: Low level inorganic minerals, male 5

source_name: Low level inorganic minerals, male

value: Low level inorganic minerals


title: Low level inorganic minerals, male 2


title: High level organic minerals, male 5

source_name: High level organic minerals, male

value: High level organic minerals


title: Low level inorganic minerals, female 1

source_name: Low level inorganic minerals, female


title: High level organic minerals, male 7


title: Low level inorganic minerals, female 2


title: Low level inorganic minerals, female 3


title: Low level inorganic minerals, female 4


title: High level organic minerals, male 4


title: High level organic minerals, male 6


title: Low level inorganic minerals, male 1


title: High level organic minerals, male 2


title: Low level inorganic minerals, female 5


title: High level organic minerals, female 5

source_name: High level organic minerals, female


title: L3_GFPminus_rep3

city: Fort Collins

first: Erin

last: Osborne Nishimura

state: CO

address: 1870 Campus Delivery, 200 W. Lake St.

department: Biochemistry and Molecular Biology

institute: Colorado State University

description:
RW089
L3_non-intestine_cells_merged.bw

data_processing:
Samples were assessed for quality and trimmed for adapter, primer, and polyX sequences by fastp (v 0.20.0) (Chen 2017; PMID: 30423086)
Trimmed reads were aligned separately to the ce11 genome using hisat2 (v 2.1.0) (Kim 2017; PMID: 31375807).
The number of reads associated with each gene model was tabulated for the C. elegans WS263 genome annotation using featureCounts (v 1.6.4) (Liao 2014; PMID: 24227677).
samtools (v 1.9) (Li 2009; PMID: 19505943), DeepTools (bamCoverage v 3.2.0) (Ramírez 2016; PMID: 27079975), and UCSC Kent Utilities were used to transform alignments into formats suitable for viewing on UCSC Genome Browser (Kent 2002; PMID: 12045153).
RNA-seq count data were filtered for detected genes (> 10 counts per million across all samples) and analyzed using DESeq2 (v 1.28.1) (Love 2014; PMID: 25516281) with default settings in the R Environment (v 4.0.3, BiocManager, v 1.30.10).
The raw counts (intestine_FACS_RNAseq_raw_counts.txt), normalized counts (intestine_FACS_RNAseq_norm_counts.txt), and normalized/variance-stabilized/log-transformed counts (intestine_FACS_RNAseq_rlog_counts.txt) are provided.
Assembly: C. elegans, ce11
Supplementary files format and content: .gtf file: c_elegans.PRJNA13758.WS263.canonical_geneset.gtf
Supplementary files format and content: .bw files were generated using bamCoverage, part of the DeepTools package
Supplementary files format and content: merged.bw files were merged by replicate using UCSC Kent Utilities
Supplementary files format and content: counts tables were generated from featureCounts tabultion and then processed within DESeq2: intestine_FACS_RNAseq_norm_counts.txt; intestine_FACS_RNAseq_raw_counts.txt; intestine_FACS_RNAseq_rlog_counts.txt

organism: Caenorhabditis elegans

source_name: sorted non-intestine cells

growth_protocol: C. elegans strains were cultered on 150 mm NGM agar plates seeded with 3 ml of OP50 liquid culture. Two rounds of synchronization were performed and then harvested at the approporate stage.

extract_protocol:
Total RNA was extracted using an miRNeasy micro kit (Qiagen 217084).
mRNA was prepared for sequencing using the NEB Next Ultra II RNA Library Prep Kit for Illumina (NEB E7770S) and Poly(A) Magnetic Isolation Module (NEB E7490S).
Libraries of a median 200 - 400 bp length were generated. Libraries RW047-RW055 were sequenced at 2 x 150 bp on a HiSeq X-ten to a read depth of 100 million paired end reads. Libraries RW057-RW089 were sequenced at 2 x 150 bp on NovaSeq 6000 to a read depth of  40 to 100 million paired end reads.

treatment_protocol: Worms were washed 3 times in sterile M9 before cell dissociation to remove excess OP50 E. coli.

value: sorted non-intestine cells

value: non-intestine

tag: biological replicate

value: 2 min SDS-DTT treatment, 30 min pronase E treatment

value: 100 strokes dounce pestle A


title: High level inorganic minerals, male 2

source_name: High level inorganic minerals, male

value: High level inorganic minerals


title: L3_GFPplus_rep3

description:
RW088
L3_intestine_cells_merged.bw

source_name: sorted intestine cells

value: sorted intestine cells

value: intestine

value: 300,000 GFP+ cells


title: L3_whole_rep3

description:
RW086
L3_whole_merged.bw

source_name: whole worms

value: whole worms

value: all

value: 10ul of packed worm pellet


title: L3_GFPplus_rep2

description:
RW085
L3_intestine_cells_merged.bw


title: High level organic minerals, male 1

value: male


title: High level organic minerals, female 4


title: High level inorganic minerals, female 3

source_name: High level inorganic minerals, female


title: High level inorganic minerals, female 1


title: L3_whole_rep2

description:
RW082
L3_whole_merged.bw


title: High level organic minerals, female 3


title: L3_cells_rep2

description:
RW083
L3_dissociated_cells_merged.bw

source_name: dissociated worm cells

value: dissociated worm cells

value: 70ul of cell suspension


title: L3_GFPminus_rep1

description:
RW081
L3_non-intestine_cells_merged.bw


title: L1_GFPminus_rep3

description:
RW077
L1_non-intestine_cells_merged.bw


title: L1_cells_rep3

description:
RW075
L1_dissociated_cells_merged.bw


title: L1_GFPplus_rep3

description:
RW076
L1_intestine_cells_merged.bw


title: High level inorganic minerals, male 1


title: L3_cells_rep1

description:
RW079
L3_dissociated_cells_merged.bw


title: embryo_GFPplus_rep3

description:
RW065
embryo_intestine_cells_merged.bw

value: embryo

value: 20 min chitinase, 5 min pronase E treatment

value: 100 strokes 21 gague syringe needle


title: L3_whole_rep1

description:
RW078
L3_whole_merged.bw


title: L3_cells_rep3

description:
RW087
L3_dissociated_cells_merged.bw


title: embryo_GFPminus_rep3

description:
RW066
embryo_non-intestine_cells_merged.bw

value: sorted non-intestine cells


title: High level inorganic minerals, female 4

value: female


title: embryo_whole_rep3

description:
RW064
embryo_whole_merged.bw


title: embryo_GFPminus_rep2

description:
RW063
embryo_non-intestine_cells_merged.bw

value: non-intestine


title: embryo_GFPplus_rep2

description:
RW062
embryo_intestine_cells_merged.bw


title: L1_whole_rep3

description:
RW074
L1_whole_merged.bw


title: embryo_whole_rep2

description:
RW060
embryo_whole_merged.bw


title: embryo_cells_rep2

description:
RW061
embryo_dissociated_cells_merged.bw


title: L3_GFPminus_rep2

description:
RW084
L3_non-intestine_cells_merged.bw

value: 2 min SDS-DTT treatment, 30 min pronase E treatment

value: 100 strokes dounce pestle A


title: High level inorganic minerals, female 6

value: High level inorganic minerals


title: embryo_GFPminus_rep1

description:
RW059
embryo_non-intestine_cells_merged.bw


title: embryo_GFPplus_rep1

description:
RW058
embryo_intestine_cells_merged.bw

value: sorted intestine cells

value: intestine