title: Bacteria-injected larvae, 5 day + 13h, replicate 5

city: Wageningen

first: Parth

last: Shah

state: Gelderland

address: Droevendaalsesteeg 1

department: Laboratory of Entomology

country: Netherlands

institute: Wageningen University

data_processing:
Raw data filtering was performed to remove reads with adaptor contamination.
Clean paired-end reads were mapped on Hermetia illucens genome (GCF_905115235.1) using STAR and default parameters.
Gene counts were obtained STAR (with gene count function) on the RefSeq assembly GCF_905115235.1.
Assembly: GCF_905115235.1
Supplementary files format and content: tab-delimited text file includes raw counts for each samples

organism: Hermetia illucens

source_name: larvae

growth_protocol: The larvae of Hermetia illucens were reared at 16 h light / 8 h dark cycle at 27°C and 65% humidity.

extract_protocol:
After 2 h, 6 h and 13 h post-injection, five samples (of two pooled larvae each) were collected for each time point and flash-frozen in liquid nitrogen. Total RNA was extracted with TriZol reagent and subjected to DNase treatment, protein purification and stored at -80 degree C. The quality of total RNA was evaluated using Agilent Bioanalyzer and DeNovix Bioanalyzer.
Library preparation was performed at BaseClear B.V. (Leiden, Netherlands). Sequencing libraries were sequenced paired-ended (150 bp read-length) on an Illumina NovaSeq 6000 platform.

treatment_protocol: Five-day old larvae were subjected to one of the treatments (i.e. untreated, PBS-injected or Bacteria-injected) respectively. Injection of PBS and Bacteria was performed using Hamilton needle and customised assembly apparatus. After respective treatments, the larvae were transferred back to chickenfeed diets and samples were collected at 2 h, 6 h and 13 h post-treatment. Five replicates (of two larvae pooled) were collected from each treatment at a specific timepoint.

value: larvae

tag: developmental stage

value: 5 day + 13 h

value: Pseudomonas protegens Pf-5-injected


title: Bacteria-injected larvae, 5 day + 13h, replicate 4

status: Public on Jun 01 2025

type: SRA

library_source: transcriptomic

molecule: total RNA

tag: tissue

tag: treatment


title: Sample9_HEL,ANA,rep3

city: Suzhou

first: Zimu

last: Zhang

state: Jiangsu

address: Zhongnan Street

country: China

institute: Children’s Hospital of Soochow University

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.2.0 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Transcripts per Kilobase of exon model per Million mapped reads (TPM) were calculated using a methodology adapted from the StringTie software. In brief, all isoforms of a gene were assembled and merged to generate a composite transcript model. The number of reads mapped to the exonic regions of this composite transcript model was tallied and subsequently normalized. Normalization was achieved by dividing the read count by the length of the composite transcript model (in kilobases) and then scaling the result by the size of the total mapped library (in millions of reads).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include readcount values for each Sample.

organism: Homo sapiens

source_name: HEL

extract_protocol:
Cells were harvested, and total RNA was extracted with TRIzol (Invitrogen) according to the manufacturer's protocol. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: HEL

tag: cell type

value: AML cells

value: 1 μM ANA, 72h


title: Sample11_HEL,COM,rep2

value: 1 μM ANA + 0.005 μM IDA, 72h


title: WT RDM logarithmic rep 3 - RNA-seq

city: Ann Arbor

first: Lydia

last: Freddolino

state: Michigan

address: 1150 W. Medical Center Dr., Room 3315 MSRB III

country: USA

institute: University of Michigan

data_processing:
Adapter removal using the common Illumina Truseq adapter sequences with cutadapt 3.5
Read ends were trimmed using Trimmomatic 0.39 in paired end mode, with the trimming steps ‘TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:10’
Reads were aligned using bowtie2 version 2.4.4 with ‘very sensitive’ end-to-end presets, and dovetailed alignments allowed
Surviving DNA reads with proper paired-end alignments were quantified using an in-house pipeline in which each read contributes a total signal of weight 1, divided over the length of the read. Further processing is described in detail in the accompanying paper
RNA reads were processed using Rockhopper to detect transcripts and respective expression levels, as well as significance of mutant versus wild-type expression change. The IPOD pipeline up to the alignment step was also used to quantify the number of RNA reads at each basepair position.
Assembly: E. coli U00096.3
Supplementary files format and content: For all summary/processed files, note that we provide one file per experimental condition, which represents a consolidation of all replicates for that condition, as described in the accompanying manuscript. The .bedgraph file extension refers to a 5 basepair graphing of occupancy scores, where the first column indicates the chromosome, while the second and third columns indicate the left and right, respectively, basepair positions of the 5 basepair bin a genomic position and the fourth a corresponding signal. chip_vs_inp.bedgraph files – RNA polymerase occupancy given as a log_2 ratio of extracted to input, z-scored and then used to calculate enrichment p values as described in the text. rzchipsub.bedgraph files – ChIP-subtracted IPOD-HR occupancy, z-scored and then used to calculate enrichment p values as described in the text. rockhopper_summary.txt - summary of transcript information, mutant vs wt log2(fold change) and qvalue as calculated by Rockhopper from RNAseq data. rna_positive_reads_ptmr.bedgraph - RNAseq reads per tens of millions of reads within each replicate, then the mean of replicates is calculated.  rna_negative_reads_ptmr.bedgraph - RNAseq reads per tens of millions of reads within each replicate, then the mean of replicates is calculated, and signed negative to indicate strandedness.

organism: Escherichia coli

source_name: Culture lysate

extract_protocol:
DNA samples: When resuspending frozen cell pellets, two pellets (taken from a single biological replicate) of each sample were separately resuspended with spike-in, sonicated, and then combined into one tube immediately after sonication. Individual frozen C. crescentus spike-in cell pellets were resuspended in 600 µL of 1x IPOD lysis buffer (10 mM Tris HCl, pH 8.0; 50 mM NaCl) containing 1x protease inhibitors (Roche Complete Mini, EDTA free, Roche Diagnostics GmbH, Mannheim, Germany) and 1.5 µL of ready-lyse (Epicentre, Madison, WI). The spike-in resuspension was used to resuspend one of the sample cell pellets, and then the resuspended cells were incubated for 15 minutes in a 30°C water bath. Sonication was then performed on all samples using a Branson digital sonifier with a microtip at 25% amplitude for four pulses of 5 seconds with a 5 second rest between each pulse; samples were kept in an ice/water bath during sonication. The two separate tubes for each biological sample were then combined. DNA digestion was performed by adding to the sonicated lysates 120 μg RNase A (Thermo Fisher Scientific, Waltham, MA), 12 μL DNase I (Fisher product #89835), 10.8 μL 100 mM MnCl2, and 9 μL 100 mM CaCl2, and then incubating on ice for 30 minutes. The digestion was quenched with 100 μL of 500 mM EDTA (pH 8.0), followed by clarification by centrifuge for 10 minutes at 13,000 rpm at 4°C. Aliquots were taken from the clarified lysate for IPOD-HR interface extraction, RNA polymerase chromatin immunoprecipitation, and cross-linking reversal and recovery of DNA as previously described in (Freddolino et al., 2021). The procedures described in that reference were replicated here, apart from all the 2-minute centrifuging steps instead being done in 4 minutes. For DNA recovery, standard phenol-chloroform extraction as ethanol precipitation as described in (Ausubel F, 1998), where we used Glycoblue (Ambion) as a co-precipitant, NaCl as a precipitating salt (due to the presence of SDS in our solution), and washed with ice-cold 95% ethanol to avoid loss of low molecular weight DNA and the dried DNA was resuspended in 100 μL of TEe (10 mM Tris pH 8.0; 0.1 mM EDTA pH 8.0) for input samples, 20 μL of TEe for RNAP-ChIP samples, and 50 μL of TEe for IPOD samples. RNA samples: RNA pellets were removed from -80°C and then immediately resuspended in 100 μL TE buffer (10 mM Tris pH 8.0; 1 mM EDTA pH 7.0). The resuspended pellet was treated with 1 μL lysozyme (Ready-Lyse; Lucigen, Ltd.) and incubated for 10 minutes at 4°C, followed by treatment with 10 μL proteinase K and incubation for 10 minutes at room temperature with vortexing every 2 minutes. RNA was then isolated using a Zymo RNA Clean and Concentrate 5 Kit twice for each sample, with a DNase digestion (25 μL eluate from first Zymo clean-up, 58 μL nuclease-free water, 10 μL 10X DNase Reaction Buffer, 2 μL RNase inhibitor, 5 μL Baseline Zero DNase) at 37°C for 30 minutes in-between Zymo kit clean-ups. Samples were then ribo-depleted using a NEBNext rRNA Depletion (Bacteria) Kit according to manufacturer’s instructions – with the exception that 10 μL of RNA sample, containing 1 μg of RNA, was used for probe hybridization. Following ribo-depletion, samples were again cleaned-up with the Zymo Clean and Concentrate 5 Kit and then prepared for sequencing using the NEBNext Ultra II Directional RNA Sequencing Kit
DNA samples: NEB Nebnext Ultra 2 DNA kit RNA samples: NEBNext Ultra 2 Directional RNA kit

tag: strain

tag: genotype

value: wild type

tag: media

value: MOPS Rich Defined Media (RDM) + glucose

tag: time of_harvest

value: logarithmic phase


title: WT RDM logarithmic rep 1 - RNA-seq


title: Sample10_HEL,COM,rep1


title: Bacteria-injected larvae, 5 day + 13h, replicate 3


title: ΔdamΔdcm RDM logarithmic rep 3 - IPOD RNA-pol ChIP

library_source: genomic

molecule: genomic DNA

value: {delta}dam{delta}dcm


title: Sample7_HEL,ANA,rep1


title: Δdam RDM logarithmic rep 1 - RNA-seq

value: {delta}dam


title: WT RDM logarithmic rep 2 - RNA-seq


title: Sample6_HEL,IDA,rep3


title: ΔdamΔdcm RDM logarithmic rep 1 - IPOD RNA-pol ChIP


title: Δdcm RDM logarithmic rep 3 - IPOD RNA-pol ChIP

value: {delta}dcm


title: Sample5_HEL,IDA,rep2


title: ΔdamΔdcm RDM logarithmic rep 2 - IPOD RNA-pol ChIP


title: Bacteria-injected larvae, 5 day + 6h, replicate 5

value: 5 day + 6 h


title: Bacteria-injected larvae, 5 day + 13h, replicate 1


title: Sample4_HEL,IDA,rep1


title: Sample8_HEL,ANA,rep2


title: Δdcm RDM logarithmic rep 1 - IPOD RNA-pol ChIP


title: Bacteria-injected larvae, 5 day + 13h, replicate 2


title: Δdam RDM logarithmic rep 2 - IPOD RNA-pol ChIP


title: Bacteria-injected larvae, 5 day + 6h, replicate 4


title: Sample3_HEL,control,rep3

value: DMSO


title: Δdam RDM logarithmic rep 1 - IPOD RNA-pol ChIP


title: ΔdamΔdcm RDM logarithmic rep 2 - IPOD interphase


title: Bacteria-injected larvae, 5 day + 6h, replicate 1


title: WT RDM logarithmic rep 3 - IPOD RNA-pol ChIP


title: ΔdamΔdcm RDM logarithmic rep 3 - IPOD interphase


title: CB 3_control

city: Toronto

first: Veronique

last: Voisin

state: ON

address: 101 College St, room 8-353

country: Canada

institute: University Health Network

data_processing:
Samples were then submitted to The Centre for Applied Genomics (TCAG, Toronto, Canada) for high-throughput sequencing on the Illumina Novaseq 6000
Reads were aligned with STAR v2.5.2b (Dobin et al., 2013) against hg38 and annotated with ensembl v90. Default parameters were used except for the following: chimSegmentMin 12; chimJunctionOverhangMin 12; alignSJDBoverhangMin 10; alignMatesGapMax 100000; alignIntronMax 100000; chimSegmentReadGapMax parameter 3; alignSJstitchMismatchNmax 5 1 5 5.
Read counts were generated using HTSeq v0.7.2 (Anders et al., 2015). Differential gene expression was performed using edgeR_4.0.16 in R 4.3.2 following recommended practices.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text data frame that includes raw gene count value for each sample

molecule: polyA RNA

source_name: Cord Blood

growth_protocol: Sorted AML cells from each sample were cultured for 24 hours in 24 well flat-bottom plates, in serum-free X- VIVO 10 medium with 20% BIT9500, 1% L-glutamine, 1% penicillin-streptomycin supplemented with IL-6, SCF, TPO, IL-3, G-CSF. Exceptionally, sample WT3 required the support of MS5 stroma cells expressing human soluble CSF1. MS5 stroma cells were grown in 6-well tissue culture treated plates seeded at a density of 1-1.5 × 10ˆ5 cells/well, and cultured in IMEM medium +10% FBS, 1% Pen/Strep. Cells were propagated in T75 tissue culture treated flasks and passaged every 2-4 days for up to 7-8 passages. Sorted CB cells were cultured for 48 hours in 96 well round-bottom plates, in serum-free X- VIVO 10 medium supplemented with 1 % bovine serum albumin fraction V, 1x L-glutamine, 1x penicillin-streptomycin containing the subsequent cytokines: G-CSF, SCF, TPO and IL-6.

extract_protocol:
Cells were collected and viably sorted using SYTOX Blue Dead Cell Stain (Thermo Fisher Scientific), and we proceeded to total RNA purification and DNase treatment using the RNeasy Micro kit (Qiagen).
To generate RNAseq libraries, total RNA was used as input with SMART-Seq V4 Ultra Low Input RNA kit (Clontech). Next-generation sequencing libraries were made using the Nextera XT DNA Library Preparation kit (Illumina).

treatment_protocol: FLT3-KO and OR2W5-KO were performed using CRISPR/Cas9 technology through electroporation. After electroporation, cells were cultured for 3 additional days.

value: Cord Blood

value: CONTROL (OR2W5-KO)

value: Cord blood cells (primary)

tag: sort


title: Sample2_HEL,control,rep2


title: WT RDM logarithmic rep 1 - IPOD RNA-pol ChIP


title: WT RDM logarithmic rep 2 - IPOD RNA-pol ChIP


title: Bacteria-injected larvae, 5 day + 6h, replicate 2

value: larvae


title: Sample1_HEL,control,rep1


title: Bacteria-injected larvae, 5 day + 2h, replicate 5

value: 5 day + 2 h

value: Pseudomonas protegens Pf-5-injected


title: CB 3_KO


title: Δdcm RDM logarithmic rep 1 - IPOD interphase


title: Bacteria-injected larvae, 5 day + 2h, replicate 4


title: CB 2_control


title: Δdam RDM logarithmic rep 2 - IPOD interphase


title: Δdam RDM logarithmic rep 3 - IPOD RNA-pol ChIP


title: Δdam RDM logarithmic rep 1 - IPOD interphase


title: CB 2_KO


title: Bacteria-injected larvae, 5 day + 2h, replicate 2


title: Δdcm RDM logarithmic rep 2 - IPOD RNA-pol ChIP


title: CB 1_control


title: WT RDM logarithmic rep 3 - IPOD interphase


title: Bacteria-injected larvae, 5 day + 6h, replicate 3


title: ΔdamΔdcm RDM logarithmic rep 1 - IPOD interphase


title: Δdam RDM logarithmic rep 3 - IPOD interphase


title: Δdcm RDM logarithmic rep 3 - IPOD interphase


title: Δdcm RDM logarithmic rep 2 - IPOD interphase


title: Bacteria-injected larvae, 5 day + 2h, replicate 1


title: Δdcm RDM logarithmic rep 1 - RNA-seq


title: CB 1_KO


title: PBS-injected larvae, 5 day + 13h, replicate 5

value: 5 day + 13 h

value: PBS-injected control


title: ΔdamΔdcm RDM logarithmic rep 3 - IPOD input


title: ΔdamΔdcm RDM logarithmic rep 2 - IPOD input


title: Δdcm RDM logarithmic rep 3 - IPOD input


title: Bacteria-injected larvae, 5 day + 2h, replicate 3


title: WT RDM logarithmic rep 1 - IPOD interphase


title: AML FLT3 WT (WT3)_KO

source_name: Peripheral blood

value: Peripheral blood

value: Leukemic cells  (primary)


title: ΔdamΔdcm RDM logarithmic rep 1 - IPOD input

value: MOPS Rich Defined Media (RDM) + glucose


title: Δdcm RDM logarithmic rep 2 - IPOD input

value: logarithmic phase


title: AML FLT3 WT (WT3)_control


title: PBS-injected larvae, 5 day + 13h, replicate 4


title: PBS-injected larvae, 5 day + 13h, replicate 3


title: PBS-injected larvae, 5 day + 13h, replicate 2


title: Δdcm RDM logarithmic rep 1 - IPOD input


title: Δdam RDM logarithmic rep 3 - IPOD input


title: AML FLT3 WT (WT2)_KO


title: Δdam RDM logarithmic rep 1 - IPOD input


title: AML FLT3 WT (WT2)_control


title: Δdam RDM logarithmic rep 2 - IPOD input


title: AML FLT3 WT (WT1)_control


title: WT RDM logarithmic rep 3 - IPOD input

value: wild type


title: PBS-injected larvae, 5 day + 13h, replicate 1


title: PBS-injected larvae, 5 day + 6h, replicate 5


title: WT RDM logarithmic rep 2 - IPOD input


title: AML FLT3 WT (WT1)_KO


title: WT RDM logarithmic rep 2 - IPOD interphase


title: WT RDM logarithmic rep 1 - IPOD input


title: PBS-injected larvae, 5 day + 6h, replicate 3


title: RC726 Neuroretina control

city: Philadelphia

first: Raghavi

last: Sudharsan

address: 3900 Delancey Street

institute: University of Pennsylvania

description:
Library name: RC726UTX_S2
10X Genomics

library_source: transcriptomic single cell

data_processing:
Sequencing data were processed using the Cell Ranger pipeline
Assembly: Dog10K_Boxer_Tasha/canFam6
Supplementary files format and content: Compressed Tab-separated value files and matrix market exchange format files

organism: Canis lupus familiaris

source_name: Neurtoretina

extract_protocol:
Neuroretinal punches were treated with 0.25% trypsin for 10 minutes and then dissociated into single cells using Miltenyi Biotec Neural Tissue Dissociation kit - Postnatal neurons. Cells were washed and resuspended in PBS supplemented with 0.5% BSA.
Libraries were prepared using the 10X Single Cell 3' v3.1 following manufacterer's protocol.

treatment_protocol: Dogs with normal healthy retinas were given immusuppression treatment and subretinally injected with mechanically triturated hESC-derived retinal orgaoid fragments (as described in PMC9391525).

value: Neurtoretina

value: Normal or wild-type

value: Control


title: AML FLT3 ITD (ITD3)_KO


title: RC724 Neuroretina control

description:
Library name: RC724UTX_S2
10X Genomics


title: RC726 Neuroretina overlying graft

description:
Library name: RC726TX_S2
10X Genomics

value: Overlying transplant


title: AML FLT3 ITD (ITD2)_control


title: LG5 Neuroretina control

description:
Library name: LG5UTX_S1
10X Genomics


title: 15287X236_blastomere_8-CELL-G_type_IVF_cell_number_8

city: dallas

first: Edward

last: Grow

state: TEXAS

address: 7053 beltau lane

institute: UTSW

description: cellnumber 8

library_source: genomic single cell

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

organism: Bos indicus x Bos taurus

source_name: IVF

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

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

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

value: IVF


title: AML FLT3 ITD (ITD3)_control

value: CONTROL (OR2W5-KO)


title: PBS-injected larvae, 5 day + 6h, replicate 1

value: 5 day + 6 h


title: RC724 Neuroretina overlying graft

description:
Library name: RC724TX_S2
10X Genomics


title: 15287X237_blastomere_8-CELL-H_type_IVF_cell_number_8

description: cellnumber 8


title: AML FLT3 ITD (ITD2)_KO


title: AML FLT3 ITD (ITD1)_control


title: 15287X234_blastomere_8-CELL-E_type_IVF_cell_number_8

description: cellnumber 8


title: PBS-injected larvae, 5 day + 2h, replicate 4

value: larvae


title: 15287X233_blastomere_8-CELL-D_type_IVF_cell_number_8

description: cellnumber 8


title: LG5 Neuroretina overlying graft

description:
Library name: LG5TX_S1
10X Genomics


title: PBS-injected larvae, 5 day + 2h, replicate 3

value: 5 day + 2 h


title: PBS-injected larvae, 5 day + 2h, replicate 5


title: 15287X231_blastomere_8-CELL-B_type_IVF_cell_number_8

description: cellnumber 8


title: 15287X230_blastomere_8-CELL-A_type_IVF_cell_number_8

description: cellnumber 8


title: BJ fibroblast siERH+OSKM SOX2 CUT&RUN rep2

city: Seattle

first: Ryan

middle: Lehman

last: McCarthy

state: WA

address: 1900 9th Ave

department: Pediatrics

institute: University of Washington

data_processing:
Paired-end CUT&RUN reads were mapped to the human genome build hg38 using bowtie2 (v2.3.4.1) with run parameters --local --very-sensitive --no-unal --no-mixed --no-discordant -I 10 -X 1000. A quality-filtered BAM file was generated with the command samtools (v1.16.1) view -q 5 -f 2 -bS. Global scaling factors (SF) for siERH and siControl H3K9me3 data sets were calculated using the default parameters of ChIPSeqSpikeInFree (R v3.6.3). Bigwig files for visualization were generated from indexed BAM files with command bamCoverage --smoothLength 10 --normalizeUsing CPM --scaleFactor 1/SF --ignoreForNormalization chrM (deeptools 3.5.0). BED files were generated from BAMs using the bedtools command bamToBed (bedtools v2.27.1). BED files were converted to bedgraph format using the bedtools command genomecov. Peaks were called on the bedgraph files with SEACR (v1.3), using the stringent setting and selecting the top 0.01% of regions by AUC.
Assembly: hg38
Supplementary files format and content: bigwig, bed
Library strategy: CUT&RUN

source_name: BJ

growth_protocol: Cell lines culture and condition Human BJ foreskin fibroblasts were obtained from ATCC (CRL-2522) and cultured in Eagle’s Minimum Essential Medium (EMEM, Sigma-Aldrich M2279) supplemented with 10% fetal bovine serum (FBS, Hyclone SH30071) and 2mM Glutamax (ThermoFisher 35050061) at 37oC and 5% CO¬2.

extract_protocol:
CUT&RUN targeting H3K9me3 or SOX2 was performed following the protocol from Skene et al., 2017 and Janssens et al., 2018. BJ fibroblasts were detached from cell culture plates with Accutase (STEMCELL Technologies 07920), washed, bound to magnetic concanavalin A beads, and permeabilized with a dig-wash buffer (0.1% digitonin, 20 mM HEPES pH 7.5, 75 mM NaCl, 0.5 mM Spermidine, EDTA-free protease inhibitor). Bead-bound cells were incubated with a SOX2 (CST, clone D9B8N, 23064, 1:100) or H3K9me3 antibody (abcam ab8898, 1:100) at 4C overnight. The following morning, the cells were washed twice with dig-wash buffer, incubated with pA/G-MNase for an hour at 4C, and washed twice more. After chilling cells on an ice block for 5 minutes, MNase was activated for 30 minutes by addition of 2mM CaCl2. The reaction was stopped by adding an equal volume of 2X STOP buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.1% Digitonin, 0.05 mg/mL glycogen, 5 mg/mL RNase A). Digested chromatin was extracted from permeabilized cells at 37C for 30 minutes, and DNA was purified by phenol-chloroform.
Libraries were prepared as previously described in Liu et al., 2018.

treatment_protocol: Cell culture siRNA transfection experiments All ERH knockdown experiments were performed with two cycles of siRNA transfection (Silencer Select siRNA, Thermo Fisher, s4815), three days apart. Transfections were performed in fibroblasts using 5nM final concentration of siRNA  and 2.5ul/ml final concentration of Lipofectamine RNAiMAX (Thermo Fisher #31985070). We utilized the CytoTune-iPS 2.0 Sendai reprogramming kit (ThermoFisher, A16517) to express Oct4, SOX2, KLF4 and cMyc in BJ fibroblasts. Cells were treated according to the manufacturer’s instructions three days after the second of two cycles of siRNA transfection.

value: BJ

value: fibroblast

value: siERH

tag: antibody


title: AML FLT3 ITD (ITD1)_KO

value: Peripheral blood


title: 15287X232_blastomere_8-CELL-C_type_IVF_cell_number_8

description: cellnumber 8


title: 15287X229_blastomere_552D_type_IVF_cell_number_4

description: cellnumber 4


title: PBS-injected larvae, 5 day + 6h, replicate 2

value: PBS-injected control


title: 15287X228_blastomere_552C_type_IVF_cell_number_4

description: cellnumber 4


title: 15287X227_blastomere_587F_type_IVF_cell_number_6

description: cellnumber 6


title: BJ fibroblast siERH+OSKM SOX2 CUT&RUN rep1


title: 15287X235_blastomere_8-CELL-F_type_IVF_cell_number_8

description: cellnumber 8


title: PBS-injected larvae, 5 day + 2h, replicate 2


title: 15287X226_blastomere_587E_type_IVF_cell_number_6

description: cellnumber 6


title: PBS-injected larvae, 5 day + 6h, replicate 4


title: BJ fibroblast siControl+OSKM SOX2 CUT&RUN rep2

value: siControl


title: 15287X225_blastomere_587D_type_IVF_cell_number_6

description: cellnumber 6


title: 15287X224_blastomere_587C_type_IVF_cell_number_6

description: cellnumber 6


title: BJ fibroblast siControl+OSKM SOX2 CUT&RUN rep1


title: 15287X223_blastomere_587B_type_IVF_cell_number_6

description: cellnumber 6


title: BJ fibroblast siERH H3K9me3 CUT&RUN rep3

description:
H3K9me3_siERH_fibroblast_peaks_merged.bed
H3K9me3_siERH_fibroblast_mean_scaled.bw


title: Untreated larvae, 5 day + 13h, replicate 3

value: 5 day + 13 h

value: Untreated control


title: 15287X222_blastomere_587A_type_IVF_cell_number_6

description: cellnumber 6


title: BJ fibroblast siERH H3K9me3 CUT&RUN rep2


title: IR_5Gy_72h_rep 5

city: Ljubljana

first: Bostjan

last: Markelc

state: Ljubljana

address: Zaloska cesta 2

department: Department of Experimental Oncology

country: Slovenia

institute: Institute of Oncology Ljubljana

description:
Library name: IR_5Gy_72h_rep 5
Column AE in gene_count.xls

data_processing:
Quality control was assessed with fastp.
For mapping to the reference genome HISAT2 was used.
Quantification was performed by using featurecounts.
For differential expression analysis DESeq2 and edgeR were used.
Assembly: GRCh38/hg38
Supplementary files format and content: gene_count.xls contains counts for each sample.

source_name: cell line

growth_protocol: HUVEC cells were cultured in EGM-2 MV Microvascular Endothelial Cell Growth Medium-2 BulletKitTM (Lonza), with media changes every other day. Cells were cultured until reaching approximately 70% confluency and used up to passage number 10.

extract_protocol:
Cells were trypsinized with 0.05% Trypsin. Total RNA was extracted from cell passages ranging from p4 to p10 using Total RNA Kit peqGOLD (VWR) according to the manufacturer's instructions. The purity of isolated RNA was measured spectrophotomatrically using A260/A230 ratios. To assess RNA quality, RNA Assay for LabChip GX Touch (PerkinElmer, USA) was used, according to manufacturer's protocol. Samples with an RNA Quality score abouve 9 were sent for sequencing.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.

treatment_protocol: IR was conducted with Gulmay CP225 X-RAY generator with 0.55 mm copper and 1.8 mm aluminum filtering, operated at 200 kV, 9.2 mA, with a dose rate 1.73 Gy/min. HUVECs were subjected to 2 and 5 Gy of IR.

value: cell line

value: HUVEC

value: endothelial cells

value: WT

value: irradiation with 5 Gy


title: 15287X221_blastomere_552B_type_IVF_cell_number_4

description: cellnumber 4

value: IVF


title: Untreated larvae, 5 day + 13h, replicate 1


title: BJ fibroblast siERH H3K9me3 CUT&RUN rep1


title: 15287X220_blastomere_552A_type_IVF_cell_number_4

description: cellnumber 4


title: 15287X219_blastomere_586F_type_IVF_cell_number_6

description: cellnumber 6


title: IR_5Gy_72h_rep 4

description:
Library name: IR_5Gy_72h_rep 4
Column AD in gene_count.xls


title: IR_5Gy_72h_rep 3

description:
Library name: IR_5Gy_72h_rep 3
Column AC in gene_count.xls


title: BJ fibroblast siControl H3K9me3 CUT&RUN rep3


title: Untreated larvae, 5 day + 13h, replicate 2


title: PBS-injected larvae, 5 day + 2h, replicate 1


title: Untreated larvae, 5 day + 6h, replicate 5

value: 5 day + 6 h


title: IR_5Gy_72h_rep 2

description:
Library name: IR_5Gy_72h_rep 2
Column AB in gene_count.xls


title: 15287X218_blastomere_586E_type_IVF_cell_number_6

description: cellnumber 6


title: Untreated larvae, 5 day + 13h, replicate 5

value: larvae


title: Untreated larvae, 5 day + 6h, replicate 4


title: BJ fibroblast siControl H3K9me3 CUT&RUN rep2


title: 15287X217_blastomere_586D_type_IVF_cell_number_6

description: cellnumber 6


title: IR_2Gy_72h_rep 5

description:
Library name: IR_2Gy_72h_rep 5
Column Y in gene_count.xls

value: irradiation with 2 Gy


title: BJ fibroblast siControl H3K9me3 CUT&RUN rep1

value: BJ


title: IR_5Gy_72h_rep 1

description:
Library name: IR_5Gy_72h_rep 1
Column AA in gene_count.xls


title: Untreated larvae, 5 day + 13h, replicate 4


title: Untreated larvae, 5 day + 6h, replicate 3


title: H1 siERH 2day EC biol rep3

data_processing:
RNA-seq reads (paired-end) were mapped to the mm10 or hg38 genome for mouse and human experiments respectively using STAR (2.7.10b). The mapped reads to genes were counted using featureCounts.
Assembly: hg38, mm39
Supplementary files format and content: bigwig

growth_protocol: Mouse embryo work Mouse embryo experimentation was approved by the Biological Resource Center Institutional Animal Care and Use Committee (IACUC), Agency for Science, Technology and Research (IACUC Protocol 806983). C57BL/6 wild-type 3–4-week-old female mice were superovulated using 5 IU of pregnant mare serum (PMS, National Hormone and Peptide Program) gonadotropin given intraperitoneally and 5 IU of recombinant chorionic gonadotrophin (CG, National Hormone and Peptide Program) given 48 h after and immediately before mating, according to animal ethics guidelines of the University of Pennsylvania. Embryos were flushed from oviducts of plugged females using M2 medium (Merck) and cultured in KSOM+AA (Merck) covered by mineral oil (Sigma, M-5310), at 37 °C and 5% CO2. Cell lines culture and condition Human H1 ES cells were obtained from WiCell (WA01), grown on Matrigel coated wells and cultured in mTeSR1 (Stem Cell Tech, 85850) medium at 37oC and 5% CO¬2. Medium was changed daily. Human BJ foreskin fibroblasts were obtained from ATCC (CRL-2522) and cultured in Eagle’s Minimum Essential Medium (EMEM, Sigma-Aldrich M2279) supplemented with 10% fetal bovine serum (FBS, Hyclone SH30071) and 2mM Glutamax (ThermoFisher 35050061) at 37oC and 5% CO¬2.

extract_protocol:
BJ fibroblasts grown in a 6-well dish were washed twice with cold PBS, followed by addition of 1 mL TRIzol reagent (ThermoFisher 15596026) and transferred to a chilled 1.5 mL tube using a cell scraper. The cells were homogenized by pipetting through a 25G needle attached to a 2 mL syringe 10 times. 200 µl of chloroform was added to the cells and vortexed for 15 seconds, followed by a room temperature incubation of 3 minutes. Phase separation of nucleic acids and protein was performed by centrifugation at 12,000 x g for 15 minutes at 4C. The upper aqueous phase containing RNA was then transferred to a fresh chilled tube. RNA was precipitated from the aqueous phase by adding an equal volume of isopropyl alcohol, followed by a 10 minute incubation at room temperature. The RNA was pelleted by centrifugation at 12,000 x g for 10 minutes at 4C. After removal of supernatant, the pellet was washed twice with 1 mL 75% ethanol, and resuspended in nuclease free water. RNA quality was verified using a high-sensitivity RNA screentape (Agilent 5067-5576).
1ug of total RNA was sent to Novogene, who assembled and sequenced bulk RNA-seq libraries.

treatment_protocol: Mouse embryo siRNA injection experiments Microinjections were performed using a FemtoJet (Eppendorf). For ERH knockdown experiments, mouse embryos were injected with two siRNAs (Qiagen, S104403294 & S104403287) against ERH at a total concentration of 400 nM. For knockdown experiments AllStars negative control siRNA (Qiagen, 1027281) was injected in embryos at a concentration of 400nM.  Differentiation of hESCs Prior to differentiation, for samples to be analyzed by RNA-seq, cells grown to a density of 80% were digested with Accutase (Stem Cell Technologies, 07920) for 7 min. Then, DMEM/F12 was added and gently pipetted to generate a cell suspension. After centrifugation, cells were resuspended in mTeSR1 medium with 5uM ROCK inhibitor Y-27632 (Cayman Chemical, 10005583) and seeded at 8X105-1X106 cells per well in a 6 well plate coated with Matrigel (Millipore Sigma, CLS354277) 24 hours prior to differentiation treatment. For definitive endoderm differentiation of hESCs, mTeSR1 medium was removed and cells were cultured in DMEM/F12 (Thermo Fisher, 11320033) supplemented with 10% (v/v) Fetal Bovine Serum (Hyclone, SH30071) with 100ng/ml Activin A (Peprotech, 120-14P) and 3uM CHIR99021 (Cayman Chemical, 13122). For ectoderm differentiation of hESCs, mTeSR medium was removed and cells were cultured in DMEM/F12 with 5uM Retinoic Acid (Cayman Chemical, 11017).  Cell culture siRNA transfection experiments All ERH knockdown experiments were performed with two cycles of siRNA transfection (Silencer Select siRNA, Thermo Fisher, s4815), three days apart. Transfections were performed in fibroblasts using 5nM final concentration of siRNA and in hESCs using a 10nM final concentration of siRNA and 2.5ul/ml final concentration of Lipofectamine RNAiMAX (Thermo Fisher #31985070).

value: embryonic stem cell

value: ectoderm differentiation


title: H1 siERH 2day EC biol rep2

value: siERH


title: IR_2Gy_72h_rep 4

description:
Library name: IR_2Gy_72h_rep 4
Column Y in gene_count.xls


title: 15287X216_blastomere_586C_type_IVF_cell_number_6

description: cellnumber 6


title: Untreated larvae, 5 day + 6h, replicate 2


title: Untreated larvae, 5 day + 6h, replicate 1


title: 15287X215_blastomere_586B_type_IVF_cell_number_6

description: cellnumber 6


title: IR_2Gy_72h_rep 3

description:
Library name: IR_2Gy_72h_rep 3
Column X in gene_count.xls


title: IR_2Gy_72h_rep 2

description:
Library name: IR_2Gy_72h_rep 2
Column W in gene_count.xls


title: H1 siERH 2day EC biol rep1


title: H1 siControl 2day EC biol rep3


title: 15287X214_blastomere_586A_type_IVF_cell_number_6

description: cellnumber 6


title: IR_2Gy_72h_rep 1

description:
Library name: IR_2Gy_72h_rep 1
Column V in gene_count.xls


title: 15287X213_blastomere_621H_type_IVF_cell_number_8

description: cellnumber 8


title: 15287X212_blastomere_621G_type_IVF_cell_number_8

description: cellnumber 8


title: H1 siControl 2day EC biol rep2


title: Untreated larvae, 5 day + 2h, replicate 4

value: 5 day + 2 h


title: H1 siControl 2day EC biol rep1

value: siControl


title: Ctrl_72h_rep 4

description:
Library name: Ctrl_72h_rep 4
Column T in gene_count.xls


title: Untreated larvae, 5 day + 2h, replicate 2


title: 15287X210_blastomere_621E_type_IVF_cell_number_8

description: cellnumber 8


title: 15287X211_blastomere_621F_type_IVF_cell_number_8

description: cellnumber 8


title: Untreated larvae, 5 day + 2h, replicate 1


title: Untreated larvae, 5 day + 2h, replicate 3


title: H1 siERH 1day DE biol rep3

value: endoderm differentiation


title: H1 siERH 1day DE biol rep2


title: 15287X209_blastomere_621D_type_IVF_cell_number_8

description: cellnumber 8


title: 15287X208_blastomere_621C_type_IVF_cell_number_8

description: cellnumber 8


title: Ctrl_72h_rep 1

description:
Library name: Ctrl_72h_rep 1
Column Q in gene_count.xls


title: Untreated larvae, 5 day + 2h, replicate 5

value: Untreated control


title: 15287X207_blastomere_621B_type_IVF_cell_number_8

description: cellnumber 8


title: Embryo_Zld_RNAi_Zld_Input1

city: Madison

first: Melissa

last: Harrison

state: Wisconsin

address: 6204B Biochemical Sciences Building, 440 Henry Mall

department: Biomolecular Chemistry

institute: University of Wisconsin- Madison

description:
Library name: ChIPseq_63
Zld_RNAi_Input.bw

data_processing:
Reads were aligned to the Drosophila melanogaster genome (dm6) using bowtie2 v2.4.4. Reads mapped to mitochondrial or scaffold DNA, aligned multiple times, or were unmapped were discarded.
Assembly: dm6
Supplementary files format and content: bigwig files were formed from merged replicates and z-score normalized, except for the IP bigwig from the anti-Zld  in zld-RNAi ChIP-seq which was spike-in normalized with D. virilis  chromatin.

organism: Drosophila melanogaster

source_name: Stage 5 embryo

growth_protocol: Drosophila embryos were maintained at 25˚C on molasses agarose plates and processed for experimentation 2-3 hours after egg laying.

extract_protocol:
The ChIP protocol used on fixed embryos in this study was adapted from a published protocol (Blythe and Wieschaus, 2015). Embryos were collected 2-3hrs AEL, dechorionated in 50% bleach for 3 min, and followed by a 15min fixation in .45% formaldehyde for Zld. Two replicates of 1000 stage five embryos per experiment were hand sorted under a dissecting scope to avoid contamination by older embryos. Sorted embryos were homogenized in 1mL of RIPA buffer (50 mM Tris-HCl pH 8.0, 0.1% SDS, 1% Triton X-100, 0.5% sodium deoxycholate, and 150 mM NaCl) and underwent 11 cycles of sonication for 20s at 20% output on full duty cycle. For Zld ChIP in zld-RNAi, a spike-in of fixed and sonicated D. virilis was added before removing 2% input. IPs were incubated with 7 μl antibody overnight at 4C and purified using Protein A magnetic beads (Invitrogen). After washing and eluting purified IP, DNA from IPs and inputs were treated with 90µg of RNAseA for 30mins at 37˚C and decrosslinked by adding 100µg of Proteinase K overnight at 65˚C. DNA was purified using a phenol:chloroform extraction with an overnight ethanol precipitation step to concentrate samples. Libraries for inputs and IPs were prepared using the commercial NEB Next Ultra II kit.
Libraries were contructed using the NEB Next II Ultra kit. Sequencing was completed on the Illumina NovaSeq X Plus using 150bp pair end reads.

value: Stage 5 embryo

value: Zld (Harrison et al., 2010)


title: H1 siERH 1day DE biol rep1


title: H1 siControl 1day DE biol rep2


title: 15287X206_blastomere_621A_type_IVF_cell_number_8

description: cellnumber 8


title: IR_5Gy_24h_rep 4

description:
Library name: IR_5Gy_24h_rep 4
Column O in gene_count.xls

value: cell line

value: HUVEC

value: endothelial cells


title: Ctrl_72h_rep 2

description:
Library name: Ctrl_72h_rep 2
Column R in gene_count.xls

value: WT


title: Embryo_Zld_RNAi_Zld_IP1

description:
Library name: ChIPseq_61
Zld_RNAi_IP.bw


title: 15287X205_blastomere_622G_type_IVF_cell_number_7

description: cellnumber 7

value: IVF


title: IR_5Gy_24h_rep 5

description:
Library name: IR_5Gy_24h_rep 5
Column P in gene_count.xls

value: irradiation with 5 Gy


title: Ctrl_72h_rep 3

description:
Library name: Ctrl_72h_rep 3
Column S in gene_count.xls


title: H1 siControl 1day DE biol rep1


title: Ctrl_72h_rep 5

description:
Library name: Ctrl_72h_rep 5
Column U in gene_count.xls


title: Embryo_Zld_RNAi_Zld_Input2

description:
Library name: ChIPseq_64
Zld_RNAi_Input.bw


title: IR_5Gy_24h_rep 3

description:
Library name: IR_5Gy_24h_rep 3
Column N in gene_count.xls


title: H1 siERH biol rep2


title: H1 siERH biol rep3


title: Embryo_GFPCBP_Zld_Input2

description:
Library name: ChIPseq_58
Zld_GFPnej_Input.bw


title: 15287X204_blastomere_622F_type_IVF_cell_number_7

description: cellnumber 7


title: IR_5Gy_24h_rep 2

description:
Library name: IR_5Gy_24h_rep 2
Column M in gene_count.xls


title: IR_2Gy_24h_rep 5

description:
Library name: IR_2Gy_24h_rep 5
Column K in gene_count.xls

value: irradiation with 2 Gy


title: Embryo_Zld_RNAi_Zld_IP2

description:
Library name: ChIPseq_62
Zld_RNAi_IP.bw


title: Embryo_CBP_Degrad__Zld_Input2

description:
Library name: ChIPseq_60
Zld_GFPnejDeGRad_input.bw


title: 15287X203_blastomere_622E_type_IVF_cell_number_7

description: cellnumber 7


title: 15287X202_blastomere_622D_type_IVF_cell_number_7

description: cellnumber 7


title: Embryo_CBP_Degrad__Zld_IP2

description:
Library name: ChIPseq_56
Zld_GFPnejDeGRad_IP.bw


title: H1 siControl biol rep1


title: Embryo_CBP_Degrad__Zld_Input1

description:
Library name: ChIPseq_59
Zld_GFPnejDeGRad_input.bw


title: IR_2Gy_24h_rep 4

description:
Library name: IR_2Gy_24h_rep 4
Column J in gene_count.xls


title: BJ fibroblast siERH+OSKM biol rep2

value: BJ

value: fibroblast

value: siERH+OSKM


title: Embryo_GFPCBP_Zld_Input1

description:
Library name: ChIPseq_57
Zld_GFPnej_Input.bw


title: 15287X199_blastomere_622A_type_IVF_cell_number_7

description: cellnumber 7


title: Embryo_CBP_Degrad__Zld_IP1

description:
Library name: ChIPseq_55
Zld_GFPnejDeGRad_IP.bw


title: 15287X200_blastomere_622B_type_IVF_cell_number_7

description: cellnumber 7


title: 15287X198_blastomere_537A_type_IVF_cell_number_2

description: cellnumber 2


title: Embryo_GFPCBP_Zld_IP2

description:
Library name: ChIPseq_54
Zld_GFPnej_IP.bw


title: IR_2Gy_24h_rep 3

description:
Library name: IR_2Gy_24h_rep 3
Column I in gene_count.xls


title: IR_5Gy_24h_rep 1

description:
Library name: IR_5Gy_24h_rep 1
Column L in gene_count.xls


title: H1 siERH biol rep1

value: embryonic stem cell

value: siERH


title: BJ fibroblast siControl+OSKM biol rep2

value: siControl+OSKM


title: 15287X197_blastomere_620G_type_IVF_cell_number_7

description: cellnumber 7


title: H1 siControl biol rep2

value: siControl


title: H1 siControl 1day DE biol rep3

value: endoderm differentiation


title: IR_2Gy_24h_rep 2

description:
Library name: IR_2Gy_24h_rep 2
Column H in gene_count.xls


title: BJ fibroblast siERH+OSKM biol rep1


title: Ctrl_24h_rep 5

description:
Library name: Ctrl_24h_rep 5
Column F in gene_count.xls


title: BJ fibroblast siControl+OSKM biol rep1


title: Ctrl_24h_rep 4

description:
Library name: Ctrl_24h_rep 4
Column E in gene_count.xls


title: Δgp48 10H_3

city: Nanning

first: Zheng-Guo

last: He

state: Guangxi

address: 100 Daxue east road

institute: Guangxi university

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Both building index of reference genome and aligning clean reads to reference genome were used Bowtie2-2.2.3.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels .
Assembly: ASM1614v1
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes FPKM value for each sample

organism: Mycobacterium tuberculosis H37Ra

source_name: Mycobacterium tuberculosis strain H37Ra

growth_protocol: Mycobacterium tuberculosis H37Ra strains were maintained in 7H9 medium with 10% OADC, 0.2% glycerol and 0.05% Tween 80 at 37℃ 160rpm

extract_protocol:
Total RNA was isolated using RNAprep Pure Cell/Bacteria kit (Tiangen, China)
Strand-specific libraries were prepared using the NEBNext Ultra RNA Library Prep kit for Illumina (Illumina, USA) according to the manufacturer’s instructions.Library construction and sequencing were performed at Beijing Novogene Corporation.

treatment_protocol: The cells were infected by wide-type A4ZJ24 or gp48-deleted mutant phage at a MOI of 0.1 for 1h or 10h

value: Mycobacterium tuberculosis strain H37Ra

value: infected with A4ZJ24 phage

tag: phage species

value: mycobacteiophage

tag: phage genotype

value: gp48 knockdown

tag: time


title: IR_2Gy_24h_rep 1

description:
Library name: IR_2Gy_24h_rep 1
Column G in gene_count.xls

value: cell line

value: HUVEC

value: endothelial cells


title: Embryo_GFPCBP_Zld_IP1

description:
Library name: ChIPseq_53
Zld_GFPnej_IP.bw

value: Stage 5 embryo

value: Zld (Harrison et al., 2010)


title: 15287X196_blastomere_620F_type_IVF_cell_number_7

description: cellnumber 7

value: IVF


title: Δgp48 10H_2


title: 15287X195_blastomere_620E_type_IVF_cell_number_7

description: cellnumber 7


title: Δgp48 10H_1


title: M_D_hiPSC, MD6, Day14

city: Dallas

first: Leijie

last: Li

state: Texas

address: 5323 Harry Hines Blvd.

department: Molecular Biology

institute: UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER

data_processing:
Hisat2 v 2.1.0 and Stringtie v 2.1.7 pipeline
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trim Galore v 0.6.10
Trimmed sequence reads were mapped to GRCh38/GRCm39 genomics by using Hisat2 v 2.1.0
Read count extraction using StringTie v 2.1.7
Assembly: GRCh38 for human; GRCm39 for mouse
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

growth_protocol: PRKN-overexpressing mouse embryonic stem cells (PRKN-mESCs) were maintained in 2iL media and grown on Matrigel-coated plates, with 5% CO2 at 37C. PRKN-overexpressing human H9 embryonic stem cells (PRKN-hESCs) were grown in mTeSR Plus (STEMCELL) medium on Matrigel-coated (Corning) plates, with 5% CO2 at 37C.

extract_protocol:
RNA was harvested using the RNeasy Mini Plus Kit (Qiagen).
RNA libraries for RNA-seq were prepared using the SMARTer mRNA-Seq Library Prep Kit following the manufacturer's protocols.

treatment_protocol:
Mitochondria-depletion was carried out by treating PRKN-mESCs with 1 uM oligomycin A (Sigma) and antimycin A (Sigma) (A/O) for 72 hours in 2iL medium. For mitochondria-depletion of PRKN-hESCs, cells were treated with 1 uM A/O for 48 hours in mTeSR Plus. After A/O treatment, cells were washed three times with complete medium, then cultured for an additional 48 hours. After A/O treatment, washes, and 48-hour culture, cells were collected as Day 1 mitochondria-depleted cells. Medium was refreshed every day.
For Day 7 and Day 14 samples, mitochondria-depletion was carried out the same way, except after the washes, cells were cultured for only an additional 24 hours. Then, cells were grown in complete medium supplemented with 10% FBS (Gibco) and 1x CEPT (Tocris). Medium was changed every day for the first 7 days, then half of the medium was refreshed every day for the next 7 days.

value: pluripotent stem cells

value: WT

value: Mitochondria depletion supplemented with 10% FBS (Gibco) and 1x CEPT (Tocris)


title: 15287X194_blastomere_620D_type_IVF_cell_number_7

description: cellnumber 7


title: Ctrl_24h_rep 3

description:
Library name: Ctrl_24h_rep 3
Column D in gene_count.xls


title: Ctrl_24h_rep 2

description:
Library name: Ctrl_24h_rep 2
Column C in gene_count.xls


title: M_D_hiPSC, MD5, Day14


title: 15287X193_blastomere_620C_type_IVF_cell_number_7

description: cellnumber 7


title: M_D_hiPSC, MD4, Day7


title: Δgp48 1H_3


title: Ctrl_24h_ rep 1

description:
Library name: Ctrl_24h_ rep 1
Column B in gene_count.xls


title: 15287X192_blastomere_620B_type_IVF_cell_number_7

description: cellnumber 7


title: Δgp48 1H_2


title: M_D_hiPSC, MD3, Day7


title: M_D_hiPSC, MD1, Day1

value: Mitochondria depletion


title: p20 (M)

city: Bochum

first: Richard

middle: JP

last: Brown

state: NRW

address: Universitätsstr. 150

country: Germany

institute: Ruhr University

description:
Library name: 22088a0012
Name; Chromosome; Region; Expression value; TPM; RPKM; Exons; Gene ID; Gene length; ENSEMBL; Biotype; Unique gene reads; Total gene reads; Transcripts annotated; Uniquely identified transcripts; Exon length; Unique exon reads; Total exon reads; Ratio of unique to total (exon reads); Unique exon-exon reads; Total exon-exon reads; Unique intron reads; Total intron reads; Ratio of intron to total gene reads

data_processing:
CLC Genomics Workbench (Qiagen, Aarhaus)
Paired reads were mapped to the Hg38 genome scaffold, with gene and transcript annotations. Unmapped reads were saved for SARS-CoV-2 mapping.
Unmapped reads were mapped hCoV-19/Germany/BY-Bochum-1/2020 (B.1.1.70 variant; GISAID accession ID: EPI_ISL_1118929) genome to determine SARS-CoV-2 vRNA levels
For each sample, read counts for each human gene were normalised (RPKM, TPM)
Hg38 mappings were used in to identify differentialy expressed genes (DEGs) in the host between conditions (FDR <0.05)
Assembly: Hg38
Supplementary files format and content: Each sample has  .xlsx file containing processed data after Hg38 Mapping. This includes columns for Name; Chromosome; Region; Expression value; TPM; RPKM; Exons; Gene ID; Gene length; ENSEMBL; Biotype; Unique gene reads; Total gene reads; Transcripts annotated; Uniquely identified transcripts; Exon length; Unique exon reads; Total exon reads; Ratio of unique to total (exon reads); Unique exon-exon reads; Total exon-exon reads; Unique intron reads; Total intron reads; Ratio of intron to total gene reads
Supplementary files format and content: Each sample has  .xlsx file containing processed data after SARS-CoV-2 Mapping name; Chromosome; Region; Expression value; TPM; RPKM; Gene length; Unique gene reads; Total gene reads

organism:
Homo sapiens
Severe acute respiratory syndrome coronavirus 2

source_name: lung adenocarcinoma

growth_protocol: A549-A/T cells were grown in DMEM supplemented with 5% (v/v) fetal calf serum (FCS), 1% (v/v) non-essential amino acids (NEAA), 100 IU/mL penicillin, 100 μg/mL streptomycin, and 2 mM L-glutamine at 37 °C and 5% CO2.

extract_protocol:
Total RNA was then extracted using the NucleoSpin RNA kit (Macherey-Nagel) according to manufacturer’s instructions. RNA quality and quantity were analyzed using the NanoDrop One (Thermo Scientific) and Qubit.
Sequencing libraries were generated using a NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs) according to the manufacturer’s instructions.

treatment_protocol: All A549-A/T cells were infected with SARS-CoV-2 after treatment with either DMSO or MPA

value: lung adenocarcinoma

value: mycophenolic acid

tag: batch


title: 15287X191_blastomere_620A_type_IVF_cell_number_7

description: cellnumber 7


title: WT 10H_3

value: wildtype


title: 15287X190_blastomere_618P_type_IVF_cell_number_16

description: cellnumber 16


title: p20 (UTC)

description:
Library name: 22088a0011
Name; Chromosome; Region; Expression value; TPM; RPKM; Exons; Gene ID; Gene length; ENSEMBL; Biotype; Unique gene reads; Total gene reads; Transcripts annotated; Uniquely identified transcripts; Exon length; Unique exon reads; Total exon reads; Ratio of unique to total (exon reads); Unique exon-exon reads; Total exon-exon reads; Unique intron reads; Total intron reads; Ratio of intron to total gene reads

value: UTC


title: M_D_hiPSC, MD2, Day1


title: p15 (M)

description:
Library name: 22088a0010
Name; Chromosome; Region; Expression value; TPM; RPKM; Exons; Gene ID; Gene length; ENSEMBL; Biotype; Unique gene reads; Total gene reads; Transcripts annotated; Uniquely identified transcripts; Exon length; Unique exon reads; Total exon reads; Ratio of unique to total (exon reads); Unique exon-exon reads; Total exon-exon reads; Unique intron reads; Total intron reads; Ratio of intron to total gene reads


title: 15287X189_blastomere_618O_type_IVF_cell_number_16

description: cellnumber 16


title: WT 10H_1

value: Mycobacterium tuberculosis strain H37Ra

value: infected with A4ZJ24 phage


title: WT 10H_2

value: mycobacteiophage


title: M_D_hiPSC, Control2, Day0

value: Control


title: p15 (UTC)

description:
Library name: 22088a009
Name; Chromosome; Region; Expression value; TPM; RPKM; Exons; Gene ID; Gene length; ENSEMBL; Biotype; Unique gene reads; Total gene reads; Transcripts annotated; Uniquely identified transcripts; Exon length; Unique exon reads; Total exon reads; Ratio of unique to total (exon reads); Unique exon-exon reads; Total exon-exon reads; Unique intron reads; Total intron reads; Ratio of intron to total gene reads


title: M_D_hiPSC, Control1, Day0


title: 15287X188_blastomere_618N_type_IVF_cell_number_16

description: cellnumber 16


title: WT 1H_2


title: WT 1H_3


title: p9 (UTC)

description:
Library name: 22088a007
Name; Chromosome; Region; Expression value; TPM; RPKM; Exons; Gene ID; Gene length; ENSEMBL; Biotype; Unique gene reads; Total gene reads; Transcripts annotated; Uniquely identified transcripts; Exon length; Unique exon reads; Total exon reads; Ratio of unique to total (exon reads); Unique exon-exon reads; Total exon-exon reads; Unique intron reads; Total intron reads; Ratio of intron to total gene reads


title: 15287X187_blastomere_618M_type_IVF_cell_number_16

description: cellnumber 16


title: p9 (M)

description:
Library name: 22088a008
Name; Chromosome; Region; Expression value; TPM; RPKM; Exons; Gene ID; Gene length; ENSEMBL; Biotype; Unique gene reads; Total gene reads; Transcripts annotated; Uniquely identified transcripts; Exon length; Unique exon reads; Total exon reads; Ratio of unique to total (exon reads); Unique exon-exon reads; Total exon-exon reads; Unique intron reads; Total intron reads; Ratio of intron to total gene reads


title: UDCA,Expanded MAIT cells upon the stimulation of 5-OP-RU/MR1 tetramer with UDCA,HD,biol rep4

city: Wuhan

first: xiufang

last: weng

address: 13# Hangkong Rd, Wuhan, Hubei

institute: Huazhong University of Science and Technology

data_processing:
Illumina nova seq platform used for basecalling.
Raw image Data files obtained by Illumina nova are analyzed by CASAVA Base Calling and converted into Raw Data of sequencing sequences，and the results are stored in FASTQ (.fastq.gz) file format. The reference genomes and the annotation file were downloaded from ENSEMBL database (http://www.ensembl.org/index.html).
The clean reads obtained by filtering were compared to the reference sequence.Based on the comparison results, new transcript prediction, differential splicing gene detection, SNP and Indel detection, fusion gene detection and other analyses were performed.
HISAT was used to compare clean reads to reference genes. Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and RPKM (Reads per Kilobase per Million Reads) was then calculated to estimate the expression level of genes in each sample.
Assembly: Homo_sapiens.GRCh38.99.chr
Supplementary files format and content: Matrix table with read counts for every gene and every sample

source_name: peripheral blood

extract_protocol:
Total RNAs were extracted from enriched cells  using TRIzol Reagent (Invitrogen,cat. NO 15596026 ), following the methods by Chomczynski et al (DOI:10.1006/abio.1987.9999)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol:
expanded MAIT cells
expanded MAIT cells with GCDCA
expanded MAIT cells with TCDCA
expanded MAIT cells with UDCA

value: peripheral blood

value: T cell

value: MAIT

value: UDCA


title: UDCA,Expanded MAIT cells upon the stimulation of 5-OP-RU/MR1 tetramer with UDCA,HD,biol rep3


title: Δgp48 1H_1

value: gp48 knockdown


title: 15287X186_blastomere_618L_type_IVF_cell_number_16

description: cellnumber 16

value: IVF


title: UDCA,Expanded MAIT cells upon the stimulation of 5-OP-RU/MR1 tetramer with UDCA,HD,biol rep2


title: WT 1H_1


title: p5 (M)

description:
Library name: 22088a006
Name; Chromosome; Region; Expression value; TPM; RPKM; Exons; Gene ID; Gene length; ENSEMBL; Biotype; Unique gene reads; Total gene reads; Transcripts annotated; Uniquely identified transcripts; Exon length; Unique exon reads; Total exon reads; Ratio of unique to total (exon reads); Unique exon-exon reads; Total exon-exon reads; Unique intron reads; Total intron reads; Ratio of intron to total gene reads


title: p5 (UTC)

description:
Library name: 22088a005
Name; Chromosome; Region; Expression value; TPM; RPKM; Exons; Gene ID; Gene length; ENSEMBL; Biotype; Unique gene reads; Total gene reads; Transcripts annotated; Uniquely identified transcripts; Exon length; Unique exon reads; Total exon reads; Ratio of unique to total (exon reads); Unique exon-exon reads; Total exon-exon reads; Unique intron reads; Total intron reads; Ratio of intron to total gene reads


title: 15287X184_blastomere_618J_type_IVF_cell_number_16

description: cellnumber 16


title: chicken primary muscle-derived cells, ribosomes incoporated, No2

city: Fukuoka

first: Shota

last: Inoue

address: 744 Motooka Nishi-ku Fukuoka

department: Graduate School of Systems Life Sciences

country: Japan

institute: Kyushu University

description: Library name: Sample4

data_processing:
macOS v12.7.6
FastQ reads generated from the samples were processed using the fastp tool (version 0.23.4) to trim low-quality regions (with a Phred quality score cutoff of Q = 30) and remove adapter sequences
The trimmed paired-end reads were aligned to the GRCg7b reference genome (bGalGal1.mat.broiler.GRCg7b, GCA_016699485.1) using the HISAT2 program (version 2.2.1)
Gene-level read counts were extracted using featureCounts (version 2.0.1) with the cor-responding GTF file (Ensembl release-111) from the Ensembl genome browser
The read counts were then normalized by TPM
Assembly: GRCg7b
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: csv file includes TPM values for each sample
Library strategy: Ribo-Seq

organism: Gallus gallus

source_name: muscle

growth_protocol: CMCs were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
RNA was harvested using RNeasy Plus Mini Kit (Qiagen).
RNA libraries were prepared from the purified RNA using the Illumina TruSeq Stranded mRNA Sample Preparation kit.

treatment_protocol: CMCs were incorporated with ribosomes in ESGRO medium and cultured for 14 days in a humidified atmosphere with 5% CO₂ at 37°C. In the control group, CMCs were cultured under the same conditions without ribosome addition

value: muscle


title: chicken primary muscle-derived cells, ribosomes incoporated, No1

description: Library name: Sample3


title: p3 (M)

description:
Library name: 22088a004
Name; Chromosome; Region; Expression value; TPM; RPKM; Exons; Gene ID; Gene length; ENSEMBL; Biotype; Unique gene reads; Total gene reads; Transcripts annotated; Uniquely identified transcripts; Exon length; Unique exon reads; Total exon reads; Ratio of unique to total (exon reads); Unique exon-exon reads; Total exon-exon reads; Unique intron reads; Total intron reads; Ratio of intron to total gene reads


title: TCDCA,Expanded MAIT cells upon the stimulation of 5-OP-RU/MR1 tetramer with TCDCA,HD,biol rep4

value: TCDCA


title: 15287X183_blastomere_618I_type_IVF_cell_number_16

description: cellnumber 16


title: TCDCA,Expanded MAIT cells upon the stimulation of 5-OP-RU/MR1 tetramer with TCDCA,HD,biol rep3


title: p3 (UTC)

description:
Library name: 22088a003
Name; Chromosome; Region; Expression value; TPM; RPKM; Exons; Gene ID; Gene length; ENSEMBL; Biotype; Unique gene reads; Total gene reads; Transcripts annotated; Uniquely identified transcripts; Exon length; Unique exon reads; Total exon reads; Ratio of unique to total (exon reads); Unique exon-exon reads; Total exon-exon reads; Unique intron reads; Total intron reads; Ratio of intron to total gene reads


title: chicken primary muscle-derived cells, Control, No1

description: Library name: Sample1

data_processing:
macOS v12.7.6
FastQ reads generated from the samples were processed using the fastp tool (version 0.23.4) to trim low-quality regions (with a Phred quality score cutoff of Q = 30) and remove adapter sequences
The trimmed paired-end reads were aligned to the GRCg7b reference genome (bGalGal1.mat.broiler.GRCg7b, GCA_016699485.1) using the HISAT2 program (version 2.2.1)
Gene-level read counts were extracted using featureCounts (version 2.0.1) with the cor-responding GTF file (Ensembl release-111) from the Ensembl genome browser
The read counts were then normalized by TPM
Assembly: GRCg7b
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: csv file includes TPM values for each sample


title: 15287X182_blastomere_618H_type_IVF_cell_number_16

description: cellnumber 16


title: TCDCA,Expanded MAIT cells upon the stimulation of 5-OP-RU/MR1 tetramer with TCDCA,HD,biol rep2


title: p1 (M)

description:
Library name: 22088a002
Name; Chromosome; Region; Expression value; TPM; RPKM; Exons; Gene ID; Gene length; ENSEMBL; Biotype; Unique gene reads; Total gene reads; Transcripts annotated; Uniquely identified transcripts; Exon length; Unique exon reads; Total exon reads; Ratio of unique to total (exon reads); Unique exon-exon reads; Total exon-exon reads; Unique intron reads; Total intron reads; Ratio of intron to total gene reads


title: p1 (UTC)

description:
Library name: 22088a001
Name; Chromosome; Region; Expression value; TPM; RPKM; Exons; Gene ID; Gene length; ENSEMBL; Biotype; Unique gene reads; Total gene reads; Transcripts annotated; Uniquely identified transcripts; Exon length; Unique exon reads; Total exon reads; Ratio of unique to total (exon reads); Unique exon-exon reads; Total exon-exon reads; Unique intron reads; Total intron reads; Ratio of intron to total gene reads


title: S2-Zld_CuSO4_A-485_K27ac_IP2

data_processing:
Reads were aligned to the Drosophila melanogaster genome (dm6) using bowtie2 v2.4.4. Reads mapped to mitochondrial or scaffold DNA, aligned multiple times, or were unmapped were discarded.
Assembly: dm6
Supplementary files format and content: bigwig files were formed from merged replicates and z-score normalized, except for bigwigs from the anti-GFP and H3K27ac (in S2 cells) ChIP-seq in which were spike-in normalized with mouse chromatin.

growth_protocol: Drosophila embryos were maintained at 25˚C on molasses agarose plates and processed for experimentation 2-3 hours after egg laying. S2 cells were cultured in Schneider’s medium with supplemented antibiotic/antimycotic and 10% FBS at 27 ˚C.

extract_protocol:
The ChIP protocol used on fixed embryos in this study was adapted from a published protocol (Blythe and Wieschaus, 2015). Embryos were collected 2-3hrs AEL, dechorionated in 50% bleach for 3 min, and followed by a 15min fixation in formaldehyde (.45% formaldehyde for Zld and H3K27ac, 1.8% for CBPGFP). Two replicates of 1000 stage five embryos per experiment were hand sorted under a dissecting scope to avoid contamination by older embryos. Sorted embryos were homogenized in 1mL of RIPA buffer (50 mM Tris-HCl pH 8.0, 0.1% SDS, 1% Triton X-100, 0.5% sodium deoxycholate, and 150 mM NaCl) and underwent 11 cycles of sonication for 20s at 20% output on full duty cycle. For CBPGFP ChIP, a spike-in of fixed and sonicated H3.3-GFP MEF chromatin was added before removing 2% input. IPs were incubated with 6µg antibody overnight at 4?C and purified using Protein A magnetic beads (Invitrogen). After washing and eluting purified IP, DNA from IPs and inputs were treated with 90µg of RNAseA for 30mins at 37˚C and decrosslinked by adding 100µg of Proteinase K overnight at 65˚C. DNA was purified using a phenol:chloroform extraction with an overnight ethanol precipitation step to concentrate samples. Libraries for inputs and IPs were prepared using the commercial NEB Next Ultra II kit. ChIP in S2 cells was performed as previously described (Gibson et al. 2023). 5x107 cells were fixed in .8% formaldehyde for 7 min. Fixed chromatin was sonicated on a Covaris S220 for five 120s rounds with 60s delay, peak power at 170, a duty factor of 10%, and 200 cycles per burst. A spike-in of 5% MEF chromatin was added to H3K27ac sonicated chromatin before separating IPs from 2% input. IPs were incubated with antibody at 4?C for 4 hours. IP purification, RNAse treatment, decrosslinking, and DNA concentration was performed identically to the embryo ChIP protocol stated above.
Libraries were contructed using the NEB Next II Ultra kit. Sequencing was completed between the Illumina NextSeq 500 using 75bp single end reads or the Illumina Hi-Seq4000 using 50bp single end reads.

treatment_protocol: S2 cells were induced to express Zld using CuSO4, and were treated either with control DMSO drug or a CBP catalytic inhibitor A485 for 4 hours.

value: 400 uM CuSO4

tag: condition

value: H3K27ac (Active motif 39135 )


title: 15287X180_blastomere_618F_type_IVF_cell_number_16

description: cellnumber 16


title: 15287X185_blastomere_618K_type_IVF_cell_number_16

description: cellnumber 16


title: S2-Zld_CuSO4_A-485_K27ac_Input1


title: GCDCA,Expanded MAIT cells upon the stimulation of 5-OP-RU/MR1 tetramer with GCDCA,HD,biol rep4

value: GCDCA


title: UDCA,Expanded MAIT cells upon the stimulation of 5-OP-RU/MR1 tetramer with UDCA,HD,biol rep1


title: 15287X201_blastomere_622C_type_IVF_cell_number_7

description: cellnumber 7


title: S2-Zld_CuSO4_A-485_K27ac_IP1


title: 15287X178_blastomere_618D_type_IVF_cell_number_16

description: cellnumber 16


title: GCDCA,Expanded MAIT cells upon the stimulation of 5-OP-RU/MR1 tetramer with GCDCA,HD,biol rep3


title: 15287X177_blastomere_618C_type_IVF_cell_number_16

description: cellnumber 16


title: chicken primary muscle-derived cells, Control, No2

description: Library name: Sample2


title: GCDCA,Expanded MAIT cells upon the stimulation of 5-OP-RU/MR1 tetramer with GCDCA,HD,biol rep2


title: antibiotics, rep9

type: RNA

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

institute: University clinics Freiburg

hyb_protocol: Labeled fragments were hybridized to Affymetrix Clariom S arrays for 16h at 45°C with 60 rpm in an Affymetrix Hybridization oven 645.

scan_protocol: After washing and staining, the arrays were scanned with the Affymetrix GeneChip Scanner 3000 7G. CEL-files were produced from the raw data with Affymetrix GeneChip Command Console Software.

data_processing: CEL files were analysed using the oligo R package. RMA method, log2 transformed were used to normalized the probe intensities.

label: Biotin

organism: Mus musculus

source_name: allo-HCT mice, treated, day +14

label_protocol: We used the Affymetrix Clariom S kit for cDNA synthesis, amplification, and second-cycle cDNA synthesis, as well as fragmentation and labeling with Biotin, as described by the manufacturer.

growth_protocol: Mice were housed in SPF conditions for the entire duration of ABX/vehicle treatment and allo-HCT, till the day of harvest (D+14). After anesthesia, brains were homogenised and cells sorted on BD FACS Aria II before analysis.

extract_protocol: CD45int CD11b+ cells were sorted using FACS

treatment_protocol: Mice were treated for 14 days with ABX/vehicle (D-13 to D-1), underwent allo-HCT (D0) and continued on ABX/vehicle treatment for another 14 days (D+1 to D+14).

value: Sorted CD45int CD11b+ cells

value: antibiotics (ABX)

value: Brain


title: S2-Zld_CuSO4_DMSO_K27ac_Input2

value: 1000 uM CuSO4

value: DMSO


title: S2-Zld_CuSO4_A-485_K27ac_Input2


title: GCDCA,Expanded MAIT cells upon the stimulation of 5-OP-RU/MR1 tetramer with GCDCA,HD,biol rep1


title: TCDCA,Expanded MAIT cells upon the stimulation of 5-OP-RU/MR1 tetramer with TCDCA,HD,biol rep1


title: 15287X175_blastomere_618A_type_IVF_cell_number_16

description: cellnumber 16


title: GmMEKK2, SMV inoculation 14 dpi, biol rep 2

city: Hangzhou

first: Xuanbo

last: Zhong

address: 866 Yuhangtang Road

institute: Zhejiang university

description: Library name: ZMP_14d2

data_processing:
Paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) in a reference-based approach.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Assembly: Glycine_max_v4.0
Supplementary files format and content: text file include FPKM values for each Sample

organism: Glycine max

source_name: leaf

extract_protocol:
RNA degradation and contamination was monitored on 1% agarose gels.RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

value: leaf

value: SMV inoculation 14 dpi


title: GmMEKK2, SMV inoculation 14 dpi, biol rep 3

description: Library name: ZMP_14d3


title: antibiotics, rep8


title: C,Expanded MAIT cells upon the stimulation of 5-OP-RU/MR1 tetramer,HD,biol rep6

value: peripheral blood

value: T cell

value: Control


title: S2-Zld_CuSO4_DMSO_K27ac_Input1


title: S2-Zld_CuSO4_DMSO_K27ac_IP2


title: 15287X179_blastomere_618E_type_IVF_cell_number_16

description: cellnumber 16


title: 15287X174_blastomere_617P_type_IVF_cell_number_16

description: cellnumber 16


title: C,Expanded MAIT cells upon the stimulation of 5-OP-RU/MR1 tetramer,HD,biol rep4

value: MAIT


title: 15287X173_blastomere_617O_type_IVF_cell_number_16

description: cellnumber 16

value: IVF


title: S2-Zld_CuSO4_DMSO_K27ac_IP1


title: C,Expanded MAIT cells upon the stimulation of 5-OP-RU/MR1 tetramer,HD,biol rep5


title: GmMEKK2, SMV inoculation 14 dpi, biol rep 1

description: Library name: ZMP_14d1


title: vehicle, rep5

value: vehicle (VEH)


title: S2-Zld_A-485_K27ac_Input2

value: 0 uM CuSO4


title: 15287X176_blastomere_618B_type_IVF_cell_number_16

description: cellnumber 16


title: C,Expanded MAIT cells upon the stimulation of 5-OP-RU/MR1 tetramer,HD,biol rep3


title: vehicle, rep1


title: GmMEKK2, SMV inoculation 7 dpi, biol rep 2

description: Library name: ZMP_7d2

value: SMV inoculation 7 dpi


title: 15287X172_blastomere_617N_type_IVF_cell_number_16

description: cellnumber 16


title: 15287X181_blastomere_618G_type_IVF_cell_number_16

description: cellnumber 16


title: C,Expanded MAIT cells upon the stimulation of 5-OP-RU/MR1 tetramer,HD,biol rep2


title: S2-Zld_A-485_K27ac_IP2

value: H3K27ac (Active motif 39135 )


title: S2-Zld_A-485_K27ac_Input1


title: GmMEKK2, SMV inoculation 7 dpi, biol rep 1

description: Library name: ZMP_7d1


title: C,Expanded MAIT cells upon the stimulation of 5-OP-RU/MR1 tetramer,HD,biol rep1


title: 15287X169_blastomere_617I_type_IVF_cell_number_16

description: cellnumber 16


title: S2-Zld_A-485_K27ac_IP1


title: 15287X170_blastomere_617J_type_IVF_cell_number_16

description: cellnumber 16


title: NHEK cells, Liq-Rock-3, 42hours

city: Chikusa-ku

first: Hirofumi

last: Teshima

state: Aichi

address: furo-chou

institute: Nagoya university

data_processing:
Miniconda3 v 23.3.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp (parameter- quality value: 15, length required: 20)
Trimmed sequence reads were mapped to GRCh38 using HISAT2
Read count extraction were performed using stringtie
Read count normalization were performed using DESeq2 v 1.38.3
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes RPKM values and TPM values for each Sample

source_name: epidermis

growth_protocol: Normal human epidermal keratinocytes were culture in the medium CnT-Prime Epithelial Proliferating Medium followed by the 3D Airlift Medium (CELLnTEC, Switzerland) grown on the insert filter in 24-well plate.

extract_protocol:
At the 42 hrs after starting the air-exposure time, each cultrued  cells were harvested to prepare RNA using the Sepasol-I (Nacalai Tesque, Kyoto, Japan) followed by the RNA mini kit (Favorgen, Ping Tung, Taiwan)
The cDNAs were synthesized from oligo(dT)-purified RNA fraction and double stranded-cDNA was constructed

treatment_protocol: The proliferated cells were grown on the filter insert and air-exposure was started by removing the medium. In the case of rocking, the cell were cultured in the submerged with see-saw type shaking.

value: epidermis

value: cultured keratinocytes

value: wild type

value: rocking


title: GmMEKK2, SMV inoculation 0 dpi, biol rep 2

description: Library name: ZMP_CK2

value: SMV inoculation 0 dpi


title: GmMEKK2, SMV inoculation 7 dpi, biol rep 3

description: Library name: ZMP_7d3


title: S2-Zld_DMSO_K27ac_IP2

value: DMSO


title: 15287X168_blastomere_617G_type_IVF_cell_number_16

description: cellnumber 16


title: 15287X167_blastomere_617F_type_IVF_cell_number_16

description: cellnumber 16


title: NHEK cells, Liq-Rock-1, 42hours


title: wildtype, SMV inoculation 14 dpi, biol rep 2

description: Library name: NT_14d2

value: leaf

value: WT


title: 15287X166_blastomere_617E_type_IVF_cell_number_16

description: cellnumber 16


title: NHEK cells, Liq-3, 42hours

value: submerged


title: wildtype, SMV inoculation 14 dpi, biol rep 3

description: Library name: NT_14d3

value: SMV inoculation 14 dpi


title: 15287X165_blastomere_617D_type_IVF_cell_number_16

description: cellnumber 16


title: 15287X171_blastomere_617L_type_IVF_cell_number_16

description: cellnumber 16


title: wildtype, SMV inoculation 14 dpi, biol rep 1

description: Library name: NT_14d1


title: wildtype, SMV inoculation 7 dpi, biol rep 3

description: Library name: NT_7d3


title: Embryo_ZldRNAi_H3K27ac_Input2

value: Stage 5 embryo


title: GmMEKK2, SMV inoculation 0 dpi, biol rep 3

description: Library name: ZMP_CK3


title: NHEK cells, Liq-1, 42hours


title: 15287X164_blastomere_617B_type_IVF_cell_number_16

description: cellnumber 16


title: S2-Zld_DMSO_K27ac_Input2


title: Embryo_ZldRNAi_H3K27ac_IP2


title: wildtype, SMV inoculation 7 dpi, biol rep 2

description: Library name: NT_7d2


title: Embryo_ZldRNAi_H3K27ac_Input1


title: NHEK cells, Air-2, 42hours

value: air-exposure


title: GmMEKK2, SMV inoculation 0 dpi, biol rep 1

description: Library name: ZMP_CK1


title: 15287X163_blastomere_617A_type_IVF_cell_number_16

description: cellnumber 16

value: IVF


title: NHEK cells, Air-3, 42hours


title: wildtype, SMV inoculation 7 dpi, biol rep 1

description: Library name: NT_7d1


title: Embryo_ZldRNAi_H3K27ac_IP1


title: NHEK cells, Air-1, 42hours


title: 15287X161_blastomere_613L_type_IVF_cell_number_13

description: cellnumber 13


title: NHEK cells, Liq-Rock-2, 42hours


title: NHEK cells, Liq-2, 42hours


title: S2-Zld_DMSO_K27ac_IP1


title: wildtype, SMV inoculation 0 dpi, biol rep 3

description: Library name: NT_CK3


title: Embryo_WT_H3K27ac_Input2


title: 15287X160_blastomere_613K_type_IVF_cell_number_13

description: cellnumber 13


title: Embryo_WT_H3K27ac_IP2


title: WAY treatment 1

city: Kawasaki

first: Tatsuto

last: Kageyama

state: Kanagawa

address: Life Innovation Center, 3-25-22 Tonomachi

institute: Kanagawa Institute of Industrial Science and Technology

data_processing:
Data processing were conducted using NovaSeq Control Software v1.7.5, Real Time Analysis (RTA) v3.4.4, bcl2fastq2 v2.20, and DRAGEN Bio-IT Platform v3.9.3
Assembly: hg18
Supplementary files format and content: TPM, counts

source_name: hair follicle

growth_protocol: Adult human DP cells were obtained from PromoCell (Heidelberg, Germany), passaged up to passage four, and used for 2D culture.

extract_protocol:
Total RNA was extracted using an RNeasy Mini Kit (Qiagen) from DP cells 20  μM WAY267464 or LIT001 treatment for 3 days.
RNA library for RNA-seq were prepared using SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing and Nextera XT DNA Library Prep Kit

treatment_protocol: Dermal papilla cells (2 × 104 cells) were suspended in 0.5 mL culture medium supplemented with 20  μM WAY267464 or LIT001, and seeded into the wells of a 24-well cell culture plate (Corning Inc., Corning, NY, USA). Gene expression in DP cells was assessed  after 3 days of culture.

value: hair follicle

value: dermal papilla cells

value: WAY267464 treatment for 3 days.


title: LIT treatment 1

value: LIT001 treatment for 3 days.


title: wildtype, SMV inoculation 0 dpi, biol rep 2

description: Library name: NT_CK2


title: 15287X159_blastomere_613J_type_IVF_cell_number_13

description: cellnumber 13


title: 15287X162_blastomere_613M_type_IVF_cell_number_13

description: cellnumber 13


title: 15287X158_blastomere_613I_type_IVF_cell_number_13

description: cellnumber 13


title: Embryo_WT_H3K27ac_IP1

value: H3K27ac (Active motif 39135 )


title: ThIL620ng2

city: Davis

first: Gaurav

last: Sarode

state: CA

address: 6404A GBSF, 451 E. Health Sciences Dr.

department: Internal Medicine

institute: University of California, Davis

data_processing:
Raw reads (FASTQ) were processed through fastp (0.20.0), removing reads containing adapter and poly-N sequences and low-quality reads while simultaneously calculating Q20, Q30, and GC content
Paired-end clean reads were aligned to the reference genome(grcm38) using the Spliced Transcripts Alignment to a Reference (STAR) software (v2.6.1d)
FeatureCounts(v1.5.0-p3) was used to count the reads mapped to each gene; RPKM of each gene was calculated based on the length of the gene and reads mapped to the gene.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
Supplementary files format and content: Matrix tab-delimited text files with raw gene counts for every gene and every sample

source_name: liver

growth_protocol: HepG2 cells were obtained from ATCC (HB-8065, Lot: 70015966) and cultured in . Dulbecco's Modified Eagle Medium (DMEM) (cat# 11965118), 10% fetal bovine serum (Fisher Scientific, cat# FB12999102), and 1% penicillin/streptomycin (Gibco, cat# 15140122); cells were incubated at 37°C and 5% CO2. An equal number of cells were seeded in each well of 6-well or 10-cm collagen-treated cell culture plates per treatment group and incubated overnight to attach, with subsequent media changes twice per week

extract_protocol:
After pre-treatment, cells were treated  for 1, 4 and 24 hours with either,- no treatment (NT), Recombinant Human IL-6 Protein (IL-6) 1 ng/ml (low dose), IL-6 20 ng/ml (high dose, cat# 206-IL-010, R&D Systems, Minneapolis, MN), Hyper IL-6 (Recombinant human IL-6R alpha/IL-6 chimera) 1 ng/ml (low dose), and Hyper IL-6 20 ng/ml (high dose, cat# 8954-SR-025, R&D Systems, Minneapolis, MN). Untreated HepG2 control cells were washed twice with PBS and provided with fresh medium. The following day, cells were used for protein and RNA isolation.
Sequencing libraries were generated using with 1 ug of total RNA by NEBNext Ultra RNA Library Prep Kit for Illumina (Cat. no-E7530LNew England Biolabs).

treatment_protocol: HepG2 cells were pre-treated with 1% FBS with no Recombinant Human TGF-beta 1 Protein (TGF-B1) or 5 ng/ml TGF-B1 (cat#R240-B-010, R&D Systems, Minneapolis, MN) overnight.

value: liver

tag: disease

value: cancer

value: HepG2 cells

value: TGFb+Hyper IL6 20ng


title: No treatment 1


title: 15287X157_blastomere_613G_type_IVF_cell_number_13

description: cellnumber 13

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


title: 15287X156_blastomere_613F_type_IVF_cell_number_13

description: cellnumber 13


title: Embryo_GFPnej_ZldRNAi_Input2


title: brefs-inflorescences-1

city: Anseong-si, Gyeonggi-do

first: Heewon

last: Moon

address: 4726,Seodong-daero, Daedeok-myeon

country: South Korea

institute: Chung-ang university

description: replicate 1

data_processing:
Quality evaluation of the RNA-seq reads were conducted using the FastQC software (http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Low quality of raw reads was trimmed and filtered out using Trimmomatic (ver0.36) (Bolger et al. 2014).
Qualified reads (Q>30%) were only used in the mapping. Reference genome of Brassica rapa plants was obtained from Ensembl Plants (https://plants.ensembl.org/info/website/ftp/index.html).
Mapping was performed using the STAR aligner software with default parameters (Dobin et al. 2013).
Aligned reads were converted to digital counts using FeatureCounts (Liao et al. 2014). Differentially expressed genes (DEGs) were identified using edgeR (Robinson et al. 2010) based on a p-value < 0.05 and two-fold difference cut-off.
Assembly: B. rapa reference genome was obtained from Ensembl
Supplementary files format and content: bw files for individual samples

organism: Brassica rapa

source_name: inflorescences

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen, Germany) and treated with DNase I (New England Biolabs, USA) to remove genomic DNA contamination.
RNA-seq libraries were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina Inc., USA) according to the manufacturer’s instructions.

value: inflorescences

value: BrEFS knockout


title: 15287X155_blastomere_613E_type_IVF_cell_number_13

description: cellnumber 13

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


title: Embryo_GFPnej_ZldRNAi_GFP_IP2

value: GFP (Abcam ab290 )


title: brefs-inflorescences-2

description: replicate 2


title: Embryo_GFPnej_ZldRNAi_Input1


title: 15287X154_blastomere_613D_type_IVF_cell_number_13

description: cellnumber 13


title: wildtype, SMV inoculation 0 dpi, biol rep 1

description: Library name: NT_CK1

value: leaf

value: WT

value: SMV inoculation 0 dpi


title: ThIL620ng1


title: TIL620ng3

value: TGFb+IL6 20ng


title: brefs-leaves-2

description: replicate 2

source_name: leaves

value: leaves


title: Embryo_GFPnej_ZldRNAi_GFP_IP1

value: Stage 5 embryo


title: Embryo_GFPnej_Input2


title: brefs-inflorescences-3

description: replicate 3


title: 15287X153_blastomere_613C_type_IVF_cell_number_13

description: cellnumber 13

value: IVF


title: TIL620ng1


title: TIL620ng2


title: brefs-leaves-3

description: replicate 3


title: 15287X152_blastomere_613B_type_IVF_cell_number_13

description: cellnumber 13


title: Embryo_GFPnej_GFP_IP2


title: ThIL620ng3


title: Ro18-inflorescences-3

description: replicate 3


title: 15287X151_blastomere_613A_type_IVF_cell_number_13

description: cellnumber 13


title: brefs-leaves-1

description: replicate 1


title: Ro18-inflorescences-2

description: replicate 2


title: T3

description: Control TGFb treated

value: Control TGFb treated


title: Embryo_GFPnej_Input1


title: 15287X150_blastomere_619H_type_IVF_cell_number_8

description: cellnumber 8


title: Embryo_GFPnej_GFP_IP1


title: Ro18-inflorescences-1

description: replicate 1


title: 15287X149_blastomere_619G_type_IVF_cell_number_8

description: cellnumber 8


title: S2-Zld_CuSO4_A-485_Zld_Input2

value: 400 uM CuSO4


title: 15287X148_blastomere_619F_type_IVF_cell_number_8

description: cellnumber 8


title: Ro18-leaves-2

description: replicate 2


title: 15287X147_blastomere_619E_type_IVF_cell_number_8

description: cellnumber 8


title: Ro18-leaves-3

description: replicate 3


title: DU145_RR_miR-92a, rep6

city: Nantes

first: Delphine

last: Fradin

address: 8 quai Moncousu

country: France

institute: CRCI2NA, Inserm UMR1307, CNRS UMR6075

data_processing:
Pipeline details have been published by Charpentier E et al. 2018 (10.21203/rs.3.pex-1336/v1)
Assembly: Hg38
Supplementary files format and content: Matrix table of raw gene counts for all genes in all samples

source_name: DU145 RR

growth_protocol: DU145 cells were grown in RPMI+10% SVF

extract_protocol:
miRNeasy kit (Qiagen)
Libraries were prepared according to NovaSeq 6000 Sequencing Sytem's instructions accompanying the NovaSeq 6000 SP Reagent Kit (Ref# 20028401). Libraries were sequenced on the NovaSeq 6000 following the manufacturer's protocols.
3' SRP

treatment_protocol: transfection with 66nM final of miRNA mimics

tag: cell population

value: prostate cancer cell line

tag: phenotype

value: RR

tag: transfection

tag: replicate


title: DU145_RR_miR-neg, rep6

tag: cell line

value: miR control


title: S2-Zld_CuSO4_A-485_Zld_Input1

tag: treatment


title: T2

description: Control TGFb treated

tag: tissue

value: liver

value: cancer

value: HepG2 cells


title: 15287X145_blastomere_619C_type_IVF_cell_number_8

description: cellnumber 8

tag: cell type


title: T1

description: Control TGFb treated


title: DU145_RR_NT, rep6


title: 15287X144_blastomere_619B_type_IVF_cell_number_8

description: cellnumber 8


title: DU145_RR_miR-200c, rep6


title: S2-Zld_CuSO4_DMSO_Zld_Input2

tag: genotype

value: 1000 uM CuSO4

value: DMSO


title: Ro18-leaves-1

description: replicate 1


title: S2-Zld_CuSO4_A-485_Zld_IP1

value: Zld (Harrison et al., 2010)


title: DU145_RS_NT, rep6

source_name: DU145 RS

value: RS


title: S2-Zld_CuSO4_DMSO_Zld_IP2


title: 15287X143_blastomere_619A_type_IVF_cell_number_8

description: cellnumber 8

source_name: IVF


title: 15287X146_blastomere_619D_type_IVF_cell_number_8

description: cellnumber 8


title: FW_P_1

city: Nanchang

first: Biao

last: Chen

address: Zhimin street, Jingkai district

institute: Jiangxi Agricultural University

data_processing:
Cutadapt (https://cutadapt.readthedocs.io/en/stable/) was used to remove the reads containing adaptors and low-quality bases to make it suitable for analysis in next step.
HISAT2 (https://daehwankimlab.github.io/hisat2/, version: 2-2.0.4) was adopted to map the reads to duck genome (https://www.ncbi.nlm.nih.gov/genome/2793?genome_assembly_id=426073)
The mapped reads of each sample were then assembled by using StringTie (http://ccb.jhu.edu/software/stringtie/, version: stringtie-1.3.4d) with default parameters.
Then, a comprehensive transcriptome was reconstructed with the mapped reads from all samples using gffcompare software (http://ccb.jhu.edu/software/stringtie/gffcompare.shtml, version: gffcompare-0.9.8).
StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were employed to evaluate the expression levels of all transcripts and genes in each sample by calculating fragments per kilobase of exon model per Million mapped fragments (FPKM). The differentially expressed mRNAs (DEGs) and differentially expressed transcripts (DETs) were selected using the criteria |log2 fold change| ≥1 and p ≤0.05 by R package DESeq2 (http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html).
Genome_build: IASCAAS_PekingDuck_PBH1.5 (GCF_003850225.1)
Supplementary_files_format_and_content: Count, FPKM and differential expression analysis

organism: Anas platyrhynchos

source_name: pituitary

growth_protocol: All ducks were kept at room temperature and fed with the commercial dietary produced by Nanchang Huada Group (Nanchang, Jiangxi, China). The 15 ducks raised in floor-water system (FW group) were maintained at natural illumination, while the ducks raised in cages (C group) were subjected to a standard light regimen of 16 h light. All the ducks remained in good health over the duration of the experiment.

extract_protocol:
Total RNAs of 16 samples were extracted and purified using Trizol reagent following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Agilent 2100 with RIN number >7.0.  All samples were kept at -80 °C.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: At the age of 110-day, fifteen ducks were randomly selected and raised in three cages (100 × 45 × 50 cm), the others were still fed in the floor-water system.

value: pituitary

tag: strain

value: Shanma duck

value: reared in water-floor combination system

tag: age

tag: group


title: FW_P_3


title: DU145_RR_miR-neg, rep5


title: FW_P_2


title: S2-Zld_CuSO4_DMSO_Zld_Input1

tag: antibody


title: 15287X142_blastomere_616H_type_IVF_cell_number_8

city: dallas

first: Edward

last: Grow

address: 7053 beltau lane

institute: UTSW

description: cellnumber 8


title: DU145_RR_miR-92a, rep5


title: S2-Zld_CuSO4_A-485_Zld_IP2


title: S2-Zld_CuSO4_DMSO_Zld_IP1


title: C_P_4

value: reared with multilayer cages


title: 15287X141_blastomere_616G_type_IVF_cell_number_8

description: cellnumber 8

value: IVF


title: DU145_RR_miR-200c, rep5


title: FW_P_4


title: C_P_3


title: S2-Zld_A-485_Zld_Input2

value: 0 uM CuSO4