title: sample.kidney_24_1year

description:
htcf.wustl.edu/files/NeAlDBd2/Mcmahon_2328_5678/CGCTACA
all.gene_RPKM.txt
all.gene_counts.txt

value: 1 year


title: H3K27me3 lin15B 20C rep1

status: Public on Feb 21 2019

type: SRA

city: Milwaukee

first: Lisa

middle: N.

last: Petrella

state: WI

address: 1428 W. Clybourn St

department: Biological Sciences

country: USA

institute: Marquette University

library_source: genomic

data_processing:
Raw sequence reads from the Illumina HiSeq (50 bp single-end read sequencing for ChIP-seq) were mapped to the C. elegans genome (Wormbase version WS220) using Bowtie 1.1.2 with default settings.
MACS2 was used to call peaks and to create bedgraph files. The broad peak option was used for H3K9me2. The statistical cutoff q=0.01 was used. Further options used were -g ce --bdg —keep-dup=auto.
Custom scripts were used to scale bedgraph files to the same number of total reads (number depended on the histone mark).
Genome_build: ws220 (ce10)
Supplementary_files_format_and_content: bedgraph file for genome browser containing scaled read coverage
Supplementary_files_format_and_content: narrowPeak or broadPeak file with peak calls as determined by MACS2

molecule: genomic DNA

organism: Caenorhabditis elegans

source_name: H3K27me3 lin15B 20C

growth_protocol: Synchronized N2 or mutant L1s from standard NGM plates were washed off of plates and grown in standard S-basal media liquid culture with HB101 as a food source at 20°C until there were gravid adults. Adult worms were treated with standard bleaching solution to collect embryos, and embryos were incubated for 14 hours in S-basal without food to acquire synchronized L1s.  For 20°C samples F1 synchronized N2 or mutant L1s were grown in standard S-basal media liquid culture with HB101 as a food source at 20°C until there were gravid adult, they were bleached, and the resulting embryos were grown for 14 hours until all L1s then frozen in liquid nitrogen.  For 26°C samples F1 synchronized N2 or mutant L1s were grown in standard S-basal media liquid culture with HB101 as a food source at 20°C until the L4 larval stage at which point the culture was shifted to 26°C and grown until there were gravid adults.  The adults were bleached and the resulting embryos were grown for 14 hours at 26°C until all L1s then frozen in liquid nitrogen

extract_protocol:
Crosslinked samples were resuspended in FA buffer, and sonicated in a Diagenode Bioruptor (60 pulses of 30 seconds at full power with 1 minute rest in between).  Extracts were clarified and protein concentrations determined using a Bradford reagents.  Histone modifications were individually IPed using 1 μg appropriate antibodies on prepared lysates. ChIPs were performed with 0.5 mg of extract, and 2% of the extract was set aside for an input reference control.  Two methods were used for ChIP, see Sample section above to match with sample.  Method 1: ChIPs were incubated overnight at 4°C with 1% sarkosyl. Mouse IgG Dynabeads equilibrated in 100 μL FA buffer were added and incubated for 2 hours at 4°C. ChIPs were washed with the following buffers: twice with FA buffer, once with FA buffer containing 1 M NaCl, once with FA buffer containing 0.5 M NaCl, once with TEL buffer (10 mM Tris-HCl pH 8.0, 0.25 M LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA), and twice with TE buffer (10 mM Tris-HCl pH 8.0 and 1 mM EDTA). 2 elutions of 150 μL elution buffer containing TE plus 1% SDS and 250 mM NaCl were incubated at 65°C. Eluted ChIP and input samples were incubated with RNAse One for 30 min at 37°C and then proteinase K for 1 hour at 55°C. Crosslinks were reversed overnight at 65°C. DNA was purified using a Qiagen PCR clean-up column and eluted in 25 μl of water.  Method 2: ChIPs were performed using an IP-Star Compact Automated System (Diagenode) according to the manufacturers’ instructions with the following settings and reagents: the “indirect method” was used with 100 μL reaction, 80 μL Mouse IgG Dynabeads equilibrated in FA buffer; IP for 12 hr, bead incubation for 2 hr; 10 minute washes at middle speed with FA buffer containing 1 M NaCl, FA buffer containing 0.5M NaCl, TEL buffer, and TE buffer. Samples were eluted in 100 μL Elution Buffer. Eluted samples were incubated with RNAse One for 30 min at 37°C and then proteinase K for 1 hour at 55°C. Crosslinks were reversed overnight at 65°C. DNA was purified by phenol chloroform extraction, ETOH precipitated, and DNA resuspended in 20 μl of water.
Two methods were used for library construction, see Characteristics section.  Method 1: Both ChIP and input DNA samples had the ends blunted and phosphorylated with KlenowDNAP, T4 DNAP, and T4 PNK. 3’-dA overhangs are then added with Klenow Fragment (3’ to 5’exo minus), and Illumina adapters were subsequently ligated to the ends. Next, PCR amplification was performed using Illumina primers, for a total of 16 cycles. Amplified DNA libraries were size-selected on a 2% agarose gel so that fragments sized between 250-350bp were obtained; gel extraction was carried out at room temperature. Method 2: The NEBNext Ultra DNA library Prep Kit (NEB) was used following the manufacturers’ instructions.  1 ng of starting DNA was used, adapters were diluted 1:40, and AMPure beads were used for size selection before amplification to enrich for fragments corresponding to a 200 bp insert size.

treatment_protocol: Frozen late L1s were ground using a mortar and pestle with liquid nitrogen.  The resulting worm powder was resuspended in FA buffer and crosslinked for 10 minutes in 1% formaldehyde.

tag: developmental stage

tag: genotype

tag: temperature

tag: chip antibody

value: Fujifilm Wako MABI0323, #309–95259

tag: input control

value: Input lin15B 20C rep1

value: Method 1


title: P_1: control 1

first: Balazs

last: Balint

state: Csongrad

address: Vallalkozok street

country: Hungary

institute: Seqomics Ltd

library_source: transcriptomic

data_processing:
Reads were quality trimmed using CLC Genomics Workbench Tool (v 11.0). Ambiguous base limit=0, Error probability cutoff value=0.01. Reads shorter than 40 nt were discarded. A custom-masked reference sequence based on E. coli K12 MG1655 reference genome version U00096.3 was used for mapping. Masking was performed keeping only one copy of each analyzed IS type. Reads were mapped using RNA-Seq analysis package 2.16 of CLC Genomics Workbench Tool (v. 11.0). Parameters: min. read length fraction = 0.9, min. read similarity fraction = 0.95. mismatch cost = 2, insertion cost = 3, deletion cost = 3, Strand specific = Both, Maximum number of hits for a read=30, Count paired reads as two=no, Expression value= Total counts. Trimmed mean of M values (TMM) scale normalization was used. Function: calcNormFactors, Package: edgeR, Version 3.12.1 Voom log2 transformation without quantile normalization was applied. Function: voom normalize.method="none", Package: limma, Version: 3.26.9 List of differentially expressed genes was obtained with limma, using linear modeling with empirical Bayes moderation. Package: limma, Version: 3.26.9.
Genome_build: Reference sequence file: U00096.3_RepMasked.fasta, annotation file: U00096.3_1extra_IS150_IS1_IS3_IS5_IS5y_CrispR.gff3
Supplementary_files_format_and_content: *_CLC_RNA_Seq.csv: RNA-Seq read counts table exported from CLC Genomic Workbench Tool.
Supplementary_files_format_and_content: TMM_Voom_Exp_28Aug2018.csv: Normalized gene expression matrix.
Supplementary_files_format_and_content: U00096.3_RepMasked.fasta: IS_Repeat-masked reference file.

molecule: total RNA

organism: Escherichia coli str. K-12 substr. MG1655

source_name: bacterial culture

growth_protocol: The six parallel cultures were grown at 37 oC in Mineral Salts minimal medium (Hall, Mol Biol Evol 15:1) supplemented with 0.2 % glucose and Chloramphenicol to an OD540 value of 1.

extract_protocol:
Total RNA was prepared using the E.Z.N.A. Bacteria RNA Kit (Omega bio-tek, Norcross, GA, USA) following instructions of the manufacturers.
Library construction was performed using TrueSeq RNA Library Preparation Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions with slight modifications. Briefly, RNA quality and quantity measurements were performed using RNA ScreenTape and Reagents on TapeStation (all from Agilent, Santa Clara, CA, USA) and Qubit (Thermo Fisher Scientific, Waltham, MA, USA); only high quality (RIN >8.0) total RNA samples were processed. Next, 1 µg of RNA was DNaseI (Thermo Fisher Scientific, Waltham, MA, USA) treated, the ribosomal RNA depleted using RiboZero Magnetic Kit for Gram-negative bacteria (Epicentre, Madison, WI, USA) and the leftover was ethanol precipitated. The success of rRNA removal was determined by measurement on TapeStation using high-sense RNA ScreenTape and Reagents (all from Agilent, Santa Clara, CA, USA). Next, RNA was purified and fragmented; first strand cDNA synthesis was performed using SuperScript II (Thermo Fisher Scientific, Waltham, MA, USA) followed by second strand cDNA synthesis, end repair, 3’-end adenylation, adapter ligation and PCR amplification. All of the purification steps were performed using AmPureXP Beads (Beckman Coulter, Indianapolis, IN, USA). Final libraries were quality checked using D1000 ScreenTape and Reagents on TapeStation (all from Agilent, Santa Clara, CA, USA). Concentration of each library was determined using the KAPA Library Quantification Kit for Illumina (KAPA Biosystems, Wilmington, MA, USA).

treatment_protocol: Each culture was treated with the RNAprotect Bacteria Reagent (Qiagen, Leipzig, Germany).

tag: tissue

value: bacterial culture

tag: genotype/variation

value: carrying plasmid pCRISPath

tag: growth medium

value: glucose minimal medium + Chloramphenicol

tag: od


title: sample.kidney_25_3months

city: Lugano

first: Pietro

middle: Ernesto

last: Cippa

address: Via Tesserete 46

department: Nephrology

country: Switzerland

institute: Ente Ospedaliero Cantonale

description:
htcf.wustl.edu/files/NeAlDBd2/Mcmahon_2328_5678/CCGGCAG
all.gene_RPKM.txt
all.gene_counts.txt

data_processing:
Reads were aligned to the Ensemble top-level assemby with STAR, version 2.0.4b
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5
Transcript counts were produced by Sailfish version 0.6.3
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: Gene-level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalization size factors were calculated to adjust for samples for differences in library size.

organism: Homo sapiens

source_name: Kidney allograft biopsy

extract_protocol:
Clontech SMARTer
Clontech SMARTer

tag: patient

value: Patient #25

tag: time point

value: 3 months


title: H3K27me3 N2 26C rep1

value: wild-type

value: Input N2 26C rep1


title: H3K27me3 N2 20C rep1

value: Input N2 20C rep1


title: Neat1-KO rep5

city: New York

first: Pavel

last: Katsel

state: NY

address: 1 Gustave L Levy Pl

department: Psychiatry

institute: Icahn School of Medicine At Mount Sinai

data_processing:
Reads from each sample were aligned on mm10 reference genome using the STAR aligner (v2.5.0). For each sample, this produced a coordinate-sorted BAM file of mapped paired-end reads. Quantification of reads per gene was done using HTseq (v0.8.0).
A sample-by-gene read count matrix was generated for all samples by the Ensembl genes. Scaling normalization to remove composition biases in sequencing data was applied to log(CPM) (read Counts Per Million total reads) using the trimmed mean of M-values (TMM) method.
We used the voomWithQualityWeights function from the limma package to model the normalized read counts.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw reads counts for each sample and normalized abundance measurements for each sample

organism: Mus musculus

source_name: Brain

extract_protocol:
Brains were removed, flash frozen on dry ice, cerebral cortex was dissected and RNA was isolated using Promega Maxwell 16 Tissue LEV, Total RNA Purification Kit. Illumina TruSeq RNA with RiboZero Gold 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: strain

value: frontal cortex

tag: age

value: 2 months old

tag: gender

value: female


title: Neat1-KO rep4

value: 4 months old


title: sample.kidney_25_1year

description:
htcf.wustl.edu/files/NeAlDBd2/Mcmahon_2328_5678/GATGGCC
all.gene_RPKM.txt
all.gene_counts.txt


title: w16 human embryonic kidney

city: Leiden

first: Stefan

last: Semrau

address: Einsteinweg 55

department: Physics

country: Netherlands

institute: Leiden University

data_processing:
Single-cell expression was quantified using unique molecular identifiers (UMIs) by 10x Genomics’ “Cell Ranger” software.
Cells were filtered for having 2000 UMI counts or more
Genome_build: hg19
Supplementary_files_format_and_content: count_matrix: matrix of UMI counts where cells are columns and genes rows; barcode_list: list of 12bp barcodes corresponding to the columns of matrix; gene_list: HUGO and ensembl identifiers corresponding to the rows of matrix

source_name: disociated human embryonic kidney

extract_protocol:
One human embryo of w16 was isolated and the kidney dissected in cold saline solution (0.9% NaCl, Versylene Fresenius, FranceThe obtained kidney was decapsulated and kept on ice in dissociation buffer (DPBS + Penicillin 100U/ml + Streptomycin 0.1 mg/ml) before cutting it into 1 – 2 mm pieces. The pieces were washed 3 times with washing solution (Advanced DMEM F12 supplemented with: ITS commercial solution (Insulin – Transferrin – Selenium), Glutamax, Penicillin 100 U/ml and Streptomycin 0.1 mg/ml) with brief centrifugation (160g) in order to remove as many red blood cells as possible. The washed kidney tissue was then incubated with digestion solution (Trypsin/EDTA solution 0.25% and Collagenase-II 280 U/ml) and incubated overnight at 4°C. The next day, the digestion solution was removed, the kidney was rinsed with washing solution and incubated with washing solution for 30 min at 37°C with agitation. Subsequently, the sample was sequentially passed through sterile cell-strainers of 100, 70 and 40 µm pore size with the help of washing solution. The cells were then centrifuged, counted and viability was measured to be 78% (trypan blue assay) before proceeding with single-cell RNA sequencing library preparation.
10X library: Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3' Reagent Kit, Version 2 Chemistry (10x Genomics) according to the manufacturer's protocol.  Libraries were sequenced on a NextSeq500 in Mid Output mode using a version 2, 150 cycles kit (Illumina).

value: embryonic kidney


title: TS543

first: Hanna

middle: Mendes

last: Levitin

address: Department of Systems Biology 3960 Broadway, Lasker 203A

department: Department of Systems Biology

institute: Columbia University Medical Center

data_processing:
Read 1 and read 2 fastq files were generated on basespace.
12-nt cell barcodes (CBs) and 8-nt unique molecular identifiers (UMIs) were extracted from read 1. Degenerate CBs containing either 'N's or more than four consecutive 'G's were discarded. Synthesis errors, which can result in truncated 11-nt cell barcodes, were corrected.
Read 2 were trimmed to remove poly(A) tails (> dA(7)) from the 3'-ends of each read. Any resulting fragment shorter than 24 nucleotides were discarded.
Trimmed reads were then aligned to GRCh38 (GENCODE v.24) using STAR v.2.5.0 with parameters "-- sjdbOverhang 65 --twopassMode Basic --outSAMtype BAM Unsorted". Only reads with unique, strand-specific alignments to exons were kept for further analysis.
All reads with the same CB, UMI, and gene mapping were collapsed to represent a single molecule. To correct for sequencing errors in UMIs, we further collapsed UMIs that were within Hamming distance 1 of another UMI with the same barcode and gene. To correct for sequencing errors in cell barcodes, we then collapsed CBs that were within Hamming distance one of another cell barcode, had at least 20 unique IMI-gene pairs, and had at least 75% overlap of their UMI-gene pairs. A digital gene expression matrix was then generated from these corrected barcode-UMI-gene triplets.
We estimated the number of cell barcodes corresponding beads associated with cells in our microwell system using the cumulative histogram of reads associated with each barcode
To avoid dead cells and library construction artifacts, we removed cell barcodes that failed to satisfy certain criteria.  We removed all cells where >10% of molecules aligned to genes expressed from the mitochondrial genome or where the ratio of molecules aligning to whole gene bodies (including introns) to molecules aligning exclusively to exons was >1.5. These measures remove cells with compromised plasma membranes, which results in retention of mitochondrial or nuclear transcripts. We also removed cells where the number of reads per molecule (indicative of amplification efficiency) or the number of molecules per gene deviated by more than 2.5 standard deviations from the mean for a given sample.
Cell barcode and UMI information is present in read 1.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text files that contain the molecular counts for each individual cell.

molecule: polyA RNA

source_name: Glioma tumor-sphere

growth_protocol: TS543 cells were plated at density 1 x 104 viable cells/cm2 and grown as neurospheres with NeuroCult™ NS-A Basal Medium supplemented with NeuroCult™ NS-A Proliferation Supplement, 20ng/ml EGF, 10ng/ml bFGF, and 0.0002% Heparin (Stem Cell Technologies).

extract_protocol:
mRNA molecues were captured using bead-bound oligo dT(30).
Captured mRNA molecues were reverse transcriped to obtain cDNA which is then amplified by PCR reactions. The cDNA PCR reaction product was then purified with AMPure XP beads. The purified cDNA PCR product was used as the input for Nextera XT reactions to generate sequencing library.

tag: cell line


title: PJ030-core

source_name: High grade glioma tissue

value: Female

tag: location

value: left temporal

tag: diagnosis

value: Anaplastic Astrocytoma, WHO grade III

tag: ragiographic region

value: MRI contrast-enhancing core


title: Neat1-KO rep1

value: 3 months old

tag: genotype


title: PJ030-margin

value: MRI non-enhancing margin


title: Neat1-KO rep3


title: sample.kidney_26_baseline_pre

description:
htcf.wustl.edu/files/NeAlDBd2/Mcmahon_2328_5678/TGACTCT
all.gene_RPKM.txt
all.gene_counts.txt

value: Patient #26

value: pre


title: WT rep5

value: wild type


title: sample.kidney_26_baseline_post

description:
htcf.wustl.edu/files/NeAlDBd2/Mcmahon_2328_5678/CCATCAT
all.gene_RPKM.txt
all.gene_counts.txt

value: post


title: sample.kidney_26_3months

description:
htcf.wustl.edu/files/NeAlDBd2/Mcmahon_2328_5678/GGAGTCC
all.gene_RPKM.txt
all.gene_counts.txt

value: 3 months


title: WT rep2


title: sample.kidney_26_1year

description:
htcf.wustl.edu/files/NeAlDBd2/Mcmahon_2328_5678/TGGCATA
all.gene_RPKM.txt
all.gene_counts.txt

value: 1 year


title: Total TdTomato+CD11b+Dump- cells from regression group

first: Emily

last: Brown

address: 435 E 30th St

department: Medicine

institute: NYU Langone

data_processing:
quality control, Cell Ranger Single Cell Software Suite
sample de-multiplexing, Cell Ranger Single Cell Software Suite
barcode processing, Cell Ranger Single Cell Software Suite
R1 contains the barcode (first 16 bp) and UMI (following 10 bp)
R2 contains the biological read.
single cell 3' gene counting, Cell Ranger Single Cell Software Suite
alignment, Cell Ranger Single Cell Software Suite
Genome_build: mm10
Supplementary_files_format_and_content: Filtered matrix of gene expression by cell, file with barcodes and file with expressed genes.  Files are ready to be import into Seurat package or similar.

source_name: Mouse aorta

extract_protocol: The whole aorta was carefully isolated, and the perivascular fat was removed. Then the aortic tissue was cut into as small pieces as possible and incubated at 37°C for 2 hours with enzyme mixture containing DNase I (40 U/ml), liberase (4 U/ml), hyaluronidase (60 U/ml). Live TdTomato+CD11b+Dump- cells (Dump- are excluding CD3+, CD19+, CD49b+, Siglec-F+, Ly6G+ cells) were sorted out using BD FACSAriaIII. The cells are resuspended in final concentration of ~500 cells/µL in 1X HBSS containing 0.04% BSA to minimize cell loss and aggregation. ~12,000 cells are partitioned into nanoliter-scale Gel Bead-In-EMulsions (GEMs) to achieve single cell resolution for a maximum recovery of 10,000 individual cells per sample. Utilizing the v2 Chromium™ Single Cell 3' Library Kit and Chromium instrument (10x Genomics), poly-adenylated mRNA from an individual cell is tagged with a unique 16bp 10x barcode and 10bp Unique Molecular Identifier. Full length cDNA is then amplified to generate sufficient mass for library construction. Enzymatic fragmentation and size selection are used to optimize the cDNA amplicon size (~400bp) for library construction. The final library is sequence ready and contains four unique sample indexes. The concentration of the 10x single cell library will be accurately determined through qPCR (Kapa Biosystems) to produce cluster counts appropriate for the HiSeq4000 platform (Illumina). 26x98nt read lengths are generated targeting 50,000 reads per cell.

value: aorta

tag: cell type

value: monocytes and macrophages

value: 28 weeks

tag: condition

value: amelioration of atherosclerosis


title: Total TdTomato+CD11b+Dump- cells from progression group

value: severe atherosclerosis


title: sample.kidney_27_baseline_pre

description:
htcf.wustl.edu/files/NeAlDBd2/Mcmahon_2328_5678/GTAAAAA
all.gene_RPKM.txt
all.gene_counts.txt

value: Patient #27


title: mESC Dox m6a-rep1

city: Monrovia

first: Jianjun

last: Chen

state: CA

department: Systems Biology

institute: Beckman Research Institute of City of Hope

description:
mESCs_Dox_m6a_rep1-2_peak.bed
mESCs_Dox_m6A-seq_rep1-2_exomePeak_peak.txt

data_processing:
Illumina Casava1.8 software used for basecalling.
All sequenced reads were checked for quality control by using FastQC v0.11.5 with default parameters; then the processed reads were mapped to mm10 whole genome using TopHat v2.1.1 with default parameters
The m6A enriched regions were calculated by using exomePeak with default parameters.
The cutoff for significantly enriched m6A peak: p-value < 1e-5, FDR < 1e-3, fold_enrichment >= 2
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited excel files include exomePeak peak calling results for each Sample

source_name: mouse embryonic stem cells

growth_protocol: Feeder-free mESCs with doxycycline (Dox)-inducible knockdown of Setd2 were cultured as spheres in 2i medium (a serum-free N2B27 medium supplemented with MEK inhibitor PD0325901 (1 μM, Selleckchem), GSK3 inhibitor CHIR99021 (3 μM, Selleckchem), and 1,000 U/ml leukemia inhibitory factor (LIF, Millipore)) on gelatin-coated plates.

extract_protocol:
Total RNA was extracted using Direct-zol RNA MiniPrep Kit (Zymo). mRNA was further purified using Dynabeads mRNA DIRECT Kit (Thermo Fisher). mRNA was then sonicated. For IP samples, RNA was subjected to IP using m6A antibody (Synaptic Systems, 202003).
Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit (Illumina).

treatment_protocol: Cells were treated with 1 µg/ml doxycycline for 4 consecutive days to induce Setd2 knockdown.

tag: dox treatment

value: Dox + (Setd2 knockdown)

tag: ip antibody

value: m6A antibody (Synaptic Systems, 202003)

tag: replication


title: mESC Dox m6a-rep2


title: sample.kidney_27_baseline_post

description:
htcf.wustl.edu/files/NeAlDBd2/Mcmahon_2328_5678/CTGCAAT
all.gene_RPKM.txt
all.gene_counts.txt


title: WT rep1

tag: tissue

value: frontal cortex

value: 2 months old

value: female


title: sample.kidney_27_3months

description:
htcf.wustl.edu/files/NeAlDBd2/Mcmahon_2328_5678/AATTCAT
all.gene_RPKM.txt
all.gene_counts.txt


title: L-GQE sperm 60

city: Shanghai

first: Wei

last: Liu

state: Shanghai

address: 320 Yueyang Road

department: Institute of Biochemistry and Cell Biology

country: China

institute: Chinese Academy of Sciences

data_processing:
We used cutadapt to trim adapter sequece(TGGAATTCTCGGGTGCCAAGGC) and filt low quality reads of raw sequencing data.
The expression levels of the tsRNAs and classification were based on MintMAP.
The processed reads longer than 17nt were mapped to human miRNA database (miRBase version 22), allowing ±2 to be template by the corresponding genomic sequence at the 3’end (http://www.mirbase.org/).
rsRNAs were mapped to rRNA precursors in the order of 5S, 5.8S, 18S, 28S and 45S.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include RPM values for each Sample

source_name: sperm

extract_protocol:
Total cellular RNA was extracted using a TRIzol reagent (Takara).
Approximately 200 ng of total cellular RNA was used to construct a small RNA library according to the Illumina protocol

value: testis

tag: embryo quality

value: low rate of good quality  embryo


title: L-GQE sperm 59


title: L-GQE sperm 61


title: L-GQE sperm 63


title: L-GQE sperm 62


title: L-GQE sperm 64


title: mESC Ctrl m6a-rep2

description:
mESCs_Ctrl_m6a_rep1-2_peak.bed
mESCs_Ctrl_m6A-seq_rep1-2_exomePeak_peak.txt

value: Dox - (control)


title: L-GQE sperm 58


title: sample.kidney_18_baseline_pre

description:
htcf.wustl.edu/files/NeAlDBd2/Mcmahon_2328_5678/ACAGATA
all.gene_RPKM.txt
all.gene_counts.txt

tag: patient

value: Patient #18

value: pre


title: L-GQE sperm 57


title: sample.kidney_27_1year

description:
htcf.wustl.edu/files/NeAlDBd2/Mcmahon_2328_5678/AGGCGAA
all.gene_RPKM.txt
all.gene_counts.txt

tag: time point

value: 1 year


title: KO_BMDM_LPS_Input

city: Bethesda

first: Anup

last: Dey

address: 9000 Rockville Pike

department: DDB

institute: NIH/NICHD

data_processing:
ChIP-seq reads were aligned to the mouse reference genome (mm9) using Burrows-wheeler aligner using default parameter.
Peak calling was performed using SICER, with a window and gap set at 50bp with 0.01 FDR for Brd4 or at 200bp for other ChIP-seq with FDR at 0.01.
Genome_build: mm9
Supplementary_files_format_and_content: Sicer outputs were converted to wiggle file

growth_protocol: Bone marrow cells were directly cultured in DMEM-F12 media in the presence of L929 conditioned medium for 7 days. This allows generation of terminally differentiatiated pure macrophage populalation.

extract_protocol:
Cells were fixed with 1% formaldehyhyde. Nulear lysates were made  clarified by sonicatio.  DNA andprotein complexes were precipitated with antibody
ChIP-seq libraries were prepared using Ovation SP Untraflow system (part# 8030) and DR multiplex system 1-8 and 9-16 (part#8033 and 8034) on Mondrian SP workstation.

treatment_protocol: For conditional deletion of Brd4, bone marrow cells carrying Brd4 fl/fl; Ert2-cre transgenes were cultured in the presence 2uM 4hydroytamoxifen from day 1. For inflammatory stimulus just prior to harvest cells were treated with LPS (100ng/ml)  for 4 hours .

tag: strain background

tag: genotype/variation

value: Brd4Fl/Fl;Ert2-cre (KO)

value: Bone marrow derived macrophages (BMDM)

tag: treated with

value: LPS (100ng/ml) for 4hrs

tag: chip antibody

value: none (input)


title: mESC Ctrl m6a-rep1


title: WT rep4

tag: strain

tag: age

value: 4 months old

tag: gender

value: wild type


title: mESC Dox input-rep2

value: Dox + (Setd2 knockdown)


title: KO_BMDM_UT_Input

value: none (UT; untreated)


title: sample.kidney_28_baseline_pre

description:
htcf.wustl.edu/files/NeAlDBd2/Mcmahon_2328_5678/TTTGGCG
all.gene_RPKM.txt
all.gene_counts.txt

value: Patient #28


title: WT rep3

value: frontal cortex

value: 3 months old

tag: genotype


title: WT_BMDM_LPS_Input

value: Brd4Fl/Fl mice (WT)

tag: cell type


title: mESC Dox input-rep1


title: L-GQE sperm 56

value: testis

value: low rate of good quality  embryo


title: sample.kidney_28_baseline_post

description:
htcf.wustl.edu/files/NeAlDBd2/Mcmahon_2328_5678/TAACAAG
all.gene_RPKM.txt
all.gene_counts.txt

value: post


title: L-GQE sperm 55


title: WT_BMDM_UT_Input


title: sample.kidney_04_baseline_pre

description:
htcf.wustl.edu/files/pX7rOPeW/Mcmahon_2328_1234/GAGGCGT
all.gene_RPKM.txt
all.gene_counts.txt

value: Patient #04

value: pre


title: KO_BMDM_LPS_H3K122ac_ChIP-seq

value: Brd4Fl/Fl;Ert2-cre (KO)

tag: chip antibody info.

value: Abcam Cat#ab33309


title: mESC Ctrl input-rep1

tag: dox treatment

value: Dox - (control)


title: sample.kidney_04_baseline_post

description:
htcf.wustl.edu/files/pX7rOPeW/Mcmahon_2328_1234/CGTCGCT
all.gene_RPKM.txt
all.gene_counts.txt


title: WT_BMDM_LPS_H3K122ac_ChIP-seq

value: Bone marrow derived macrophages (BMDM)

value: LPS (100ng/ml) for 4hrs


title: mESC Ctrl input-rep2

tag: ip antibody


title: L-GQE sperm 52


title: mESC Dox H3K36me3-rep1 (ChIP-seq)

description:
mESCs_Dox_ChIP-seq_rep1-2_MACS_peaks.txt
mESCs_macs_shSetD2_rep1-2_peaks.bed

data_processing:
Illumina Casava1.8 software used for basecalling.
All sequenced reads were checked for quality control by using FastQC v0.11.5 with default parameters; then the processed reads were mapped to mm10 whole genome using Bowtie v1.1.2 with default parameters
The H3K36me3 enriched regions were calculated by using MACS with following parameters: -g mm --nomodel --shiftsize 147 -B -S --call-subpeaks
The cutoff for significantly enriched H3K36me3 peak: p-value < 1e-5, FDR < 0.05
Genome_build: mm10
Supplementary_files_format_and_content: *txt: tab-delimited text files containing peaks generated by MACS.
Supplementary_files_format_and_content: *bed: bed files containing significantly enriched H3K36me3 peaks.

extract_protocol:
Cell lysate was sonicated and clarified by using 0.22 µm filter. Histone-DNA complexes were isolated with H3K36me3 antibody.
Libraries were constructed by using Auto iDeal ChIP-seq kit for Histones (Diagenode, C01010057) following manufacturer's prorocol.

value: mESC

tag: treatment

value: Dox +

value: Setd2 knockdown

value: H3K36me3 (Abcam, catalog# ab9050, lot# GR166781-1)

tag: replicate


title: sample.kidney_04_1year

description:
htcf.wustl.edu/files/pX7rOPeW/Mcmahon_2328_1234/GTCTGAT
all.gene_RPKM.txt
all.gene_counts.txt

value: 1 year


title: L-GQE sperm 51

tag: tissue

tag: embryo quality


title: KO_BMDM_UT_H3K122ac_ChIP-seq

value: none (UT; untreated)


title: mESC Ctrl H3K36me3-rep2 (ChIP-seq)

description:
mESCs_Cont_ChIP-seq_rep1-2_MACS_peaks.txt
mESCs_macs_shCont_rep1-2_peaks.bed

value: Dox -

value: control


title: WT_BMDM_UT_H3K122ac_ChIP-seq

value: Brd4Fl/Fl mice (WT)


title: L-GQE sperm 50

value: testis

value: low rate of good quality  embryo


title: sample.kidney_05_baseline_pre

description:
htcf.wustl.edu/files/pX7rOPeW/Mcmahon_2328_1234/CAAGCCG
all.gene_RPKM.txt
all.gene_counts.txt

tag: patient

value: Patient #05

tag: time point

value: pre


title: KO_BMDM_LPS_H3K4me1_ChIP-seq

tag: strain background

tag: genotype/variation

value: Brd4Fl/Fl;Ert2-cre (KO)

value: Abcam Cat#ab8895


title: mESC Dox H3K36me3-rep2 (ChIP-seq)

tag: chip antibody


title: L-GQE sperm 49


title: sample.kidney_05_baseline_post

description:
htcf.wustl.edu/files/pX7rOPeW/Mcmahon_2328_1234/GCAGGGG
all.gene_RPKM.txt
all.gene_counts.txt

value: post


title: mESC Ctrl H3K36me3-rep1 (ChIP-seq)


title: KO_BMDM_UT_H3K4me1_ChIP-seq

value: Bone marrow derived macrophages (BMDM)

tag: treated with


title: L-GQE sperm 54

tag: age


title: mESC Dox input-rep2 (ChIP-seq)

value: mESC


title: sample.kidney_05_3months

description:
htcf.wustl.edu/files/pX7rOPeW/Mcmahon_2328_1234/ACGTCTG
all.gene_RPKM.txt
all.gene_counts.txt

value: 3 months


title: mESC Dox input-rep1 (ChIP-seq)

value: Dox +

value: Setd2 knockdown


title: L-GQE sperm 48


title: sample.kidney_05_1year

description:
htcf.wustl.edu/files/pX7rOPeW/Mcmahon_2328_1234/TGAGGTT
all.gene_RPKM.txt
all.gene_counts.txt

value: 1 year


title: WT_BMDM_LPS_H3K4me1_ChIP-seq

value: LPS (100ng/ml) for 4hrs


title: L-GQE sperm 53


title: sample.kidney_04_3months

description:
htcf.wustl.edu/files/pX7rOPeW/Mcmahon_2328_1234/TTTTGTC
all.gene_RPKM.txt
all.gene_counts.txt

value: Patient #04


title: L-GQE sperm 47


title: mESC Ctrl input-rep2 (ChIP-seq)

value: Dox -

value: control


title: sample.kidney_06_baseline_pre

description:
htcf.wustl.edu/files/pX7rOPeW/Mcmahon_2328_1234/TTTAACT
all.gene_RPKM.txt
all.gene_counts.txt

value: Patient #06


title: L-GQE sperm 46

value: testis

value: low rate of good quality  embryo


title: KO_BMDM_LPS_H3K4me3_ChIP-seq

value: Abcam Cat#ab8580


title: mESC Ctrl input-rep1 (ChIP-seq)


title: L-GQE sperm 45


title: KO_BMDM_UT_H3K4me3_ChIP-seq

value: Brd4Fl/Fl;Ert2-cre (KO)

value: none (UT; untreated)


title: sample.kidney_06_3months

description:
htcf.wustl.edu/files/pX7rOPeW/Mcmahon_2328_1234/ACCCACT
all.gene_RPKM.txt
all.gene_counts.txt


title: sample.kidney_06_baseline_post

description:
htcf.wustl.edu/files/pX7rOPeW/Mcmahon_2328_1234/TCAACTG
all.gene_RPKM.txt
all.gene_counts.txt

value: post


title: L-GQE sperm 44


title: sample.kidney_06_1year

description:
htcf.wustl.edu/files/pX7rOPeW/Mcmahon_2328_1234/CAATATC
all.gene_RPKM.txt
all.gene_counts.txt


title: sample.kidney_07_baseline_pre

description:
htcf.wustl.edu/files/pX7rOPeW/Mcmahon_2328_1234/GGGTCAA
all.gene_RPKM.txt
all.gene_counts.txt

value: Patient #07

value: pre


title: WT_BMDM_LPS_H3K4me3_ChIP-seq

value: Brd4Fl/Fl mice (WT)

value: Bone marrow derived macrophages (BMDM)


title: KO_BMDM_LPS_H4tetraac_ChIP-seq

value: EMD Millipore Cat#06-866


title: sample.kidney_07_baseline_post

description:
htcf.wustl.edu/files/pX7rOPeW/Mcmahon_2328_1234/AGATACT
all.gene_RPKM.txt
all.gene_counts.txt


title: Wnt-independent G564NS

city: Toronto

first: Nishani

last: Rajakulendran

state: Ontario

address: 144 College St. Room 950, Leslie Dan Faculty of Pharmacy

department: Pharmaceutical Sciences

country: Canada

institute: University of Toronto

data_processing:
RNA-seq reads were processed with RNA-seq the bioinformatics pipeline of BCBIO toolkit (https://github.com/chapmanb/bcbio-nextgen). Splicing-aware alignment was conducted using STAR (Dobin et al 2013) and read counts calculation with featureCounts (Liao et al 2014).
Differential expression analysis was performed with edgeR package (McCarthy et al, 2012; Robinson et al 2010) in R (R Core Team, 2017) according to the user’s guide. (https://bioconductor.org/packages/release/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf).
Genome_build: grch37
Supplementary_files_format_and_content: Files include tpm values for each Sample (GSCs_counts.txt) and differential expression analysis per gene (GSCs_DE.csv)

source_name: Glioblastoma Stem Cells

growth_protocol: Adherent cultures grown on Laminin coated plates

extract_protocol:
GSCs were dissociated, flash frozen, and RNA was harvested using Trizol reagent.
polyA capture

treatment_protocol: no treatment

value: Glioblastoma Stem Cell (GSC)

tag: cell line

tag: phenotype

value: Wnt-independent


title: WT_BMDM_UT_H3K4me1_ChIP-seq

tag: cell type

value: Abcam Cat#ab8895


title: sample.kidney_07_3months

description:
htcf.wustl.edu/files/pX7rOPeW/Mcmahon_2328_1234/GTCGATA
all.gene_RPKM.txt
all.gene_counts.txt

value: 3 months


title: L-GQE sperm 42


title: Wnt-independent G361NS


title: Wnt-dependent G523NS

value: Wnt-dependent


title: Wnt-independent G440NS


title: Wnt-independent G510NS


title: KO_BMDM_UT_H4tetraac_ChIP-seq

tag: chip antibody info.


title: Wnt-dependent G477NS


title: WT_BMDM_LPS_H4tetraac_ChIP-seq

value: LPS (100ng/ml) for 4hrs


title: sample.kidney_07_1year

description:
htcf.wustl.edu/files/pX7rOPeW/Mcmahon_2328_1234/GCTTAGA
all.gene_RPKM.txt
all.gene_counts.txt

value: 1 year


title: L-GQE sperm 40

value: testis

value: low rate of good quality  embryo


title: sample.kidney_08_baseline_pre

description:
htcf.wustl.edu/files/pX7rOPeW/Mcmahon_2328_1234/GGTCCTC
all.gene_RPKM.txt
all.gene_counts.txt

value: Patient #08


title: L-GQE sperm 39


title: WT_BMDM_UT_H4tetraac_ChIP-seq

value: none (UT; untreated)


title: Wnt-dependent G472NS


title: L-GQE sperm 38


title: KO_BMDM_LPS_H3K9ac_ChIP-seq

value: Brd4Fl/Fl;Ert2-cre (KO)

value: EMD Millipore Cat#07-352


title: L-GQE sperm 43


title: Wnt-dependent G432NS


title: sample.kidney_08_baseline_post

description:
htcf.wustl.edu/files/pX7rOPeW/Mcmahon_2328_1234/TGTTTGT
all.gene_RPKM.txt
all.gene_counts.txt

value: post


title: WT_BMDM_UT_H3K4me3_ChIP-seq

value: Brd4Fl/Fl mice (WT)

value: Abcam Cat#ab8580


title: KO_BMDM_UT_H3K9ac_ChIP-seq

value: Bone marrow derived macrophages (BMDM)


title: L-GQE sperm 41


title: L-GQE sperm 36


title: WT_BMDM_LPS_H3K9ac_ChIP-seq


title: sample.kidney_08_3months

description:
htcf.wustl.edu/files/pX7rOPeW/Mcmahon_2328_1234/CCGGACC
all.gene_RPKM.txt
all.gene_counts.txt


title: sample.kidney_08_1year

description:
htcf.wustl.edu/files/pX7rOPeW/Mcmahon_2328_1234/CTCCCGA
all.gene_RPKM.txt
all.gene_counts.txt


title: L-GQE sperm 35


title: WT_BMDM_UT_H3K9ac_ChIP-seq


title: L-GQE sperm 34


title: L-GQE sperm 33


title: KO_BMDM_UT_H3K27ac_ChIP-seq

value: Abcam Cat#ab4729


title: M2T3_MEL2 ESC 20% O2

city: Parkville

first: James

last: Spyrou

state: VIC

address: Royal Parade

department: School of BioSciences

country: Australia

institute: The University of Melbourne

description:
M2T3_CC0U1ANXX_GAGTGG_L004
processed data file: M2.DESeq2.tabular.txt

data_processing:
FASTQ Groomer version 1.1.1 was used to convert data files to the Sanger Quality score format.
Trim Galore! version 0.4.3.1 was used to trim adapters from the ends of reads.
Reads were aligned to the UCSC GRCh37/hg19 reference genome with RNA STAR version 2.5.2b-0.
featureCounts version 1.4.6.p5 was used to measure gene expression as counted reads.
DESeq2 version 1.14.1 was used to identify differentially expressed genes (DEGs) and their fold changes from count data.
Genome_build: hg19
Supplementary_files_format_and_content: FeatureCounts tabular files were generated with featureCounts version 1.4.6.p5 and contain raw count values and Ensembl Gene IDs (ENSG). DESeq2 tabular files were generated using DESeq2 version 1.14.1; tabular files contain Ensembl Gene IDs (ENSG), mean normalised counts, log2(fold change), standard error of the log2(fold change), Wald statistic, p-value, and p-value adjusted with the Benjamini-Hochberg procedure which controls false discovery rate (FDR), for each gene.

source_name: MEL2 ESC 20% O2

growth_protocol: iPSC were generated by reprogramming NHDF with Sendai viruses containing OKSM under 20% oxygen (A-iPSC) or 5% oxygen (P-iPSC), and cultured on Matrigel-coated 6-well Falcon culture plates in mTeSR1 medium. MEL2 human ESC were cultured on Matrigel-coated 6-well Falcon culture plates.

extract_protocol:
A-iPSC, P-iPSC and MEL2 hESC were lysed and total RNA was isolated using an RNeasy Plus Mini Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Once established, cells from each line were sub-cultured in atmospheres of both 20% (atmospheric) and 5% (physiological) oxygen.

value: MEL2 iPSC

tag: culture condition

value: 20% oxygen

tag: passages


title: M2F2_MEL2 ESC 5% O2

description:
M2F2_CC0U1ANXX_GTTTCG_L004
processed data file: M2.DESeq2.tabular.txt

source_name: MEL2 ESC 5% O2

value: 5% oxygen


title: M2F1_MEL2 ESC 5% O2

description:
M2F1_CC0U1ANXX_CCGTCC_L004
processed data file: M2.DESeq2.tabular.txt


title: KO_BMDM_LPS_H3K27ac_ChIP-seq


title: M2T2_MEL2 ESC 20% O2

description:
M2T2_CC0U1ANXX_GTGAAA_L004
processed data file: M2.DESeq2.tabular.txt


title: M2F3_MEL2 ESC 5% O2

description:
M2F3_CC0U1ANXX_ATTCCT_L004
processed data file: M2.DESeq2.tabular.txt


title: L-GQE sperm 32


title: L-GQE sperm 37


title: sample.kidney_09_3months

description:
htcf.wustl.edu/files/pX7rOPeW/Mcmahon_2328_1234/TACAGAC
all.gene_RPKM.txt
all.gene_counts.txt

value: Patient #09

value: 3 months


title: WT_BMDM_LPS_H3K27ac_ChIP-seq

value: LPS (100ng/ml) for 4hrs


title: L-GQE sperm 31

value: testis


title: sample.kidney_09_1year

description:
htcf.wustl.edu/files/pX7rOPeW/Mcmahon_2328_1234/ATGACAG
all.gene_RPKM.txt
all.gene_counts.txt

value: 1 year


title: WT_BMDM_UT_H3K27ac_ChIP-seq


title: sample.kidney_10_baseline_pre

description:
htcf.wustl.edu/files/pX7rOPeW/Mcmahon_2328_1234/CGGTGGC
all.gene_RPKM.txt
all.gene_counts.txt

value: Patient #10

value: pre


title: M5F3_P-iPSC 5% O2

description:
iPSC were derived from NHDF under 5% oxygen culture
M5F3_CC0U1ANXX_CTTGTA_L004
processed data file: M5.DESeq2.tabular.txt

source_name: P-iPSC 5% O2

value: NHDF-derived iPSC

tag: reprogramming condition


title: M5F2_P-iPSC 5% O2

description:
iPSC were derived from NHDF under 5% oxygen culture
M5F2_CC0U1ANXX_ACTTGA_L004
processed data file: M5.DESeq2.tabular.txt


title: L-GQE sperm 30

value: low rate of good quality  embryo


title: KO_BMDM_LPS_p65_ChIP-seq

value: Brd4Fl/Fl;Ert2-cre (KO)

value: Santa Cruz Cat#sc-372


title: sample.kidney_10_baseline_post

description:
htcf.wustl.edu/files/pX7rOPeW/Mcmahon_2328_1234/TACATGG
all.gene_RPKM.txt
all.gene_counts.txt

value: post


title: sample.kidney_09_baseline_post

description:
htcf.wustl.edu/files/pX7rOPeW/Mcmahon_2328_1234/TCCCAGC
all.gene_RPKM.txt
all.gene_counts.txt


title: KO_BMDM_UT_p65_ChIP-seq

value: Bone marrow derived macrophages (BMDM)

value: none (UT; untreated)


title: L-GQE sperm 29


title: L-GQE sperm 28


title: WT_BMDM_LPS_p65_ChIP-seq

value: Brd4Fl/Fl mice (WT)


title: sample.kidney_10_3months

description:
htcf.wustl.edu/files/pX7rOPeW/Mcmahon_2328_1234/GTACGGC
all.gene_RPKM.txt
all.gene_counts.txt


title: M5F1_P-iPSC 5% O2

description:
iPSC were derived from NHDF under 5% oxygen culture
M5F1_CC0U1ANXX_TGACCA_L004
processed data file: M5.DESeq2.tabular.txt


title: sample.kidney_10_1year

description:
htcf.wustl.edu/files/pX7rOPeW/Mcmahon_2328_1234/GCCGTTT
all.gene_RPKM.txt
all.gene_counts.txt


title: M2T1_MEL2 ESC 20% O2

description:
M2T1_CC0U1ANXX_AGTTCC_L004
processed data file: M2.DESeq2.tabular.txt

value: MEL2 iPSC

value: 20% oxygen


title: sample.kidney_09_baseline_pre

description:
htcf.wustl.edu/files/pX7rOPeW/Mcmahon_2328_1234/GCAACGC
all.gene_RPKM.txt
all.gene_counts.txt

value: Patient #09


title: L-GQE sperm 26


title: KO_BMDM_LPS_PolII_ChIP-seq

value: PolII

value: Biolegend cat. # CTD4H8


title: WT_BMDM_UT_p65_ChIP-seq


title: M5T1_P-iPSC 20% O2

description:
iPSC were derived from NHDF under 5% oxygen culture
M5T1_CC0U1ANXX_CGATGT_L004
processed data file: M5.DESeq2.tabular.txt

source_name: P-iPSC 20% O2

value: 5% oxygen


title: M5T2_P-iPSC 20% O2

description:
iPSC were derived from NHDF under 5% oxygen culture
M5T2_CC0U1ANXX_GCCAAT_L004
processed data file: M5.DESeq2.tabular.txt


title: sample.kidney_11_baseline_pre

description:
htcf.wustl.edu/files/pX7rOPeW/Mcmahon_2328_1234/TGATTAC
all.gene_RPKM.txt
all.gene_counts.txt

value: Patient #11


title: sample.kidney_11_baseline_post

description:
htcf.wustl.edu/files/pX7rOPeW/Mcmahon_2328_1234/CCTAATC
all.gene_RPKM.txt
all.gene_counts.txt


title: M4F3_A-iPSC 5% O2

description:
iPSC were derived from NHDF under 20% oxygen culture
M4F3_CC0U1ANXX_GGCTAC_L004
processed data file: M4.DESeq2.tabular.txt

source_name: A-iPSC 5% O2


title: KO_BMDM_UT_PolII_ChIP-seq


title: L-GQE sperm 24

value: testis


title: sample.kidney_11_3months

description:
htcf.wustl.edu/files/pX7rOPeW/Mcmahon_2328_1234/CATCGCG
all.gene_RPKM.txt
all.gene_counts.txt

value: 3 months


title: L-GQE sperm 25


title: WT_BMDM_LPS_PolII_ChIP-seq

value: LPS (100ng/ml) for 4hrs


title: M5T3_P-iPSC 20% O2

description:
iPSC were derived from NHDF under 5% oxygen culture
M5T3_CC0U1ANXX_TAGCTT_L004
processed data file: M5.DESeq2.tabular.txt

value: NHDF-derived iPSC


title: sample.kidney_11_1year

description:
htcf.wustl.edu/files/pX7rOPeW/Mcmahon_2328_1234/CACCTCC
all.gene_RPKM.txt
all.gene_counts.txt

value: 1 year


title: L-GQE sperm 23

value: low rate of good quality  embryo


title: M4F2_A-iPSC 5% O2

description:
iPSC were derived from NHDF under 20% oxygen culture
M4F2_CC0U1ANXX_CAGATC_L004
processed data file: M4.DESeq2.tabular.txt


title: WT_BMDM_UT_PolII_ChIP-seq


title: M4F1_A-iPSC 5% O2

description:
iPSC were derived from NHDF under 20% oxygen culture
M4F1_CC0U1ANXX_TTAGGC_L004
processed data file: M4.DESeq2.tabular.txt


title: sample.kidney_12_baseline_pre

description:
htcf.wustl.edu/files/pX7rOPeW/Mcmahon_2328_1234/ACTGTCG
all.gene_RPKM.txt
all.gene_counts.txt

value: Patient #12

value: pre


title: L-GQE sperm 22


title: L-GQE sperm 27


title: L-GQE sperm 21


title: sample.kidney_12_baseline_post

description:
htcf.wustl.edu/files/pX7rOPeW/Mcmahon_2328_1234/GTTCTCA
all.gene_RPKM.txt
all.gene_counts.txt

value: post


title: KO_BMDM_UT_BRD4_ChIP-seq

value: Brd4Fl/Fl;Ert2-cre (KO)

value: Bone marrow derived macrophages (BMDM)

value: none (UT; untreated)


title: M4T3_A-iPSC 20% O2

description:
iPSC were derived from NHDF under 20% oxygen culture
M4T3_CC0U1ANXX_GATCAG_L004
processed data file: M4.DESeq2.tabular.txt

source_name: A-iPSC 20% O2

value: 20% oxygen


title: M4T2_A-iPSC 20% O2

description:
iPSC were derived from NHDF under 20% oxygen culture
M4T2_CC0U1ANXX_ACAGTG_L004
processed data file: M4.DESeq2.tabular.txt


title: L-GQE sperm 20


title: sample.kidney_12_3months

description:
htcf.wustl.edu/files/pX7rOPeW/Mcmahon_2328_1234/TTGCCCC
all.gene_RPKM.txt
all.gene_counts.txt


title: WT_BMDM_LPS_BRD4_ChIP-seq

value: Brd4Fl/Fl mice (WT)


title: M4T1_A-iPSC 20% O2

description:
iPSC were derived from NHDF under 20% oxygen culture
M4T1_CC0U1ANXX_ATCACG_L004
processed data file: M4.DESeq2.tabular.txt


title: WT_BMDM_UT_BRD4_ChIP-seq

value: none (untreated)


title: HepG2_shMETTL14_6h_rep2 (RNA-seq)

description:
mRNA half-life.txt
RNAseq_Raw_and_RPKM.txt

data_processing:
FASTQs are trimmed by cutadapt to remove low quality ends and adapters
All sequenced reads were aligned to the combined reference sequences consisting of human (GRCh37; 34,618 genes) and 92 synthetic RNA spike-in controls (ERCC) using TopHat.
HTSeq (v0.6.1p1) is used to determine the read counts per human gene and ERCC, and 14,212 genes with read counts >= 1 in all 32 samples are retained for further analysis. The relative expression of each gene is calculated as the ratio of its read count to the total read counts of all 92 ERCC controls, and gene expression is shown to be highly reproducible (Pearson correlation coefficient > 0.995) between two replicates of the same condition.Therefore, the average gene expression of two replicates of the same condition is used to represent the gene expression in that condition.
The constant of mRNA decay (Kdecay) is calculated by fitting an exponential decay model to gene expression across four time points (0 hr steady state, 1 hr, 3hr, and 6 hr), and mRNA half life is then calculated as ln2 / Kdecay.
Genome_build: human GRCh37
Supplementary_files_format_and_content: tab-delimited text files include mRNA half-life and gene expression matrix

source_name: HepG2 cells

growth_protocol: The human hepatocellular carcinoma cell line HepG2 (ATCC HB-8065) was maintained in EMEM medium (ATCC) supplemented with 10% FBS (Invitrogen, Carlsbad, CA), 2 mM L-Glutamine and 1% penicillin-streptomycin. Lentivirus were produced in HEK293T cells by co-transfecting individual shRNA construct with packaging vectors (pMD2.G, pMDLg/pRRE and pRSV-Rev) into HEK293T cells in 60 mm cell culture dish using X-tremeGENE HP DNA Transfection Reagent (Roche Diagnostics, Grenzach-Wyhlen, Germany). The lentivirus particles were harvested at 48 and 72 hours after transfection and directly added into HepG2 cells with 4 μg/mL polybrene. After two rounds of infection, cells were selected for at least two passages by adding 1 μg/mL puromycin into growth medium.

extract_protocol:
The total RNA was extracted by miRNeasy Kit (Qiagen).
For RNA sequencing, equal amount of ERCC RNA spike-in control (Thermo Fisher Scientific) was added to the total RNA samples as internal controls before library construction. Sequencing libraries were prepared using TruSeq SR Cluster Kit V4-cBot-HS (illumina).

treatment_protocol: HepG2 cells with stably expressed shRNAs against SETD2 or METTL14 were seeded into 6-well plates to get 50% confluency after 24 hours. Cells were then treated with 5 μg/mL actinomycin D and collected at indicated time points.

tag: shRNA

tag: treatment

value: 5 ug/mL actinomycin D


title: sample.kidney_13_baseline_pre

description:
htcf.wustl.edu/files/pX7rOPeW/Mcmahon_2328_1234/TGCTGGG
all.gene_RPKM.txt
all.gene_counts.txt

value: Patient #13


title: L-GQE sperm 18

tag: tissue

value: testis

tag: embryo quality


title: HepG2_shMETTL14_6h_rep1 (RNA-seq)

tag: time point


title: sample.kidney_13_baseline_post

description:
htcf.wustl.edu/files/pX7rOPeW/Mcmahon_2328_1234/TCAAACA
all.gene_RPKM.txt
all.gene_counts.txt

tag: patient


title: sample.kidney_13_3months

description:
htcf.wustl.edu/files/pX7rOPeW/Mcmahon_2328_1234/AGCGCCG
all.gene_RPKM.txt
all.gene_counts.txt

value: 3 months


title: L-GQE sperm 16


title: L-GQE sperm 17


title: HepG2_shMETTL14_3h_rep2 (RNA-seq)


title: KO_LPS_Rep1

data_processing:
Pair -end reads were aligned to M.musculus reference genome using Burrows-Wheeler Aligner (BWA) with default parameters.
Transcript abundance was quantified using rpkm for genes (Ramskold et.al 2009)
EdgeR software was used to determine differentially expressed genes  with p-values<0.01 and FDR 0.1
Genome_build: mm9

source_name: Bone marrow derived macrophages

growth_protocol: Bone marrow cells were cultured in DMEM/L929 supernatant/10% FCS in the presence of 4uM 4-hydroxytamoxifen resulting in Ert2-Cre mediated deletion of Brd4 floxed allele. After 7 days in culture bone marrow derived macrophages were either stimulated with 100ng/ml LPS for 4 hours or left untreated

extract_protocol: Total RNA was extracted using Rneasy mini kit (Qiagen). Oligo-dT selection was performed using Dynal magnetic beads (Invitrogen), Fragmented RNA was reverse transcribed, purified and library was prepared including ligation of barcode using Mondrian SP (Nugen) and Ovation SP Ultraflow library system (Nugen). Library DNA was subjected to sequencing in Illumina Hiseq 2000.

tag: genotype

value: C57Bl6, Brd4Floxed :Ert2-Cre

value: Mcrophages were stimulated with LPS for 4 hours


title: KO_LPS_Rep2


title: KO_BMDM_LPS_BRD4_ChIP-seq

tag: strain background

tag: genotype/variation

value: LPS (100ng/ml) for 4hrs

tag: chip antibody


title: sample.kidney_13_1year

description:
htcf.wustl.edu/files/pX7rOPeW/Mcmahon_2328_1234/ATCGAGC
all.gene_RPKM.txt
all.gene_counts.txt

source_name: Kidney allograft biopsy

value: 1 year


title: HepG2_shMETTL14_3h_rep1 (RNA-seq)

tag: cell line


title: L-GQE sperm 15

tag: age

value: low rate of good quality  embryo


title: KO_Untreated_Rep1

value: Unstimulated macrophages


title: HepG2_shMETTL14_1h_rep2 (RNA-seq)


title: L-GQE sperm 14


title: WT_LPS_Rep2

value: C57Bl6, Brd4Floxed


title: HepG2_shMETTL14_1h_rep1 (RNA-seq)


title: sample.kidney_14_baseline_pre

description:
htcf.wustl.edu/files/pX7rOPeW/Mcmahon_2328_1234/GTATTTG
all.gene_RPKM.txt
all.gene_counts.txt

value: Patient #14

value: pre


title: L-GQE sperm 19


title: L-GQE sperm 13


title: HepG2_shMETTL14_0h_rep2 (RNA-seq)

value: untreated


title: WT_LPS_Rep1


title: sample.kidney_12_1year

description:
htcf.wustl.edu/files/pX7rOPeW/Mcmahon_2328_1234/TAGGTAA
all.gene_RPKM.txt
all.gene_counts.txt

value: Patient #12


title: L-GQE sperm 12


title: HepG2_shMETTL14_0h_rep1 (RNA-seq)


title: sample.kidney_14_1year

description:
htcf.wustl.edu/files/pX7rOPeW/Mcmahon_2328_1234/TCGAGAT
all.gene_RPKM.txt
all.gene_counts.txt


title: WT_Untreated_Rep2


title: KO_Untreated_Rep2


title: sample.kidney_15_baseline_pre

description:
htcf.wustl.edu/files/pX7rOPeW/Mcmahon_2328_1234/GACACAG
all.gene_RPKM.txt
all.gene_counts.txt

value: Patient #15


title: HepG2_shSETD2_6h_rep2 (RNA-seq)


title: sample.kidney_15_baseline_post

description:
htcf.wustl.edu/files/pX7rOPeW/Mcmahon_2328_1234/ACCTGAA
all.gene_RPKM.txt
all.gene_counts.txt

value: post


title: L-GQE sperm 10


title: L-GQE sperm 11


title: Input lin37 26C rep3

source_name: Input lin37 26C

tag: developmental stage

tag: temperature

value: Method 2


title: L-GQE sperm 9


title: sample.kidney_15_3months

description:
htcf.wustl.edu/files/pX7rOPeW/Mcmahon_2328_1234/TGGTCTC
all.gene_RPKM.txt
all.gene_counts.txt


title: HepG2_shSETD2_3h_rep2 (RNA-seq)

value: 5 ug/mL actinomycin D


title: H3K4me3 lin37 20C rep1

source_name: H3K4me3 lin37 20C

value: Fujifilm Wako MABI0304, #305–34819

tag: input control

value: Input lin37 20C rep1


title: sample.kidney_14_baseline_post

description:
htcf.wustl.edu/files/pX7rOPeW/Mcmahon_2328_1234/CTGGTGG
all.gene_RPKM.txt
all.gene_counts.txt


title: HepG2_shSETD2_3h_rep1 (RNA-seq)


title: sample.kidney_15_1year

description:
htcf.wustl.edu/files/pX7rOPeW/Mcmahon_2328_1234/TACTCTA
all.gene_RPKM.txt
all.gene_counts.txt


title: HepG2_shSETD2_1h_rep2 (RNA-seq)


title: sample.kidney_14_3months

description:
htcf.wustl.edu/files/pX7rOPeW/Mcmahon_2328_1234/ACTCCAA
all.gene_RPKM.txt
all.gene_counts.txt

value: 3 months


title: sample.kidney_01_baseline_pre

description:
Mcmahon_2230_2/GAGGCGT
all.gene_RPKM.txt
all.gene_counts.txt

value: Patient #01


title: Input lin35 20C rep3

source_name: Input lin35 20C


title: L-GQE sperm 6

value: testis


title: H3K4me3 lin35 26C rep1

source_name: H3K4me3 lin35 26C

value: Input lin35 26C rep1


title: H3K4me3 lin35 20C rep2

source_name: H3K4me3 lin35 20C

value: Input lin35 20C rep3


title: L-GQE sperm 7

value: low rate of good quality  embryo


title: WT_Untreated_Rep1

value: C57Bl6, Brd4Floxed

value: Unstimulated macrophages


title: sample.kidney_01_baseline_post

description:
Mcmahon_2230_2/TTTAACT
all.gene_RPKM.txt
all.gene_counts.txt


title: L-GQE sperm 5


title: H3K4me3 lin15B 26C rep1

source_name: H3K4me3 lin15B 26C

value: Input lin15B 26C rep1


title: HepG2_shSETD2_0h_rep2 (RNA-seq)

value: untreated


title: HepG2_shSETD2_6h_rep1 (RNA-seq)


title: HepG2_shSETD2_1h_rep1 (RNA-seq)


title: sample.kidney_01_3months

description:
Mcmahon_2230_2/GGTCCTC
all.gene_RPKM.txt
all.gene_counts.txt


title: L-GQE sperm 4

source_name: sperm


title: H3K4me3 lin15B 20C rep1

source_name: H3K4me3 lin15B 20C

value: Input lin15B 20C rep1


title: H3K4me3 N2 26C rep2

source_name: H3K4me3 N2 26C

value: wild-type

value: Input N2 26C rep2


title: HepG2_shSETD2_0h_rep1 (RNA-seq)

description:
mRNA half-life.txt
RNAseq_Raw_and_RPKM.txt


title: L-GQE sperm 8


title: sample.kidney_01_1year

description:
Mcmahon_2230_2/CGGTGGC
all.gene_RPKM.txt
all.gene_counts.txt

value: 1 year


title: sample.kidney_02_baseline_pre

description:
Mcmahon_2230_2/ACTGTCG
all.gene_RPKM.txt
all.gene_counts.txt

value: Patient #02

value: pre


title: L-GQE sperm 3


title: HepG2_shCtrl_6h_rep2 (RNA-seq)

value: non-specific control

value: 5 ug/mL actinomycin D


title: HepG2_shCtrl_6h_rep1 (RNA-seq)


title: L-GQE sperm 1


title: L-GQE sperm 2


title: H3K4me3 N2 20C rep1

source_name: H3K4me3 N2 20C

value: Fujifilm Wako MABI0304, #305–34819

value: Input N2 20C rep1

value: Method 2


title: H3K36me3 lin37 26C rep3

source_name: H3K36me3 lin37 26C

value: Fujifilm Wako MABI0333, #300–952

value: Input lin37 26C rep3


title: sample.kidney_02_3months

description:
Mcmahon_2230_2/GAGTACG
all.gene_RPKM.txt
all.gene_counts.txt

value: 3 months


title: HepG2_shCtrl_3h_rep2 (RNA-seq)


title: H3K27me3 lin37 26C rep1

source_name: H3K27me3 lin37 26C

value: Fujifilm Wako MABI0323, #309–95259

value: Input lin37 26C rep1


title: sample.kidney_02_1year

description:
Mcmahon_2230_2/ACAGATA
all.gene_RPKM.txt
all.gene_counts.txt


title: H-GQE sperm 23

value: testis

value: high rate of good quality embryo


title: H-GQE sperm 22


title: H3K27me3 lin37 20C rep1

source_name: H3K27me3 lin37 20C

value: Input lin37 20C rep1


title: sample.kidney_03_baseline_pre

description:
Mcmahon_2230_2/CTCAATG
all.gene_RPKM.txt
all.gene_counts.txt

value: Patient #03


title: HepG2_shCtrl_1h_rep1 (RNA-seq)


title: H-GQE sperm 21


title: sample.kidney_03_baseline_post

description:
Mcmahon_2230_2/AAATGCA
all.gene_RPKM.txt
all.gene_counts.txt

value: post


title: H-GQE sperm 20


title: HepG2_shCtrl_0h_rep2 (RNA-seq)

value: untreated


title: sample.kidney_03_3months

description:
Mcmahon_2230_2/ACGCGGG
all.gene_RPKM.txt
all.gene_counts.txt


title: HepG2_shCtrl_0h_rep1 (RNA-seq)


title: H-GQE sperm 19


title: N2 input rep1

city: Berlin

first: Baris

last: Tursun

address: Robert-Rössle-Str. 10

country: Germany

institute: Max Delbrück Center for Molecular Medicine

data_processing:
Basecalling and Demultiplexing was done with Illumina bcl2fastq v2.18.0.12 software.
ChIP-seq reads were mapped using bowtie2 v2.3.2  in paired end mode with default settings (-D 15 -R 2 -N 0 -L 22 -i S,1,1.15)  and allowing up to one alignment per read (-k 1 ) to version ce10 of the worm genome assembly.
Peaks were called for each replicate using the MACS v2.1.0 module callpeak with those settings: ( -g ce -keep-dup auto -q 0.05 - nomodel -extsize 300).
Genome_build: ce10
Supplementary_files_format_and_content: Bigwig files were generated by converting bam files to bed files using bedtools bamtobed v2.25.0 , followed by an extension of each alignment region by 200 bases up and down-stream, respectively. Regions overlapping chromosome borders were clipped. Then base resolution coverage score was calculated and scaled to reads-per-million by dividing each position by one million. Finally the scaled coverage track was exported to a bigwig file .    NarrowPeak files were generated during the peak calling process and the format follows the ENCODE narrowPeak format specifications.

source_name: whole worm

growth_protocol: C. elegans strains were maintained on OP50 bacteria and NGM agar plates at 15ºC. Worms were transferred to fresh food once a week.

extract_protocol:
Synchronized L4s  were washed with M9 buffer and flash-frozen as “worm popcorn” in liquid nitrogen. The popcorn was pulverized using a biopulverizer before further grinding to a fine powder using a mortar. The powder was dissolved in 10 vol 1,1 % formaldehyde in PBS+1 mM PMSF and fixed for 10 min with gentle rocking. Quenching was achieved by adding 2,5 M Glycine to a final concentration of 125 mM and gently rocking for 5 min. After centrifugation the pellet was washed with ice-cold PBS+1 mM PMSF, before it was resuspended in FA-buffer (50 mM HEPES/KOH pH 7,5, 1mM EDTA, 1% Triton X-100, 0,1 % sodium deoxycholate, 150 mM NaCl) + 1 % Sarkosyl + protease inhibitor and sonicated twice using a Bioruptor (15 times, 15 sec ON, 15 sec OFF; high settings) followed by 15 min centrifugation at full speed, 4°C. The supernatant was taken off (approx. 2-4 mg protein) and incubated either with MRG-1 antibody (Novus) or with buffer ON at 4°C on a rotator. Next, samples were incubated with µMACS ProteinA beads (Milteny Biotec) for 1 h on ice before they were applied to µMACS magnetic M columns that were equilibrated using FA buffer. The columns with bound material were washed 2x using FA buffer followed by washing with FA buffer + 1 mM NaCl and FA buffer + 500 mM NaCl. After further washing with TEL buffer (0,25 mM LiCl, 1 % sodium deoxycholate, 1 mM EDTA) and 2x with TE buffer, the samples were eluted using elution buffer (1 % SDS, 250 mM NaCl, 10 mM Tris pH 8,0, 1mM EDTA). The fixation was reverse crosslinked using 2 µl of 10 mg/ml Proteinase K at 50°C for 1 h followed by incubation at 65°C ON. The DNA was purified using the QIAquick PCR purification kit in a final volume of 40 µl.
Libraries were prepared using the NEXTflex qCHIP-Seq v2 kit (NOVA-5130-12) according to manufacturer’s instructions.

treatment_protocol: For experiments, worms were synchronized by bleaching and L1 larvae were put on OP50 containing plates and grown at 25°C until most of the animals reached L4 stage.

tag: strain

tag: Stage

value: MRG-1 antibody (Novus bio)


title: N2 input rep2


title: N2 input rep3


title: sample.kidney_03_1year

description:
Mcmahon_2230_2/GGAGTCC
all.gene_RPKM.txt
all.gene_counts.txt

value: 1 year


title: sample.kidney_02_baseline_post

description:
Mcmahon_2230_2/GTATTTG
all.gene_RPKM.txt
all.gene_counts.txt

value: Patient #02


title: HepG2 DRB HA-METTL14 (ChIP-seq)

description:
HepG2_macs_METL14_DRB_peaks.bed
HepG2_macs_METTL14_DRB_peaks.txt

data_processing:
Illumina Casava1.8 software used for basecalling.
All sequenced reads were checked for quality control by using FastQC v0.11.5 with default parameters; then the processed reads were mapped to hg19 whole genome using Bowtie v1.1.2 with default parameters
The METTL14 enriched regions were calculated by using SICER with default parameters
The cutoff for significantly enriched METTL14 peak: FDR < 1e-4
Genome_build: hg19
Supplementary_files_format_and_content: bed files containing METTL14 peaks identified by SICER

source_name: HepG2 cells

growth_protocol: The human hepatocellular carcinoma cell line HepG2 (ATCC HB-8065) was maintained in EMEM medium (ATCC) supplemented with 10% FBS (Invitrogen, Carlsbad, CA), 2 mM L-Glutamine and 1% penicillin-streptomycin.

extract_protocol:
METTL14 ChIP experiment was performed using iDeal ChIP-seq Kit for Transcription Factors (Diagenode) following the manufacturer’s protocol. Briefly, HepG2 cells transduced with HA-tagged METTL14 were crosslinked with formaldehyde, lysed, and subjected to chromatin shearing by sonication in a Bioruptor Pico (Diagenode) with 30s on/30s off for 20 cycles. Immunoprecipitation was performed using 2 µg anti-HA antibody (11867423001, Roche).
Product DNA (including IP product and the Input control) was decrosslinked and subjected to library construction using KAPA Hyper Prep Kit (Roche). Libraries were purified using AxyPrep Mag PCR Clean-up kit (Thermo Fisher Scientific). Each library was quantified using a Qubit fluorometer (Thermo Fisher Scientific) and the size distribution assessed using the 2100 Bioanalyzer (Agilent Technologies). The amplified libraries were hybridized to the Illumina single end flow cell and amplified using the cBot (Illumina). Single end reads of 50 nt were generated on Illumina HiSeq2500.

treatment_protocol: For overexpression, PLJM1 vectors with METTL14 cDNA fused with HA-tag at N-terminal and EGFP at C-terminal, along with 2nd generation packaging vectors (pMD2.G and psPAX2), were co-transfected into HEK293T cells using X-tremeGENE HP DNA Transfection Reagent. The lentivirus particles were harvested at 48 and 72 hours after transfection and were used for infection of target cells with the supplement polybrene. After two rounds of infection, cells were selected with 1 μg/ml puromycin. GFP-high cells were then sorted by flow cytometry to make sure that the stable cells have relatively high expression of METTL14. HepG2 cells were treated with or withour 100µM DRB for 3 hours.

tag: ip antibody

value: HA antibody (11867423001, Roche)

value: DRB

tag: replication


title: HepG2_shCtrl_3h_rep1 (RNA-seq)

tag: shRNA

value: non-specific control

tag: treatment

value: 5 ug/mL actinomycin D


title: BNST_Male_8c

city: Cambridge

first: Evan

last: Macosko

state: Ma

address: 75 Ames St, Broad Institute

institute: Broad Institute

description:
Male8_BNST
single-nuclei gene expression data
BNST_region_neur_Mal_matrix.mtx
BNST_region_neur_Mal_barcodes.csv
BNST_region_neur_Mal_genes.csv
BNST_only_Mal_matrix.mtx
BNST_only_Mal_barcodes.csv
BNST_only_Mal_genes.csv

data_processing:
Genome_build: mm10_premrna
Mouse:  R1:28 bp, R2:91 bp
Sequencing reads were demultiplexed and aligned against the mm10_premrna mouse genome build for BNST samples using 10x Cell Ranger v3.0.2; sequencing reads were demultiplexed and aligned against the GRCh38_premrna build for SN samples using 10x Cell Ranger v2.2
Digital gene expression matrices (with gene expression counts) were generated by Cell Ranger software (v3.0.2 for BNST samples, v2.2 for SN samples)
Digital gene expression matrices were analyzed and subset to specific regions using LIGER (v0.3)
Supplementary_files_format_and_content:
digital gene expression matrix (sparse format): matrix market format, rows = genes/transcripts, columns = barcodes/cells
barcodes list: names of barcodes/cells for corresponding DGE matrix file
genes list: names of transcripts/genes for corresponding DGE matrix file
BNST_only: nuclei determined to be neurons localized specifically to BNST
BNST_region_neur: nuclei determined to be neurons localized to the larger BNST region

source_name: Bed nucleus of the stria terminalis

extract_protocol:
Perfused frozen tissues were finely minced and dissociated in an extraction media a based on that of Carter et al. 2009 with 0.1% Triton for 10 minutes. Extracted nuclei were washed in 30 mLs of media based on that of Carter et al. 2009 and pelleted by bucket centrifuge. Nuclei were filtered through a 40 um FlowMi filter before FACS sorting for singlets using a DAPI signal.
10X Chromium Single Cell 3' (V2 or V3) (manufacturer's protocol).  Mouse: V3, human: V2.

tag: Sex

value: Male

tag: tissue

value: Bed nucleus of the stria terminalis


title: N2 rep3


title: N2 rep2


title: H-GQE sperm 18

tag: embryo quality


title: HepG2 DRB input (ChIP-seq)


title: H-GQE sperm 17


title: HepG2_shCtrl_1h_rep2 (RNA-seq)

tag: time point


title: N2 rep1


title: HepG2 HA-METTL14 rep2 (ChIP-seq)

description:
HepG2_macs_METTL14_peaks.bed
HepG2_macs_METTL14_peaks.txt


title: H-GQE sperm 16


title: H-GQE sperm 15


title: BNST_Male_8a


title: HepG2 HA-METTL14 rep1 (ChIP-seq)


title: BNST_Male_8b


title: glp-4 input rep3


title: BNST_Male_7b

description:
Male7_BNST
single-nuclei gene expression data
BNST_region_neur_Mal_matrix.mtx
BNST_region_neur_Mal_barcodes.csv
BNST_region_neur_Mal_genes.csv
BNST_only_Mal_matrix.mtx
BNST_only_Mal_barcodes.csv
BNST_only_Mal_genes.csv


title: glp-4 input rep2


title: HepG2 input rep2 (ChIP-seq)


title: H-GQE sperm 14


title: H-GQE sperm 13


title: BNST_Male_7a


title: BNST_Male_6a

description:
Male6_BNST
single-nuclei gene expression data
BNST_region_neur_Mal_matrix.mtx
BNST_region_neur_Mal_barcodes.csv
BNST_region_neur_Mal_genes.csv
BNST_only_Mal_matrix.mtx
BNST_only_Mal_barcodes.csv
BNST_only_Mal_genes.csv


title: H-GQE sperm 12


title: BNST_Male_5b

description:
Male5_BNST
single-nuclei gene expression data
BNST_region_neur_Mal_matrix.mtx
BNST_region_neur_Mal_barcodes.csv
BNST_region_neur_Mal_genes.csv
BNST_only_Mal_matrix.mtx
BNST_only_Mal_barcodes.csv
BNST_only_Mal_genes.csv


title: H-GQE sperm 11


title: glp-4 rep2


title: BNST_Male_5a


title: H-GQE sperm 10


title: glp-4 rep1


title: BNST_Male_3a

description:
Male3_BNST
single-nuclei gene expression data
BNST_region_neur_Mal_matrix.mtx
BNST_region_neur_Mal_barcodes.csv
BNST_region_neur_Mal_genes.csv
BNST_only_Mal_matrix.mtx
BNST_only_Mal_barcodes.csv
BNST_only_Mal_genes.csv


title: H-GQE sperm 9


title: H-GQE sperm 8


title: BNST_Male_4a

description:
Male4_BNST
single-nuclei gene expression data
BNST_region_neur_Mal_matrix.mtx
BNST_region_neur_Mal_barcodes.csv
BNST_region_neur_Mal_genes.csv
BNST_only_Mal_matrix.mtx
BNST_only_Mal_barcodes.csv
BNST_only_Mal_genes.csv


title: SN_SubjectMD6063_c

description:
SubjectMD6063_SN
single-nuclei gene expression data
SN_MD6063_matrix.mtx
SN_MD6063_barcodes.csv
SN_MD6063_genes.csv

data_processing:
Genome_build: GRCh38_premrna
Human:  R1:26 bp, R2:98 bp
Sequencing reads were demultiplexed and aligned against the mm10_premrna mouse genome build for BNST samples using 10x Cell Ranger v3.0.2; sequencing reads were demultiplexed and aligned against the GRCh38_premrna build for SN samples using 10x Cell Ranger v2.2
Digital gene expression matrices (with gene expression counts) were generated by Cell Ranger software (v3.0.2 for BNST samples, v2.2 for SN samples)
Digital gene expression matrices were analyzed and subset to specific regions using LIGER (v0.3)
Supplementary_files_format_and_content:
digital gene expression matrix (sparse format): matrix market format, rows = genes/transcripts, columns = barcodes/cells
barcodes list: names of barcodes/cells for corresponding DGE matrix file
genes list: names of transcripts/genes for corresponding DGE matrix file

source_name: Substantia nigra

tag: individual

value: Subject MD6063

value: Substantia nigra


title: H-GQE sperm 7

value: testis


title: SN_SubjectMD6063_b


title: BNST_Male_2b

description:
Male2_BNST
single-nuclei gene expression data
BNST_region_neur_Mal_matrix.mtx
BNST_region_neur_Mal_barcodes.csv
BNST_region_neur_Mal_genes.csv
BNST_only_Mal_matrix.mtx
BNST_only_Mal_barcodes.csv
BNST_only_Mal_genes.csv


title: BNST_Male_1b

description:
Male1_BNST
single-nuclei gene expression data
BNST_region_neur_Mal_matrix.mtx
BNST_region_neur_Mal_barcodes.csv
BNST_region_neur_Mal_genes.csv
BNST_only_Mal_matrix.mtx
BNST_only_Mal_barcodes.csv
BNST_only_Mal_genes.csv


title: H-GQE sperm 6

value: high rate of good quality embryo


title: SN_SubjectMD6060_b

description:
SubjectMD6060_SN
single-nuclei gene expression data
SN_MD6060_matrix.mtx
SN_MD6060_barcodes.csv
SN_MD6060_genes.csv

value: Subject MD6060


title: BNST_Male_2a


title: H-GQE sperm 5


title: SN_SubjectMD6063_a


title: BNST_Male_1a


title: glp-4 input rep1

tag: chip antibody


title: glp-4 rep3


title: HepG2 input rep1 (ChIP-seq)

tag: cell line


title: SN_SubjectMD6060_a


title: BNST_Female_7a

description:
Female7_BNST
single-nuclei gene expression data
BNST_region_neur_Fem_matrix.mtx
BNST_region_neur_Fem_barcodes.csv
BNST_region_neur_Fem_genes.csv
BNST_only_Fem_matrix.mtx
BNST_only_Fem_barcodes.csv
BNST_only_Fem_genes.csv

value: Female


title: SN_SubjectMD5893_c

description:
SubjectMD5893_SN
single-nuclei gene expression data
SN_MD5893_matrix.mtx
SN_MD5893_barcodes.csv
SN_MD5893_genes.csv

value: Subject MD5893


title: BNST_Female_6c

description:
Female6_BNST
single-nuclei gene expression data
BNST_region_neur_Fem_matrix.mtx
BNST_region_neur_Fem_barcodes.csv
BNST_region_neur_Fem_genes.csv
BNST_only_Fem_matrix.mtx
BNST_only_Fem_barcodes.csv
BNST_only_Fem_genes.csv


title: H-GQE sperm 2

tag: age


title: SN_SubjectMD5893_b


title: H-GQE sperm 3


title: SN_SubjectMD5893_a


title: BNST_Female_6b


title: SN_SubjectMD5862_c

description:
SubjectMD5862_SN
single-nuclei gene expression data
SN_MD5862_matrix.mtx
SN_MD5862_barcodes.csv
SN_MD5862_genes.csv

value: Subject MD5862


title: H-GQE sperm 1


title: Hb_supernat_polyp_2

city: Irapuato

first: Cei

last: Abreu-Goodger

state: Guanajuato

address: Km. 9.6 Libramiento Nte Carr Leon-Irapuato

country: Mexico

institute: Langebio - Cinvestav

data_processing:
All libraries were quality checked with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), reaper v16-098 (https://www.ebi.ac.uk/~stijn/reaper/reaper.html) was used to remove the Illumina small RNA Adapter sequences, and PullSeq 1.0.2 (https://github.com/bcthomas/pullseq) to keep reads that were at least 16 nucleotides long.
Tally v16-098 (https://www.ebi.ac.uk/~stijn/reaper/tally.html) was used to collapse all reads to a single occurrence in a FASTA file, keeping the counts of each read in the header. These are provided as processed files.
The alignment component of ShortStack 3.8.3 was used, with parameters: --nostitch, --mismatches 2, --mmap u, --bowtie_m 500 and --ranmax 500.
All the sRNA-seq results for each genome were used to predict novel ncRNA producing regions or clusters. All libraries for each genome were combined as a single input, and ShortStack 3.8.3 was used with the following parameters: --pad 10, --mincov 10, --dicermin 18, --dicermax 32. All the clusters were then split at exon-intron boundaries.
In order to obtain a level of expression for each sRNA-producing cluster, mapped reads were counted using the findOverlaps function from GenomicRanges R package with parameters minoverlap=16 and ignore.strand=TRUE. Only reads between 20-25nt were counted. Count tables were produced for each genome, where each cluster is a row and each library a column. These are provided as supplementary files.
Genome_build: The reference genome assembly for H. bakeri genome was nHp_v2.0 from http://parasite.wormbase.org/Heligmosomoides_polygyrus_prjeb15396 and for C. elegans WBcel235 from http://parasite.wormbase.org/Caenorhabditis_elegans_prjna13758.
Supplementary_files_format_and_content: Contains all reads of at least 16 nucleotides collapsed to a unique occurrences and saved in FASTA format. Read count is included in the tab files.

organism: Heligmosomoides polygyrus bakeri

source_name: Input supernatant

growth_protocol: CBA x C57BL/6 F1 (CBF1) mice were infected with L3 infective-stage H. bakeri larvae by gavage and adult nematodes were collected from the small intestine 14 days post infection. The nematodes were washed and maintained in serum-free media in vitro.

extract_protocol:
Total RNA was treated with RNA 5' Polyphosphatase (Epicenter) following manufacturer's instructions, before library preparation.
Total RNA was extracted using a miRNAeasy mini kit (Qiagen) following manufacturer's instructions. RNA was treated with Turbo DNA-free kit (Thermo Fisher) to remove residual DNA.
Libraries were prepared using the CleanTag small RNA library prep kit according to manufacturer’s instructions, using total RNA from adult worms (30 ng), and sucrose-gradient purified EVs (equivalent 1E10 EVs measured by Nanosight, Malvern). For all samples, 1:12 dilutions of both adapters were used with 18 amplification cycles (TriLink BioTechnologies). Fragments between 140-170bp were size selected and sequenced on an Illumina HiSeq high output v4 50bp SE in Edinburgh Genomics.

value: Input supernatant

tag: agent

value: polyphosphatase

tag: treatment protocol

value: Nematodes were disrupted in 700 µl of Qiazol (Qiagen) using mechanical disruption with 5 mm stainless steel beads (Qiagen) on a Tissue Lyser II (30hz for 2 min twice; Qiagen)


title: BNST_Female_5b

description:
Female5_BNST
single-nuclei gene expression data
BNST_region_neur_Fem_matrix.mtx
BNST_region_neur_Fem_barcodes.csv
BNST_region_neur_Fem_genes.csv
BNST_only_Fem_matrix.mtx
BNST_only_Fem_barcodes.csv
BNST_only_Fem_genes.csv


title: MF-2

city: Guiyang

first: Huiqing

last: Yan

state: Guizhou

address: Guizhou Normal University

department: School of Life Science

institute: Guizhou Normal University

data_processing:
150bp paired-end reads were generated via Illumina HiSeqTM 3000
Raw data of fastq format were firstly processed through trimmomatic by default parameters. The clean reads were selected from raw data with filtering out adaptor-only reads, reads with more than 5% N bases unknown, and low-quality reads (reads containing more than 50% bases with Q-value≤10).
The clean reads were assembled de novo using the Trinity assembly program. The Trinity software first combined reads with a certain length of overlap to form contigs, then reads were mapped back to the contigs. After that contigs were clustered into transcripts using the paired-end reads, and redundancies in these transcripts were then removed to obtain unigenes. The genome assembly of was used as the genomic reference.
Bowtie2and RSEM (RNA-Seq by Expectation-Maximization) were used to map clean reads to the assembled transcriptome and evaluate the abundance of each transcript, respectively. To compare the expression levels of transcripts in different samples, FPKM (fragments per kilobase of transcript per million mapped reads) for normalization and to present the expression of transcripts was used
Genome_build: De novo assembly
Supplementary_files_format_and_content: FPKMs

organism: Rosa roxburghii

source_name: Mature Fruit

growth_protocol: Wild Rose roxburghii were planted in Guizhou Normal University, Guizhou, China (26°42.408'N, 106°67.353'E) for transcriptomic analyses.

extract_protocol:
Using Trizol method (Invitrogen, Life Technologies)+ RNAiso-mate (Takara, Japan), which is used for extracting tissues contained high levels of polyphenols, according the manufacturer’s protocol, total RNA was extracted from two biological replicates (three plants per replicate) for each genotype.
NanoDrop ND 1000 (NanoDrop technologies) was used to initially calculate the quality and quantity of the extracted RNA, and then the RNA Integrity Number (RIN) value was assessed by Agilent Technologies 2100 Bioanalyzer (Agilent). Only when the value of RIN was higher than 8, the RNA was used to prepare the c-DNA library according to the TruSeq RNA Sample Prep v2 protocol

tag: authority

value: Rosa roxburghii Tratt

value: Mature Fruit

tag: developmental stage

value: 120 days after flowering

tag: phenotype

value: Normal


title: BNST_Female_6a

tag: strain


title: SN_SubjectMD5862_b

value: Male


title: SN_SubjectMD5862_a


title: Hb_supernat_polyp_1


title: MF-1


title: SN_SubjectMD5840_c

description:
SubjectMD5840_SN
single-nuclei gene expression data
SN_MD5840_matrix.mtx
SN_MD5840_barcodes.csv
SN_MD5840_genes.csv

value: Subject MD5840


title: BNST_Female_5a

value: Bed nucleus of the stria terminalis


title: H-GQE sperm 4


title: YF-3

source_name: Young Fruit

value: Young Fruit

value: 50 days after flowering


title: BNST_Female_4b

description:
Female4_BNST
single-nuclei gene expression data
BNST_region_neur_Fem_matrix.mtx
BNST_region_neur_Fem_barcodes.csv
BNST_region_neur_Fem_genes.csv
BNST_only_Fem_matrix.mtx
BNST_only_Fem_barcodes.csv
BNST_only_Fem_genes.csv


title: YF-2


title: BNST_Female_4a


title: BNST_Female_3c

description:
Female3_BNST
single-nuclei gene expression data
BNST_region_neur_Fem_matrix.mtx
BNST_region_neur_Fem_barcodes.csv
BNST_region_neur_Fem_genes.csv
BNST_only_Fem_matrix.mtx
BNST_only_Fem_barcodes.csv
BNST_only_Fem_genes.csv


title: SN_SubjectMD5828_c

description:
SubjectMD5828_SN
single-nuclei gene expression data
SN_MD5828_matrix.mtx
SN_MD5828_barcodes.csv
SN_MD5828_genes.csv

value: Subject MD5828

value: Substantia nigra


title: H-3

source_name: Flower

value: Flower

value: blooming flower


title: YF-1


title: H-2


title: SN_SubjectMD5840_a


title: BNST_Female_3b

value: Female


title: SN_SubjectMD5828_b


title: H-1


title: MF-3


title: SN_SubjectMD5828_a


title: BNST_Female_2a

description:
Female2_BNST
single-nuclei gene expression data
BNST_region_neur_Fem_matrix.mtx
BNST_region_neur_Fem_barcodes.csv
BNST_region_neur_Fem_genes.csv
BNST_only_Fem_matrix.mtx
BNST_only_Fem_barcodes.csv
BNST_only_Fem_genes.csv


title: BNST_Female_3a


title: Hb_adult_polyp_3

source_name: Adult worms

value: Adult worms


title: SN_SubjectMD5840_b


title: S-3

source_name: Stem

value: Stem

value: The new shoots on one-year


title: SN_SubjectMD5534_f

description:
SubjectMD5534_SN
single-nuclei gene expression data
SN_MD5534_matrix.mtx
SN_MD5534_barcodes.csv
SN_MD5534_genes.csv

value: Subject MD5534


title: SN_SubjectMD5534_e


title: S-2

value: Rosa roxburghii Tratt


title: Hb_adult_polyp_2

value: polyphosphatase

value: Nematodes were disrupted in 700 µl of Qiazol (Qiagen) using mechanical disruption with 5 mm stainless steel beads (Qiagen) on a Tissue Lyser II (30hz for 2 min twice; Qiagen)


title: Hb_adult_polyp_1


title: S-1

value: Normal


title: SN_SubjectMD5534_d


title: SN_SubjectMD5534_c


title: BNST_Female_1a

description:
Female1_BNST
single-nuclei gene expression data
BNST_region_neur_Fem_matrix.mtx
BNST_region_neur_Fem_barcodes.csv
BNST_region_neur_Fem_genes.csv
BNST_only_Fem_matrix.mtx
BNST_only_Fem_barcodes.csv
BNST_only_Fem_genes.csv


title: Hb_adult_monop_2

extract_protocol:
Total RNA was used directly for library preparation.
Total RNA was extracted using a miRNAeasy mini kit (Qiagen) following manufacturer's instructions. RNA was treated with Turbo DNA-free kit (Thermo Fisher) to remove residual DNA.
Libraries were prepared using the CleanTag small RNA library prep kit according to manufacturer’s instructions, using total RNA from adult worms (30 ng), and sucrose-gradient purified EVs (equivalent 1E10 EVs measured by Nanosight, Malvern). For all samples, 1:12 dilutions of both adapters were used with 18 amplification cycles (TriLink BioTechnologies). Fragments between 140-170bp were size selected and sequenced on an Illumina HiSeq high output v4 50bp SE in Edinburgh Genomics.


title: SN_SubjectMD5534_b


title: L-3

source_name: Leaf

value: Leaf

value: mature leaves without petioles


title: ros1a-sperm

city: San Francisco

first: M.

middle: Yvonne

last: Kim

address: 3rd st.

institute: UC San Francisco

data_processing:
Sequenced reads were trimmed using Trim Galore! With --clip_R1 9 parameter.
trimmed reads were mapped to msu7 rice reference genome using bismark --p 4 --non-directional parameters.
methylated cytosine / (methylated cytosine + unmethylated cytosine) was calculated for every cytosine.
methylated cytosine / (methylated cytosine + unmethylated cytosine) was calculated for every 50 base pair window.
Genome_build: MSU7
Supplementary_files_format_and_content: tab-delimited 50 bp window CG, CHG, and CHH methylation.

organism: Oryza sativa

source_name: rice sperm

extract_protocol:
Wild-type and ros1a/+ O. sativa cv. Nipponbare harboring a UBQ::H2B-GFP transgene were grown at 26 ºC in a 13/11 hr light/dark cycled chamber. Rice pollen was harvested from unopened flowers with elongated stamen. Pollen grains were burst open via osmotic pressure in 370 mOsmol/kg H2O mannitol solution for 5 minutes at room temperature. Sperm cells and vegetative cell nuclei were isolated using the differential interference contrast microscopy and GFP fluorescent microscopy, respectively, under a BX-71 inverted fluorescence microscope (Olympus, Tokyo, Japan). The sperm cells and vegetative cell nuclei were washed once in 370 mOsmol/kg H2O mannitol solution and stored at -80C.
Bisulfite sequencing libraries were constructed as described Smallwood et al., Nature Methods (2014)

tag: genotype/variation

value: ros1a/+ heterozygous

tag: cultivar

value: Nipponbare

tag: cell type

value: sperm


title: Hb_adult_monop_1


title: SN_SubjectMD5534_a

tag: Sex

value: Substantia nigra


title: L-1

tag: tissue


title: WT-vegetative

source_name: rice vegetative cell

value: WT

value: vegetative cell


title: WT-sperm


title: sci3-me-759

status: Public on Feb 20 2019

city: Seattle

first: Junyue

last: Cao

state: WA

address: Foege Building S-210, 3720 15th Ave NE

department: Department of Genome Sciences

institute: University of Washington

description: sci-RNA-seq3 library

data_processing:
For sc-RNA-seq processing, read alignment and gene count matrix generation for single cell RNA-seq of co-assay was the same with sci-RNA-seq ("J. Cao et al., Comprehensive single cell transcriptional profiling of a multicellular organism by combinatorial indexing. bioRxiv, 104844 (2017).") with minor modifications: Reads were mapped to a chimeric reference genome of human (hg19) and mouse (mm10) for RNA-seq from A594, HEK293T and NIH/3T3 cells, and mouse (mm10) only for RNA-seq from mouse kidney experiment with STAR/v 2.5.2b, with gene annotations (GENCODE V19 for human; GENCODE VM11 for mouse). For mixed-species experiment, the percentage of uniquely mapping reads for genomes of each species was calculated. Cells with over 80% of UMIs assigned to one species were regarded as species-specific cells, with the remaining cells classified as mixed cells or “collisions”.
Genome_build: mouse reference genome (mm10)
Supplementary_files_format_and_content: Processed data files include a cell annotation csv  file, gene annotation csv file, and a gene count sparse matrix file
Supplementary_files_format_and_content: Cell annotation file: sample is cell id of each single cell with the reverse transcription and ligation barcode attached; tsne_1 and tsne_2 are cell coordinates after t-SNE dimension reduction.
Supplementary_files_format_and_content: Gene annotation file including gene id, gene type and gene short name.
Supplementary_files_format_and_content: A sparse matrix file: each row corresponds to gene id (with gene information in the gene_annotation.csv; each column corresponds to each cell (with cell source information in the cell_annotation.csv); each value in the matrix corresponds to UMI count.

source_name: mouse embryos

growth_protocol: The C57BL/6 mice were obtained from The Jackson Laboratory (Bar Harbor, ME) and plug matings were set up. Noon on the day of the vaginal plug was considered as embryonic day (E) 0.5. Dissections were done as previously described76 and all embryos were immediately snap frozen in liquid nitrogen. All animal procedures were in accordance with institutional, state, and government regulations (IACUC protocol 4378-01).

extract_protocol:
Mouse embryos from different development stages were processed together to reduce batch effect. Each mouse embryo was minced into small pieces by blade in 1 mL ice-cold cell lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630 from77, modified to also include 1% SUPERase In and 1% BSA) and transferred to the top of a 40um cell strainer (Falcon). Tissues were homogenized with the rubber tip of a syringe plunger (5ml, BD) in 4ml cell lysis buffer. The filtered nuclei were then transferred to a new 15ml tube (Falcon) and pelleted by centrifuge at 500xg for 5min and washed once with 1ml cell lysis buffer. The nuclei were fixed in 4ml ice cold 4% paraformaldehyde (EMS) for 15min on ice. After fixation, the nuclei were washed twice in 1ml nuclei wash buffer (cell lysis buffer without IGEPAL), and re-suspended in 500ul nuclei wash buffer. The samples were split to two tubes with 250ul in each tube and flash frozen in liquid nitrogen. We estimated the nuclei extraction efficiency based on extracted nuclei number vs. expected total nuclei number in each embryo and the nuclei extraction efficiency range from 60% to 85%.
Thawed nuclei are permeabilized with 0.2% tritonX-100 (in nuclei wash buffer) for 3 minutes on ice, and briefly sonicated (Diagenode, 12s on low power mode) to reduce nuclei clumping.  The nuclei were then washed once with nuclei wash buffer and filtered through 1ml Flowmi cell strainer (Flowmi). Filtered nuclei were spun down at 500xg for 5min and resuspended in nuclei wash buffer.    Nuclei from each mouse embryo were then distributed into several individual wells in four 96-well plates. The links between well id and mouse embryo were recorded for downstream data processing. For each well, 80,000 nuclei (16 µL) were mixed with 8 µl of 25 µM anchored oligo-dT primer (5′- /5Phos/CAGAGCNNNNNNNN[10bp barcode]TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT-3′, where “N” is any base; IDT) and 2 µL 10 mM dNTP mix (Thermo), denatured at 55°C for 5 min and immediately placed on ice. 14 µL of first-strand reaction mix, containing 8 µL 5X Superscript IV First-Strand Buffer (Invitrogen), 2 µl 100 mM DTT (Invitrogen), 2 µl SuperScript IV reverse transcriptase (200 U/μl, Invitrogen), 2 μL RNaseOUT Recombinant Ribonuclease Inhibitor (Invitrogen), was then added to each well. Reverse transcription was carried out by incubating plates by gradient temperature (4°C 2 minutes, 10°C 2 minutes, 20°C 2 minutes, 30°C 2 minutes, 40°C 2 minutes, 50°C 2 minutes and 55°C 10 minutes).    After ligation reaction, 60µL nuclei dilution buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 1% BSA) was added into each well. Nuclei from all wells were pooled together and spun down at 500xg for 10min. Nuclei were then resuspended in nuclei wash buffer and redistributed into another four 96-well plates with each well including  4µL T4 ligation buffer (NEB), 2µL T4 DNA ligase (NEB), 4µL Betaine solution (5M, Sigma-Aldrich), 6µL nuclei in nuclei wash buffer, 8µL barcoded ligation adaptor (100uM, 5’- GCTCTG[9bp or 10bp barcode A]/ideoxyU/ACGACGCTCTTCCGATCT[reverse complement of barcode A]-3’) and 16µL 40% PEG 8000 (Sigma-Aldrich). The ligation reaction was done at 16°C for 3 hours.    After RT reaction, 60µL nuclei dilution buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 1% BSA) was added into each well. Nuclei from all wells were pooled together and spun down at 600xg for 10min. Nuclei were washed once with nuclei wash buffer and filtered with 1ml Flowmi cell strainer (Flowmi) twice, counted and redistributed into eight 96-well plates with each well including 2,500 nuclei in 5µL nuclei wash buffer and 5µL elution buffer (Qiagen). 1.33 μl mRNA Second Strand Synthesis buffer (NEB) and 0.66 μl mRNA Second Strand Synthesis enzyme (NEB) were then added to each well, and second strand synthesis was carried out at 16°C for 180 min.    For tagmentation, each well was mixed with 11 μL Nextera TD buffer (Illumina) and 1 μL i7 only TDE1 enyzme (62.5nM, Illumina), and then incubated at 55°C for 5 min to carry out tagmentation. The reaction was then stopped by adding 24 μL DNA binding buffer (Zymo) per well and incubating at room temperature for 5 min. Each well was then purified using 1.5x AMPure XP beads (Beckman Coulter). In the elution step, each well was added with 8µL nuclease free water, 1µL 10X USER buffer (NEB), 1µL USER enzyme (NEB) and incubated at 37°C for 15 min. Another 6.5µL elution buffer was added into each well. The AMPure XP beads were removed by magnetic stand and the elution product was transferred into a new 96-well plate.    For PCR amplification, each well (16µL product) was mixed with 2μL of 10 μM indexed P5 primer (5′-AATGATACGGCGACCACCGAGATCTACAC[i5]ACACTCTTTCCCTACACGACGCTCTTCCGATCT-3′; IDT), 2 μL of 10 μM P7 primer (5′-CAAGCAGAAGACGGCATACGAGAT[i7]GTCTCGTGGGCTCGG-3′, IDT), and 20 μL NEBNext High-Fidelity 2X PCR Master Mix (NEB). Amplification was carried out using the following program: 72°C for 5 min, 98°C for 30 sec, 12-14 cycles of (98°C for 10 sec, 66°C for 30 sec, 72°C for 1 min) and a final 72°C for 5 min.

tag: genetic background

value: B6 background


title: sci3-me-760

description: sci-RNA-seq3 library


title: sci3-me-758

description: sci-RNA-seq3 library


title: ros1a-vegetative


title: sci3-me-757

description: sci-RNA-seq3 library


title: sci3-me-755

description: sci-RNA-seq3 library


title: sci3-me-756

description: sci-RNA-seq3 library


title: Hb_adult_monop_3

value: Adult worms


title: sci3-me-753

description: sci-RNA-seq3 library


title: sci3-me-752

description: sci-RNA-seq3 library


title: sci3-me-750

description: sci-RNA-seq3 library


title: sci3-me-748

description: sci-RNA-seq3 library


title: sci3-me-751

description: sci-RNA-seq3 library


title: sci3-me-749

description: sci-RNA-seq3 library


title: sci3-me-746

description: sci-RNA-seq3 library


title: sci3-me-747

description: sci-RNA-seq3 library


title: sci3-me-745

description: sci-RNA-seq3 library


title: L-2


title: sci3-me-740

description: sci-RNA-seq3 library


title: sci3-me-742

description: sci-RNA-seq3 library


title: sci3-me-744

description: sci-RNA-seq3 library


title: sci3-me-743

description: sci-RNA-seq3 library


title: sci3-me-739

description: sci-RNA-seq3 library


title: sci3-me-754

description: sci-RNA-seq3 library


title: sci3-me-735

description: sci-RNA-seq3 library


title: sci3-me-737

description: sci-RNA-seq3 library


title: sci3-me-736

description: sci-RNA-seq3 library


title: sci3-me-731

description: sci-RNA-seq3 library


title: sci3-me-732

description: sci-RNA-seq3 library


title: sci3-me-733

description: sci-RNA-seq3 library


title: sci3-me-729

description: sci-RNA-seq3 library


title: sci3-me-730

description: sci-RNA-seq3 library


title: sci3-me-725

description: sci-RNA-seq3 library


title: sci3-me-726

description: sci-RNA-seq3 library


title: sci3-me-741

description: sci-RNA-seq3 library


title: sci3-me-724

description: sci-RNA-seq3 library


title: sci3-me-721

description: sci-RNA-seq3 library


title: sci3-me-720

description: sci-RNA-seq3 library


title: sci3-me-723

description: sci-RNA-seq3 library


title: sci3-me-717

description: sci-RNA-seq3 library


title: sci3-me-734

description: sci-RNA-seq3 library


title: sci3-me-738

description: sci-RNA-seq3 library


title: sci3-me-714

description: sci-RNA-seq3 library


title: sci3-me-715

description: sci-RNA-seq3 library


title: sci3-me-718

description: sci-RNA-seq3 library


title: sci3-me-712

description: sci-RNA-seq3 library


title: sci3-me-713

description: sci-RNA-seq3 library


title: sci3-me-716

description: sci-RNA-seq3 library


title: sci3-me-711

description: sci-RNA-seq3 library


title: sci3-me-710

description: sci-RNA-seq3 library


title: sci3-me-709

description: sci-RNA-seq3 library


title: sci3-me-722

description: sci-RNA-seq3 library


title: sci3-me-719

description: sci-RNA-seq3 library


title: sci3-me-708

description: sci-RNA-seq3 library


title: sci3-me-702

description: sci-RNA-seq3 library


title: sci3-me-705

description: sci-RNA-seq3 library


title: sci3-me-706

description: sci-RNA-seq3 library


title: sci3-me-704

description: sci-RNA-seq3 library


title: sci3-me-703

description: sci-RNA-seq3 library


title: sci3-me-698

description: sci-RNA-seq3 library


title: sci3-me-700

description: sci-RNA-seq3 library


title: sci3-me-701

description: sci-RNA-seq3 library


title: sci3-me-699

description: sci-RNA-seq3 library


title: sci3-me-697

description: sci-RNA-seq3 library


title: sci3-me-695

description: sci-RNA-seq3 library


title: sci3-me-693

description: sci-RNA-seq3 library


title: sci3-me-692

description: sci-RNA-seq3 library


title: sci3-me-691

description: sci-RNA-seq3 library


title: sci3-me-689

description: sci-RNA-seq3 library


title: sci3-me-687

description: sci-RNA-seq3 library


title: sci3-me-688

description: sci-RNA-seq3 library


title: sci3-me-686

description: sci-RNA-seq3 library


title: sci3-me-707

description: sci-RNA-seq3 library


title: sci3-me-690

description: sci-RNA-seq3 library


title: sci3-me-685

description: sci-RNA-seq3 library


title: sci3-me-684

description: sci-RNA-seq3 library


title: sci3-me-682

description: sci-RNA-seq3 library


title: sci3-me-683

description: sci-RNA-seq3 library


title: sci3-me-696

description: sci-RNA-seq3 library


title: sci3-me-680

description: sci-RNA-seq3 library


title: sci3-me-681

description: sci-RNA-seq3 library


title: sci3-me-678

description: sci-RNA-seq3 library


title: sci3-me-679

description: sci-RNA-seq3 library


title: sci3-me-677

description: sci-RNA-seq3 library


title: sci3-me-676

description: sci-RNA-seq3 library


title: sci3-me-675

description: sci-RNA-seq3 library


title: sci3-me-694

description: sci-RNA-seq3 library


title: sci3-me-674

description: sci-RNA-seq3 library


title: sci3-me-672

description: sci-RNA-seq3 library


title: sci3-me-673

description: sci-RNA-seq3 library


title: sci3-me-671

description: sci-RNA-seq3 library


title: sci3-me-670

description: sci-RNA-seq3 library


title: sci3-me-667

description: sci-RNA-seq3 library


title: sci3-me-665

description: sci-RNA-seq3 library


title: sci3-me-664

description: sci-RNA-seq3 library


title: sci3-me-668

description: sci-RNA-seq3 library


title: sci3-me-662

description: sci-RNA-seq3 library


title: sci3-me-661

description: sci-RNA-seq3 library


title: sci3-me-660

description: sci-RNA-seq3 library


title: sci3-me-666

description: sci-RNA-seq3 library


title: sci3-me-659

description: sci-RNA-seq3 library


title: sci3-me-663

description: sci-RNA-seq3 library


title: sci3-me-658

description: sci-RNA-seq3 library


title: sci3-me-657

description: sci-RNA-seq3 library


title: sci3-me-656

description: sci-RNA-seq3 library


title: sci3-me-669

description: sci-RNA-seq3 library


title: sci3-me-655

description: sci-RNA-seq3 library


title: sci3-me-653

description: sci-RNA-seq3 library


title: sci3-me-654

description: sci-RNA-seq3 library


title: sci3-me-651

description: sci-RNA-seq3 library


title: sci3-me-652

description: sci-RNA-seq3 library


title: sci3-me-649

description: sci-RNA-seq3 library


title: sci3-me-650

description: sci-RNA-seq3 library


title: sci3-me-646

description: sci-RNA-seq3 library


title: sci3-me-645

description: sci-RNA-seq3 library


title: sci3-me-647

description: sci-RNA-seq3 library


title: sci3-me-644

description: sci-RNA-seq3 library


title: sci3-me-642

description: sci-RNA-seq3 library


title: sci3-me-641

description: sci-RNA-seq3 library


title: sci3-me-648

description: sci-RNA-seq3 library


title: sci3-me-643

description: sci-RNA-seq3 library


title: sci3-me-640

description: sci-RNA-seq3 library


title: sci3-me-638

description: sci-RNA-seq3 library


title: sci3-me-637

description: sci-RNA-seq3 library


title: sci3-me-639

description: sci-RNA-seq3 library


title: sci3-me-636

description: sci-RNA-seq3 library


title: sci3-me-633

description: sci-RNA-seq3 library


title: sci3-me-631

description: sci-RNA-seq3 library


title: sci3-me-630

description: sci-RNA-seq3 library


title: sci3-me-628

description: sci-RNA-seq3 library


title: sci3-me-629

description: sci-RNA-seq3 library


title: sci3-me-627

description: sci-RNA-seq3 library


title: sci3-me-624

description: sci-RNA-seq3 library


title: sci3-me-623

description: sci-RNA-seq3 library


title: sci3-me-626

description: sci-RNA-seq3 library


title: sci3-me-625

description: sci-RNA-seq3 library


title: sci3-me-622

description: sci-RNA-seq3 library


title: sci3-me-621

description: sci-RNA-seq3 library


title: sci3-me-619

description: sci-RNA-seq3 library


title: sci3-me-617

description: sci-RNA-seq3 library


title: sci3-me-616

description: sci-RNA-seq3 library


title: sci3-me-634

description: sci-RNA-seq3 library


title: sci3-me-635

description: sci-RNA-seq3 library


title: sci3-me-618

description: sci-RNA-seq3 library


title: sci3-me-615

description: sci-RNA-seq3 library


title: sci3-me-632

description: sci-RNA-seq3 library


title: sci3-me-613

description: sci-RNA-seq3 library


title: sci3-me-608

description: sci-RNA-seq3 library


title: sci3-me-611

description: sci-RNA-seq3 library


title: sci3-me-610

description: sci-RNA-seq3 library


title: sci3-me-607

description: sci-RNA-seq3 library


title: sci3-me-606

description: sci-RNA-seq3 library


title: sci3-me-605

description: sci-RNA-seq3 library


title: sci3-me-620

description: sci-RNA-seq3 library


title: sci3-me-604

description: sci-RNA-seq3 library


title: sci3-me-603

description: sci-RNA-seq3 library


title: sci3-me-609

description: sci-RNA-seq3 library


title: sci3-me-602

description: sci-RNA-seq3 library


title: sci3-me-601

description: sci-RNA-seq3 library


title: sci3-me-599

description: sci-RNA-seq3 library


title: sci3-me-600

description: sci-RNA-seq3 library


title: sci3-me-612

description: sci-RNA-seq3 library


title: sci3-me-596

description: sci-RNA-seq3 library


title: sci3-me-597

description: sci-RNA-seq3 library


title: sci3-me-598

description: sci-RNA-seq3 library