title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_E9_AD012

extract_protocol:
Approximately two weeks after the AAVretro injection, brains were extracted from the 56-63 day old INTACT mice, immediately submerged in ice-cold slicing buffer (2.5mM KCl, 0.5mM CaCl2, 7mM MgCl2, 1.25mM NaH2PO4, 110mM sucrose, 10mM glucose and 25mM NaHCO3) that was bubbled with carbogen, and sliced into 0.6 mm coronal sections starting from the frontal pole. From each AAVretro-injected brain, the slices were kept in the ice-cold dissection buffer from which selected brain regions (Supplementary Table 1) were manually dissected under a fluorescent dissecting microscope (Olympus SZX16), following the Allen Mouse Common Coordinate Framework (CCF), Reference Atlas, Version 3 (2015) (Extended Data Fig. 1). The dissected brain tissues were transferred to prelabeled microcentrifuge tubes, immediately frozen in dry ice, and subsequently stored at -80oC.   For each dissected brain region, samples from 2 males and 2 females were pooled separately as biological replicates for nuclei preparation. The 2-mL glass tissue dounce homogenizer and pestles (Sigma-Aldrich D8938-1SET) were pre-chilled on ice. Nuclei were prepared using a modified protocol as reported by Lacar et al., 201622. In summary, the frozen brain tissues were transferred to the dounce homogenizer with 1 mL ice-cold NIM buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT (Sigma 646563), 10μl of protease inhibitor (Sigma P8340)), with 0.1% Triton X-100 and 5μM Hoechst 33342 (Invitrogen H3570), and gently homogenized on ice with the pestle 10-15 times. The homogenate was transferred to pre-chilled microcentrifuge tubes and centrifuged at 1000 rcf for 8 min at 4oC to pellet the nuclei. The pellet was resuspended in 1 mL ice-cold NIM buffer, and again centrifuged at 1000 rcf for 8 min at 4oC. The pellet was then resuspended in 450 μL of ice-cold NSB buffer (0.25M sucrose, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT, 9ul of Protease inhibitor), and filtered through 40μM cell strainer. The filtered nuclei suspension was incubated on ice for at least 30 minutes with 50μl of nuclease-free BSA for at least 10 minutes, then incubated with GFP antibody, Alexa Fluor 488 (Invitrogen, A-21311) and anti-NeuN antibody (EMD Millipore MAB377) conjugated with Alexa Fluor 647 (Invitrogen A20173). GFP+/NeuN+ single nuclei were isolated using fluorescence-activated nuclei sorting (FANS) on a BD Influx sorter with 100μm nozzle, and sorted into 384-well plates preloaded with 2μl of digestion buffer for snmC-seq215 (20 mL digestion buffer consists of 10 mL M-digestion buffer (2×, Zymo D5021-9), 1 ml Proteinase K (20 mg, Zymo D3001-2-20), 9 mL water, and 10 µL unmethylated lambda DNA (100 pg/µL, Promega, D1521)). The collected plates were incubated at 50oC for 20 minutes then stored at -20 oC.
The bisulfite conversion and library preparation were performed following the detailed snmC-seq2 protocol as previously described (Luo, C. et al., Nat. Commun. 2018, 9(1):3824.). The snmC-Seq2 libraries were sequenced on Illumina Novaseq 6000 using the S4 flow cell 2 x 150 bp mode.

value: VIS

value: female


title: M59_Sperm_Atrazine_ChIP

status: Public on Nov 19 2020

type: SRA

city: Pullman

first: Michael

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

country: USA

institute: WSU

library_source: genomic

data_processing:
Basic read quality was verified using summaries produced by FastQC. The raw reads were trimmed and filtered using Trimmomatic. The reads for each ChIP sample were mapped to the Rnor 6.0 rat genome using Bowtie2 with default parameter options. The mapped read files were then converted to sorted BAM files using SAMtools.
To identify DHRs, the reference genome was broken into 1000 bp windows. Genomic windows with a mean of less than 10 mapped reads per sample were removed prior to further analysis. The MEDIPS R package was then used to calculate differential coverage between control and exposure sample groups as well as disease and non-disease groups. The edgeR p-value was used to determine the relative difference between the two groups for each genomic window.
Windows with an edgeR p-value less than an arbitrarily selected threshold were considered DHRs. The DHR edges were extended until no genomic window with a p-value less than 0.1 remained within 1000 bp of the DHR.
CpG density and other information was then calculated for the DHR based on the reference genome.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: The results of the edgeR analysis in CSV format. This includes raw read counts for each genomic window as well as the calculated p-value and other summary values.

molecule: genomic DNA

organism: Rattus norvegicus

source_name: Sperm

growth_protocol: Female and male rats of an outbred strain Hsd:Sprague Dawley SD (Harlan) at 70 to 100 days of age were fed ad lib with a standard rat diet and ad lib tap water. The gestating female rats treated were designated as the F0 generation. F1- F3 generation control and atrazine lineages were housed in the same room and racks with lighting, food and water. All experimental protocols for the procedures with rats were pre-approved by the Washington State University Animal Care and Use Committee (protocol IACUC # 6252).

extract_protocol:
For each sample, the epididymis was dissected free of fat and connective tissue, then, after cutting open the cauda, placed into 6 ml of phosphate buffer saline (PBS) for 20 minutes at room temperature. Further incubation at 4ºC will immobilize the sperm.  The tissue was then minced, the released sperm pelleted at 4ºC 3,000 x g for 10 min, then resuspended in NIM buffer and stored at -80ºC for further processing.   An appropriate amount of rat sperm suspension was used for ChIP analysis. Rat sperm samples were sonicated and then pretreated with 50 µl 1M DTT in each sample tube. Samples were then incubated for 2h at RT on rotation. 123 mg of NEM dissolved in 1 mL of milliQ water in a 56ºC incubator. 120 µL of NEM added to each sample and then incubated for 30 min at RT on rotation. Chromatin prepared with  400 µl "Buffer 1 Stock" (see cited ChIP protocol), 102 mg sucrose and 0.5 µl 1M DTT. Samples then centrifuged at  2,500 rpm 5 min at RT. Supernatant discarded. Sperm resuspended in 1 ml 1X PBS and centrifuged at 2,500 rpm 5 min at RT. Supernatant discarded. Sperm resuspended in 130 µl of “Complete Buffer” (“Buffer 1 stock” + detergents) and placed in 130 µl Covaris tubes. Incubate 20 minutes on ice. Covaris program set to to the desired program: Chromatin shearing 10 min, Peak power: 75.0, Duty factor: 10.0, Cycles/Burst: 200. Program run for each tube. Samples removed from Covaris tube and placed it in 1.5 ml tube and centrifuged at 12,500 rpm 10 min at RT. Supernatant then collected and protease inhibitor cocktail ((20X) by dissolving 1 tablet in 500 µl MilliQ H2O) is added (11 µl of this solution per sample). Samples run on aa 1.5 % agarose gel to check bands size before resuming the IP protocol. Each sample had 3 µl of antibody (Ab anti-histone H3, CT, pan, clone A3S Millipore cat #05-928) added and were placed at 4ºC on rotation O/N. Samples then washed with magnetic beads (ChIP grade protein magnetic beads, Cell Signal, at 4ºC). 40 µl of beads for each sample were washed: placed on DynaMag-2 for two minutes and supernatant removed without disturbing the beads. Resuspended with 1 ml of 1X IP buffer, then repeat wash process once. Supernatant removed and resuspended in 350 µl of 1x IP. 40 µl of beads added to each sample and placed on rotation at 4ºC for 3 h. Tubes were then washed on DynaMag with 1X IP 3-4 times. With the final wash, beads resuspended in 300 µl “MeDIP digestion buffer." 3 µl of Proteinase K 20 mg/ml added to each tube and placed on rotation at 56ºC, 4 h (or O/N). Samples centrifuged quickly, then supernatant placed in new 1.5 ml tubes. 300 µl of phenol/chloroform/isoamyalcohol added to each tube and Centrifuged at 12,500 rpm 10 min at RT. The aqueous phase was placed in a new 1.5 ml tube and 2 µl of Glycoblue, one tenth vol of 3 M sodium acetate (NaOAc) and 2 vol of ethanol were added to each sample. Samples then precipitated O/N at 20ºC (O/N precipitation necessary for better yields). Tubes centrifuged at 12,500 rpm 30 min at 4ºC. Supernatant removed and 500 µl of 70% EtOH added. Centrifuged at 12,500 rpm 10 min at 4ºC. Supernatant removed and samples air dried 5-10 min. Pellets resuspended in 25 µl milliQ H2O. DNA concentration measured in Qubit with brDNA kit.
ChIP DNA was used to create libraries for next generation sequencing (NGS) using the NEBNext Ultra DNA Library following the manufacturer’s protocol  and indexing each sample individually with NEBNext Multiplex Oligos for Illumina.

treatment_protocol: Outbred Sprague Dawley gestating female rats (F0 generation) were administered an intraperitoneal dose of 25 mg/kg body weight of atrazine (4% of rat oral LD50 [41] and 50% of NOAEL). These doses were administered at 90 days of age, during embryonic days 8-14 (E8-E14) of fetal gonadal sex determination. The F1 generation offspring was directly exposed as a fetus and F2 generation grand-offspring exposed as the germline in the F1 generation. These were each bred at 90 days of age within the lineage. The F3 generation great-grand-offspring is required to establish the transgenerational inheritance generation of ancestral exposure. A control lineage was established that used F0 gestating rats exposed to the vehicle control dimethyl sulfoxide (DMSO).

tag: strain

value: Sprague Dawley

tag: Sex

value: Male

tag: tissue

value: Sperm

tag: treatment

value: DMSO

tag: measurement

value: ChIP

tag: disease

tag: lineage

value: Atrazine


title: Bovine endometrium_6_sPIF

city: Aberystwyth

first: Ruth

middle: Elizabeth

last: Wonfor

state: Ceredigion

address: Penglais

department: IBERS

country: United Kingdom

institute: Aberystwyth University

description: Sample 12

library_source: transcriptomic

data_processing:
All raw paired-end data were imported into the open source platform Galaxy (version 17.01), hosted by IBERS, Aberystwyth University
Raw paired-end data were submitted to FastQC analysis (Galaxy version 0.69).
Raw paired-end data were trimmed and clipped using Trimmomatic (Galaxy Version 0.36.0)
Trimmed data were submitted to FastQC analysis (Galaxy version 0.69) to assess read quality post trimming
Trimmed data were then aligned to produce BAM files using Bowtie 2 (Galaxy version 2.2.6)
BAM files were assessed for read abundance for annotated genes using the featureCounts package (Galaxy version 1.4.6.p5)
Counts for the two sequencing runs of samples 9-14 were added together in Excel.
Bioconductor package deSeq2 (as part of the R software package (version 3.4.0)) was used to determine the differential expression of genes using the read abundance data
Genome_build: UMD 3.1 (Ensembl version 89)
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and each sample

molecule: total RNA

organism: Bos taurus

source_name: Endometrium

growth_protocol: Endometrial tissue explants were dissected from bovine uteri post slaughter. An 8mm biopsy punch was used and the endometrium dissected away from the myometrium with sterile scissors. Tissue was randomly sampled from the intercaruncular tissue in the first third of the uterine horn closest to the utero-tubular junction, ipsilateral of the ovary staged as being in the follicular stage of the oestrous cycle. Explants were cultured in 6 well plates (one per well) with 3 mL of RPMI 1640 media, supplemented with 50 IU/mL penicillin, 50 µg/mL streptomycin and 2.5 µg/mL amphotericin B. Explants were incubated in a sterile incubator at 37 oC and 5 % CO2 for a total 30 h.

extract_protocol:
Total RNA was extracted using the Norgen Total RNA purification plus kit following the manufacturer’s instructions, with the addition of the use of a bead beater with the lysis buffer to aid tissue disruption.
Total RNA was prepared for sequencing using the TruSeq v2 RNA-Seq kit, using the manufacturer’s protocol, up to the validate library step. Following the enrichment of cDNA fragments with adapters, the cDNA was quantified using a Qubit 2.0, dsDNA broad range assay. Each sample was diluted to 10 nM with 10 nM Tris HCl and 0.5 % Tween-20 in nuclease free water. Samples were pooled and subsequently diluted to 2 nM with elution buffer (Qiagen, Manchester, UK) and then to 1 nM with 0.1 M sodium hydroxide, before being held at room temperature for 5 minutes to denature the DNA. Following denaturation, the samples were diluted to 10 pM in hybridisation buffer and loaded onto a cBot to cluster cDNA onto two lanes of a V4 High output flow cell. Samples were paired-end sequenced on an Illumina HiSeq 2500 and base pairs per read were set to 126 bp. Samples 9-14 were sequenced twice due to low reads due to the sequencing process compared to samples 1-8

treatment_protocol: Immediately after extraction, explant tissue from each animal was cultured either in medium alone or with the addition of sPIF (100nM) for 24 hours. Medium was then changed and replaced with the fresh medium alone or containing sPIF (100nM) for a further 6h.

value: Treated with sPIF for 30h

value: Endometrial explant


title: M58_Sperm_Atrazine_ChIP

value: multiple (kidney, lean)


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_E9_AD004

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 INTACT reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10 INTACT
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

organism: Mus musculus

source_name: C57BL/6J P56 Mouse Brain

growth_protocol: All experimental procedures using live animals were approved by the Salk Institute Animal Care and Use Committee. The knock-in mouse line, R26R-CAG-loxp-stop-loxp-Sun1-sfGFP-Myc (INTACT) was used for most experiments4 and they were maintained on a C57BL/6J background. 42-49 day old adult male and female INTACT mice were used for the retrograde labeling experiment.

treatment_protocol: To label neurons projecting to regions of interest, injections of rAAV2-retro-Cre (produced by Salk Vector Core or Vigene, 2x10^12 to 1x10^13 viral genomes/ml, produced with capsid from Addgene plasmid #81070 packaging pAAV-EF1a-Cre from Addgene plasmid #55636) were made into both hemispheres of the INTACT mice. Animals were anesthetized with either ketamine/xylazine or isoflurane, placed in a stereotaxic frame, and 0.1 to 0.5 microliters of AAV was injected by pressure into stereotaxic coordinates corresponding to the desired projection target.

tag: age

value: brain

tag: source

tag: target

value: SSp

tag: gender

value: male


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_E9_AD006


title: RNA-Seq: WT_Activated B cells Replicate 3

city: Amsterdam

first: Fred

last: van Leeuwen

address: Plesmanlaan 121

department: Gene Regulation

country: Netherlands

institute: Netherlands Cancer Institute

data_processing:
The 65 bp single end reads were mapped to the aligned against the mouse reference genome (Ensembl build 38) using TopHat (version 2.1.0).
TopHat was supplied with a known set of gene models based on Ensembl GTF version 77 and was guided to use the first-strand as the library-type. As additional parameters --prefilter-multihits and –no coverage were used.
Genecounts were generated using a custom script that gives the same output as HTSeq-count.
Genome_build: Ensembl GRCm38
Supplementary_files_format_and_content: Tab-separated file with number of reads per gene/sample.

source_name: WT Spleen B cells in vitro activated

growth_protocol: Single cells suspensions were prepared from the spleen of 6-8-week-old mice and subjected to erylysis.

extract_protocol:
MACS sorted CD19+ cells were resuspended in Trizol (Ambion Life Technologies) and total RNA was extracted according to the manufacturer’s protocol.
Library preparation was performed on RNA samples with a measured RNA Integrity Number (RIN) between 8.0 and 10.0. Strand-specific libraries were generated using the TruSeq Stranded mRNA sample preparation kit (Illumina Inc.) according to manufacturer’s instructions (Illumina, Part # 15031047 Rev. E). RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Following erythrocyte lysis, naïve splenic B cells were enriched by the depletion of CD43 expressing cell using biotinylated anti-CD43 antibody (Clone S7, BD Biosciences), BD IMag Streptavidin Particles Plus and the IMag® system (BD Biosciences), as described by the manufacturer. Following CD43 depletion, cells were MACS sorted for CD19+ as Naive B cells.For activated B cells, the CD43- cells were activated with 5 μg/ml of Lipopolysaccharide (Escherichia Coli LPS, 055:B5, Sigma) and rIL-4 in complete IMDM medium (IMDM supplemented with 8% FCS, 100 mM pen/strep and 100 mM β-mercaptoethanol) at a density of 105 cells/well in 24 well plates. rIL4 was used at a concentration of 10 ng/ml. Two days after the stimulation, cells were MACS sorted for CD19+ as Activated B cells.

tag: cell type

value: B cell

value: Stimulated with LPS and IL-4 for 2 days

tag: genotype


title: RNA-Seq: WT_Activated B cells Replicate 2


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_E9_AD002


title: M57_Sperm_Atrazine_ChIP


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_E9_AD001


title: Bovine endometrium_5_sPIF

description: Sample 10


title: M56_Sperm_Atrazine_ChIP

value: lean


title: RNA-Seq: WT_Activated B cells Replicate 1


title: Bovine endometrium_5_Control

description: Sample 9

value: no treatment


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_E8_AD012

value: VIS

value: Pons

value: female


title: RNA-Seq: DOT1L_KO_Activated B cells Replicate 3

source_name: KO Spleen B cells in vitro activated


title: Bovine endometrium_4_sPIF

description: Sample 8


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_E8_AD010


title: M55_Sperm_Atrazine_ChIP

value: Sprague Dawley

value: Male

value: Sperm


title: M54_Sperm_Atrazine_ChIP

value: Atrazine

value: ChIP


title: CHIP_DMC1_Hellsctrl_1

city: Montpellier cedex 5

first: Julie

middle: A. J.

last: Clement

address: 141, rue de la Cardonille

department: IGH

country: France

institute: CNRS

description:
17144FL-07-03_S4_L002
DMC1-SSDS of the Hellsctrl mouse, replicate 1

data_processing:
Base-calling was performed  using CASAVA
All reads were trimmed to 50bp before processing because fragment length in both experiment are short (mean around 100bp). Sequencing up to 150bp was linked to facility organization.
Using trimmomatic, adapters were then removed and reads with sequencing quality lower than 28 were discarded.
Reads were aligned to the mm10 genome using Bowtie2 (for 5hMeDIP-seq, with only R1 reads) or BWA and its modified algorithm proposed in Khil et al., 2012  (for DMC1 ChIP-SSDS).
Reads that were unmapped or duplicated were filtered out in each experiment.
DMC1 ChIP-SSDS peaks were called using MACS2.
IDR method was used to deal with replicates for DMC1 peaks. Final peaksets were built from merged replicates, according to the IDR method.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig were built from merged replicates after alignment step for DMC1 ChIP-SSDS and 5hMeDIP-seq experiments. Input from B6 was subtracted for 5hMeDIP of B6, Spo11KO and HellscKO mice; input from RJ2 was subtracted for 5hMeDIP of RJ2.

extract_protocol:
For DMC1-SSDS experiment : Cell suspension was prepared by filtering homogenized tissue, then lysed. Lysates were sonicated and chromatin complexes were isolated with appropriate antibody. For 5hMeDIP-seq : genomic DNA was extracted by phenol/chloroform extraction  from a population of  ~95% pure leptotene/zygotene (L/Z) spermatocytes, obtained from synchronized FAC-sorted testes.
For DMC1 experiment, standard library construction was performed with the Illumina Trueseq protocol (Illumina, IP-202-9001DOC) with an additional step of kinetic enrichment as described in Khil et al. 2012. For 5hMeDIP-seq, Illumina adaptors were added to sonicated gDNA with NEB Next Ultra library preparation kit (NEB7370S), without the final PCR step. hMeDIP was then performed with Active Motif hMeDIP kit (AM, 55010) according to the manufacturers’ manual. Enriched fragments were then amplified by PCR, as recommended by the NEB Next Ultra library preparation kit.
Single Stranded DNA Sequencing (SSDS) method described in Khil et al. 2012 for DMC1 ChIPseq ; 5hMeDIP for 5hMeDIP-seq experiment

tag: genotype/variation

value: Hellsfl/{delta}

tag: age/time point

value: adult

tag: tissue/cells

value: whole-testis

tag: chip antibody

value: Santa Cruz, goat polyclonal anti-DMC1, C-20, lot #D2215

tag: protocol


title: Bovine endometrium_4_Control

description: Sample 7

value: Endometrial explant


title: Bovine endometrium_6_Control

description: Sample 11


title: M53_Sperm_Atrazine_ChIP

tag: strain

tag: Sex


title: RNA-Seq: DOT1L_KO_Activated B cells Replicate 1

value: B cell

tag: treatment


title: Bovine endometrium_3_sPIF

description: Sample 6

value: Treated with sPIF for 30h

tag: tissue


title: RNA-Seq: WT_Naïve B cells (CD43-) Replicate 3

source_name: WT Spleen B cells

value: Spleen B cells


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_E8_AD006

value: brain

value: SSp


title: M52_Sperm_Atrazine_ChIP

tag: measurement

tag: disease

value: multiple (testis, lean)


title: RNA-Seq: WT_Naïve B cells (CD43-) Replicate 2


title: M51_Sperm_Atrazine_ChIP

value: late puberty

tag: lineage


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_E8_AD002

tag: age

tag: source

value: VIS

value: female


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_E7_AD012

tag: target

value: Pons

tag: gender


title: RNA-Seq: WT_Naïve B cells (CD43-) Replicate 1

tag: cell type

tag: genotype


title: Bovine endometrium_2_sPIF

description: Sample 4


title: M50_Sperm_Atrazine_ChIP

value: Sprague Dawley

value: Male

value: Sperm

value: Atrazine


title: Bovine endometrium_3_Control

description: Sample 5

value: no treatment


title: RNA-Seq: DOT1L_KO_Naïve B cells (CD43-) Replicate 3

source_name: KO Spleen B cells


title: Bovine endometrium_2_Control

description: Sample 3


title: M49_Sperm_Atrazine_ChIP

value: ChIP

value: multiple (late puberty, prostate, lean)


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_E7_AD010


title: Bovine endometrium_1_sPIF

description: Sample 2

value: Endometrial explant


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_E7_AD008

value: male


title: RNA-Seq: DOT1L_KO_Naïve B cells (CD43-) Replicate 2

value: B cell

value: Spleen B cells


title: RNA-Seq: DOT1L_KO_Activated B cells Replicate 2

value: Stimulated with LPS and IL-4 for 2 days


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_E8_AD008

value: brain


title: M48_Sperm_Atrazine_ChIP

value: multiple (late puberty, testis, kidney, lean)


title: Bovine endometrium_1_Control

description: Sample 1


title: RNA-Seq: DOT1L_KO_Naïve B cells (CD43-) Replicate 1


title: M47_Sperm_Atrazine_ChIP


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_E7_AD007

value: VIS


title: WTNS_FM_Rep3 RNA-Seq

city: New York

first: Richard

last: Koche

state: New York

institute: Memorial Sloan Kettering Cancer Center

data_processing:
RNA-seq reads were filtered for quality and 3' trimmed for adapter sequences using trimgalore
Reads were aligned to mouse assembly hg38 using STAR (v2.6.0a) with default parameters.
Read count tables were created using HTSeq v0.9.1.
To create density files, the signal was normalised using the scalefactors from DESeq2 converted to BigWig using BEDTools.
Genome_build: hg38
Supplementary_files_format_and_content: BigWig files containing read densities normalized using DESeq2

organism: Homo sapiens

source_name: Full media

growth_protocol: Cells were seeded in full media; the following day media was changed to either estrogen depleted media (for DMSO and E2 groups) or same DMEM/F12 50/50 full media (for FM); cells were incubated for 72h; the day of cell harvesting media was refreshed

extract_protocol:
Cells were snap frozen and RNA was extracted with RNeasy Kit from Qiagen (#74106), DNase treatment was performed during the extraction
Libraries were performed by Genewiz

treatment_protocol: DMSO and E2 conditions were subjected to DMSO or E2 treatment for 6h

tag: cell line


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_E7_AD004

value: SSp


title: ChIP-seq: B_Cell_H3K79me2_WT_Activated_rep3

data_processing:
ChIP-seq reads were aligned to the mm10 genome assembly using BWA-MEM version 0.7.17-r1188 with the following argument: ‘-M’
Duplicates were removed with picard’s MarkDuplicates version 2.12 with the following arguments:’VALIDATION_STRINGENCY=LENIENT REMOVE_DUPLICATES=true’
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files were generated using bamCoverage version 3.0.1 from deepTools with the following arguments: ‘-of bigwig --binSize 25 --normalizeUsing RPGC --ignoreForNormalization chrM --effectiveGenomeSize 2652783500’; Scores represents reads per genomic content.

extract_protocol:
Flow cytometrically purified cells were cross-linked, and chromatin lysates were prepared. Histone-DNA complexes were isolated with antibodies.
Library preparation was done using KAPA LTP Library preparation kit using the manufacturer’s protocol with slight modifications. Briefly, after end-repair and A-tailing adaptor were ligated followed by SPRI clean-up. Libraries were amplified by PCR and fragments between 250-450 bp were selected using AMPure XP beads (Beckman Coultier). The libraries were analyzed for size and quantity of DNAs on a 2100 Bioanalyzer using a High Sensitivity DNA Kit (Agilent), diluted and pooled in multiplex sequencing pools. The libraries were sequenced as 65 base single reads on a HiSeq2500 (Illumina).

treatment_protocol: CD43 depleted splenocytes were activated in vitro for three days with LPS + IL-4

value: In vitro activatedSpleen CD19+ CD3-

value: H3K79me2 (Milipore 04-835)


title: M45_Sperm_Atrazine_ChIP

value: Sprague Dawley

value: Male


title: WTNS_FM_Rep1 RNA-Seq


title: WTNS_FM_Rep2 RNA-Seq


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_E7_AD002

value: female


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_E7_AD001


title: M44_Sperm_Atrazine_ChIP

value: Sperm

value: Atrazine

value: multiple (obese, tumor)


title: ChIP-seq: B_Cell_H3K79me2_WT_Naive_rep3

value: Spleen CD19+ CD3-


title: M43_Sperm_Atrazine_ChIP

value: ChIP


title: ChIP-seq: B_Cell_H3K79me2_WT_Activated_rep1

value: In vitro activated Spleen CD19+ CD3-


title: WTNS_E2_Rep3 RNA-Seq

source_name: E2 1h Induction


title: ChIP-seq: B_Cell_H3K79me2_WT_Naive_rep2


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_E6_AD012

value: Pons


title: M42_Sperm_Atrazine_ChIP

value: lean


title: WTNS_E2_Rep1 RNA-Seq


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_E6_AD007

value: brain

value: male


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_E6_AD010

value: VIS


title: WTNS_E2_Rep2 RNA-Seq


title: M41_Sperm_Atrazine_ChIP

value: testis


title: WTNS_DMSO_Rep2 RNA-Seq

source_name: DMSO control


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_E6_AD006

value: SSp


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_E6_AD004


title: WTNS_DMSO_Rep3 RNA-Seq


title: M46_Sperm_Atrazine_ChIP


title: ChIP-seq: B_Cell_H3K79me2_WT_Naive_rep1

value: H3K79me2 (Milipore 04-835)


title: RNA_zic2_2

city: San Joan d'Alacant

first: Eloísa

last: Herrera

address: Av Ramon y Cajal s/n

department: Instituto Neurociencias Alicante

country: Spain

institute: CSIC-UMH

description:
processed data file:
RNAseq_Zic2.tdf

data_processing:
All sequenced datasets adapters were trimmed using cutadapt v1.18 (Martin, 2011) and aligned to mm10. Only reads with mapq > 30. Data was processed with the extensive use of custom scripts, and Samtools (v1.9) (Li et al., 2009), bedtools v2.26.0 (Quinlan and Hall, 2010). RNA-seq data: Reads were aligned with STAR (v2.5.0c) (Dobin et al., 2013). To retrieve differentially expressed genes (DEG), mapped reads were counted with HTSeq v0.6.1 (Anders et al., 2015). ChIPseq data: Reads were aligned using bowtie2 (v2.2.9) (Langmead and Salzberg, 2012). Peak calling for Zic2 ChIP-seq was run using MACS2 (v2.1) (Zhang et al., 2008).
Genome_build: mm10
Supplementary_files_format_and_content: tdf files from whole genome alignments normalized to RPM (read per million sequenced reads).

molecule: polyA RNA

source_name: Zic2 RGCs

growth_protocol: Mice were kept in a timed pregnancy breeding colony at the Instituto de Neurociencias (IN). The animal protocols were approved by the IN Animal Care and Use Committee and met European and Spanish regulations.

extract_protocol: Whole retinas or spinal cords were dissected from embryos at E16, chopped, crosslinked with 1.1% PFA at room temperature for 20 minutes and quenched with glycine. Then, chromatin was sheared by biorruptor sonication. 10  micrograms of Chromatin were used for each IP. Diluted chromatin was incubated overnight at 4ºC with the specific antibody against mouse Zic2 at 1/500 (Millipore, AB15392) or IgG isotype control pre-immune serum at 1/500 (Abcam, ab27478). Immunoprecipitated chromatin was treated with RNAse and Protein Kinase and purified using Quiaquick PCR purification Kit (Quiagen, ID:28104). Inputs, control IgG and anti-zic2 ChIP samples were sent for library preparation and NGS service to Fasteris SA (Switzerland).

value: C57/DBA F1

value: retinal ganglion cells (RGC)

value: expressing Zic2

value: male and female


title: WTNS_DMSO_Rep1 RNA-Seq


title: M39_Sperm_Atrazine_ChIP

value: Sprague Dawley

value: Male

value: Sperm

value: Atrazine


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_E6_AD002

value: female


title: SY242CS_FM_Rep3 RNA-Seq


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_E6_AD001


title: M38_Sperm_Atrazine_ChIP

value: ChIP

value: late puberty


title: M37_Sperm_Atrazine_ChIP

value: multiple (late puberty, testis, lean)


title: SY242CS_FM_Rep2 RNA-Seq


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_E5_AD012

value: brain

value: Pons


title: RNA_GFP2

description:
processed data file:
RNAseq_GFP.tdf

source_name: GFP RGCs

value: expressing GFP


title: M36_Sperm_Atrazine_ChIP


title: SY242CS_FM_Rep1 RNA-Seq


title: RNA_GFP1

description:
processed data file:
RNAseq_GFP.tdf


title: M35_Sperm_Atrazine_ChIP


title: SY242CS_E2_Rep3 RNA-Seq


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_E5_AD010

value: VIS


title: RNA_zic2_3

description:
processed data file:
RNAseq_Zic2.tdf


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_E5_AD008

value: male


title: M40_Sperm_Atrazine_ChIP


title: M34_Sperm_Atrazine_ChIP

value: multiple (late puberty, prostate)


title: SY242CS_E2_Rep2 RNA-Seq


title: ERF97ox.43oC.IgG.rep2

first: Joanne

last: Chory

address: 10010 N Torrey Pines Rd

department: Plant Biology Laboratory

institute: Salk Institute for Biological Studies

data_processing:
Base calling was done by RTA 1.17.20 (Illumina, CA).
Demultiplexing was done by CASAVA 1.8.2 (Illumina, CA).
Reads were aligned by bowtie2 version 2.2.7 against the Arabidopsis TAIR10 genome assembly with default parameters.
SAMtools was used to merge biological ChIP-seq replicates.
MACS2 version 2.2.5 was used to call peaks using q value 0.001 with IP from ERF97ox by anti-IgG antibody as a control.
Genome_build: Arabidopsis reference genome (TAIR10)
Supplementary_files_format_and_content: bigwig files contains coordinates for an interval and an average read coverage (RPKM)

organism: Arabidopsis thaliana

source_name: Whole seedling

growth_protocol: Seedlings grew under 16 h/8 h light/dark cycle condition with 100 µmol.m-2.s-1 light intensity at 22 °C on 1/2 Linsmaier and Skoog (LS) medium for 7 days

extract_protocol:
Please see accompanying publication for detailed protocol. Briefly, ChIP-seq experiments for Col, ERF95, and ERF97 were performed as described (Kaufmann et al., 2010) using 7 day-old seedlings .  Monoclonal anti-HA antibody (11867423001, Millipore-Sigma) and IgG antibody (015-000-003, Jackson Immuno Research) was used in the experiment.
Libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Plates with 7-day-old seedlings were sealed with waterproof tape and submerged  in a 43 oC water bath for 22 min

value: Whole seedling

value: Basal heat treatment

tag: treat time

value: 22 degreesC for 7 days, then 43 degreesC for 22 min


title: SY242CS_E2_Rep1 RNA-Seq


title: RNA_zic2_1

description:
processed data file:
RNAseq_Zic2.tdf

value: C57/DBA F1

value: retinal ganglion cells (RGC)

value: expressing Zic2

value: male and female


title: ERF97ox.43oC.IgG.rep1


title: M32_Sperm_Atrazine_ChIP

value: Sprague Dawley

value: Male

value: Sperm

value: Atrazine

value: testis


title: ERF97ox.43oC.HA.rep2


title: M33_Sperm_Atrazine_ChIP

value: ChIP


title: SY242CS_DMSO_Rep3 RNA-Seq


title: RNA_GFP3

description:
processed data file:
RNAseq_GFP.tdf

value: expressing GFP


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_E5_AD006

value: brain

value: VIS

value: SSp

value: female


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_E5_AD004

value: male


title: ERF97ox.43oC.HA.rep1

value: Whole seedling

value: Basal heat treatment

value: 22 degreesC for 7 days, then 43 degreesC for 22 min


title: SY242CS_DMSO_Rep2 RNA-Seq


title: M29_Sperm_Atrazine_ChIP


title: ERF95ox.43oC.HA.rep2


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_E5_AD002


title: SY242CS_DMSO_Rep1 RNA-Seq


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_E5_AD001


title: ERF95ox.43oC.HA.rep1


title: M28_Sperm_Atrazine_ChIP

value: lean


title: ERF97ox.22oC.HA.rep2

value: no treatment

value: 22 degreesC for 7 days


title: M27_Sperm_Atrazine_ChIP

value: Sprague Dawley

value: Male

value: multiple (prostate, lean)


title: S250F_FM_Rep3 RNA-Seq


title: S250F_FM_Rep2 RNA-Seq


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_E4_AD012

value: Pons


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_E5_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_E4_AD010


title: ERF97ox.22oC.HA.rep1


title: M26_Sperm_Atrazine_ChIP

value: Sperm

value: Atrazine

value: ChIP

value: multiple (testis, obese)


title: S250F_FM_Rep1 RNA-Seq


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_E4_AD008

value: brain

value: VIS


title: M25_Sperm_Atrazine_ChIP


title: ERF95ox.22oC.HA.rep2


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_E4_AD007

value: male


title: M31_Sperm_Atrazine_ChIP


title: M24_Sperm_Atrazine_ChIP


title: S250F_E2_Rep2 RNA-Seq


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_E4_AD006

value: SSp

value: female


title: Col.22oC.HA.rep2

value: Whole seedling


title: S250F_E2_Rep1 RNA-Seq


title: Col.22oC.HA.rep1


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_E4_AD002


title: M22_Sperm_Atrazine_ChIP


title: S250F_DMSO_Rep2 RNA-Seq


title: M21_Sperm_Atrazine_ChIP

value: multiple (testis, prostate, lean)


title: S250F_DMSO_Rep3 RNA-Seq


title: ERF97ox-43C2

data_processing:
BRB-SeqTools (https://brb.nci.nih.gov/seqtools/) was used to calculate the raw counts of each gene. In detail, the RNA-seq raw reads were aligned to Arabidopsis reference genome (TAIR10) using TopHat version 2.1.1 with bowtie2-2.3.1 and gene-level raw counts data files were generated using HTSeq version 0.6.1. The raw counts were applied to Bioconductor package edgeR in R language to get the Reads Per Kilobase of transcript per Million mapped reads (RPKM) of each gene, and to identify the differentially expressed genes (DEGs).
Genome_build: Arabidopsis reference genome (TAIR10)
Supplementary_files_format_and_content: tab-delimited text files include raw counts of each gene for each sample

extract_protocol:
Total RNA was isolated from pooled (> 100 individual plants of the same genotype) whole seedlings using the RNeasy Plant Mini Kit (Qiagen, Hilden, Germany) with dsDNase treated.
500 ng total RNA of each sample was used to prepare the RNA-seq libraries using the TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, USA). Single-end sequencing was run on Illumina HiSeq 2500 sequencing machine (Illumina).

treatment_protocol: Plates with 7 days old seedlings were sealed with waterproof tape and submerged  in a 43 oC water bath for 22 min

value: Basal heat treatment

value: 22 C for 7 days, then 43 C for 22 min


title: M20_Sperm_Atrazine_ChIP

value: Sprague Dawley


title: ERF97ox-43C1


title: ERF95ox-43C2


title: S250F_DMSO_Rep1 RNA-Seq


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_E3_AD012


title: M19_Sperm_Atrazine_ChIP

value: Male

value: multiple


title: ERF95ox.22oC.HA.rep1

value: no treatment

value: 22 degreesC for 7 days


title: null_FM_Rep3 RNA-Seq


title: S250F_E2_Rep3 RNA-Seq


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_E3_AD008

value: Pons


title: ERF95ox-43C1


title: Col-43C2


title: M18_Sperm_Control_ChIP

value: Sperm

value: Atrazine

value: ChIP

value: Control


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_E3_AD007

value: brain

value: VIS

value: male


title: null_FM_Rep2 RNA-Seq


title: M23_Sperm_Atrazine_ChIP

value: kidney


title: null_FM_Rep1 RNA-Seq


title: M17_Sperm_Control_ChIP

value: multiple (kidney, lean)


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_E4_AD004

value: SSp


title: Col-43C1

value: Basal heat treatment

value: 22 C for 7 days, then 43 C for 22 min

value: Whole seedling


title: M16_Sperm_Control_ChIP

value: Sprague Dawley

value: Male


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_E4_AD001


title: null_E2_Rep3 RNA-Seq


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_E3_AD002

value: female


title: null_E2_Rep2 RNA-Seq


title: ERF97ox-22C2

value: no treatment

value: 22 C for 7 days


title: ChIP-seq: B_Cell_H3K79me2_WT_Activated_rep2

value: In vitro activated Spleen CD19+ CD3-

tag: chip antibody

value: H3K79me2 (Milipore 04-835)


title: M15_Sperm_Control_ChIP

value: Sperm

value: Atrazine

value: ChIP

value: obese

value: Control


title: M14_Sperm_Control_ChIP


title: ERF97ox-22C1


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_E2_AD010

value: brain

value: VIS

value: Pons


title: null_DMSO_Rep3 RNA-Seq


title: ERF95ox-22C2


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_E2_AD006

value: SSp


title: null_E2_Rep1 RNA-Seq


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_E3_AD004

value: male


title: M13_Sperm_Control_ChIP

value: Sprague Dawley


title: M12_Sperm_Control_ChIP

value: Male


title: null_DMSO_Rep2 RNA-Seq


title: ERF95ox-22C1

value: Whole seedling


title: Col-22C2

value: no treatment


title: M11_Sperm_Control_ChIP


title: Col-22C1

value: 22 C for 7 days


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_E2_AD002

value: female


title: null_DMSO_Rep1 RNA-Seq


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_E1_AD012


title: H247Y_FM_Rep3 RNA-Seq


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_E1_AD010


title: M9_Sperm_Control_ChIP


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_E3_AD001


title: M8_Sperm_Control_ChIP


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_E1_AD008


title: ICO_1179

city: Guangzhou

first: Haoyu

last: Wu

address: Kai Yuan Avenue 190

country: China

institute: GIBH

data_processing:
An average of 20 million paired-end reads were aligned to human genome (hg38) using STAR  (2.7.0f) with the default settings.
The number of mapped fragments was quantified at gene level using featurecount (1.6.4) with the following parameters, -p -g gene_name, based on Gencode annotation (v30).
The R package DESeq2 (1.22.2 on R 3.5.1) was used for differential gene expression analysis and for generating PCA and heatmap plots. Vst normalized counts were generated using vst function from DESeq2, and transformed to Z-scores.
Pheatmap package was used to generate heatmap plots using either vst normalized counts or Z-scores as input. Pathway analyses were performed by Enrichr web tool using the significantly differentially expressed genes as input with default settings.
Genome_build: hg38
Supplementary_files_format_and_content: Raw_gene_counts_matrix.txt

source_name: human cholangiocyte organoids

growth_protocol: Huch et al. Cell 2015 and Soroka et al. Hepatology 2018

extract_protocol:
Total RNA was collected after removal of the culture medium by adding 700µl of QIAzol lysis reagent (Qiagen) to a 24 well containing organoids (two 25µL BME/matrigel domes). RNA was isolated using the miRNeasy kit (Qiagen) according to the manufacturer’s protocol16 and the concentration was measured using a NANOdrop 2000 (ThermoFisher)
500 ng of total RNA was used for library construction using KAPA RNA Hyper + RiboErase HMR kit (Roche 08098140702)

treatment_protocol: No treatment applied

value: human cholangiocyte organoids generated from intrahepatic bile duct


title: H247Y_FM_Rep2 RNA-Seq


title: H247Y_FM_Rep1 RNA-Seq


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_E1_AD007


title: ICO_1166


title: H247Y_E2_Rep3 RNA-Seq


title: M6_Sperm_Control_ChIP

value: Sperm


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_E1_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_E1_AD004


title: H247Y_E2_Rep1 RNA-Seq


title: M5_Sperm_Control_ChIP

value: Atrazine


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_E1_AD002


title: ECO_1179

value: human cholangiocyte organoids generated from extrahepatic bile duct


title: ECO_1166


title: M4_Sperm_Control_ChIP

value: ChIP

value: late puberty


title: ECO_1172


title: H247Y_E2_Rep2 RNA-Seq


title: H247Y_DMSO_Rep3 RNA-Seq


title: BCO_1179

value: human cholangiocyte organoids generated from bile


title: M3_Sperm_Control_ChIP

value: multiple (late puberty, obese)

value: Control


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_E1_AD001

value: brain

value: VIS

value: SSp


title: H247Y_DMSO_Rep2 RNA-Seq


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_E12_AD012

value: Pons


title: BCO_1172


title: ICO_1172


title: H247Y_DMSO_Rep1 RNA-Seq


title: M2_Sperm_Control_ChIP

value: Sprague Dawley

value: Male


title: M7_Sperm_Control_ChIP

value: kidney


title: M1_Sperm_Control_ChIP


title: EIN2C-EIN3DB/ein3-1eil-1 4 hour ethylene ChIP-seq input

city: Austin

first: Hong

last: Qiao

state: TEXAS

address: 2506 speedway, NMS5.324

department: Department of Molecular Biosciences

institute: The University of Texas at Austin

data_processing:
Illumina Casava1.7 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to TAIR10 whole genome using bwa with default parameters
For RNAseq, differentially expressed genes were calculated by Cuffdiff version 2.2.1, using Col-0 RNAseq data (GSM2051305 and GSM2051306) as control.
For ChIP-seq, peaks significantly enriched in ChIP-seq tags were identified by Model-based Analysis for ChIP-Seq (MACS2, version 2.1.0.20150603).
Genome_build: tair10
Supplementary_files_format_and_content: differentially expressed genes generated using Cuffdiff (version 2.2.1) and peak files are generated using MACS2 (version 2.1.0.20150603) software.

source_name: whole seedling

growth_protocol: Arabidopsis seeds were  dark-grown at 24 ºC for 3 days

extract_protocol:
RNA was harvested using Trizol reagent from seedlings. EIN2C-EIN3DB proteins were extracted from seedlings and EIN2C-EIN3DB-DNA complexes were isolated with EIN2 antibody.
RNAseq: Libraries were prepared according to NEB instructions of the RNA Library Kit (NEB #E7420S/L); ChIPseq: Libraries were prepared according to NEB instructions of the ChIP-seq Library Kit (NEB #E6240S/L)

treatment_protocol: Treated with air (hydrocarbon-free air (Zero grade air, AirGas)) or ethylene (hydrocarbon-free air with 10 parts per million  (ppm) ethylene) for 4 hours

value: whole seedling

tag: agent

value: ethylene treated for 4 hours

tag: genotype/variation

value: EIN2C-EIN3DB in ein3-1eil-1 background


title: BCO_1166


title: F266L_FM_Rep3 RNA-Seq


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_E12_AD007

tag: strain

value: male


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_E12_AD010

value: female


title: ERCP_91

value: human cholangiocyte organoids generated from ERCP


title: EIN2C-EIN3DB/ein3-1eil-1 4 hour ethylene ChIP-seq, rep2

tag: antibody


title: F266L_FM_Rep2 RNA-Seq


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_E12_AD006

tag: tissue


title: ERCP_90


title: EIN2C-EIN3DB/ein3-1eil-1 4 hour ethylene ChIP-seq, rep1


title: F266L_FM_Rep1 RNA-Seq


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_E12_AD004


title: F266L_E2_Rep3 RNA-Seq


title: EIN2C-EIN3DB/ein3-1eil-1 4 hour air ChIP-seq input

value: air treated for 4 hours


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_E12_AD001


title: ERCP_89


title: EIN2C-EIN3DB/ein3-1eil-1 4 hour air ChIP-seq, rep2


title: F266L_E2_Rep2 RNA-Seq


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_E11_AD012


title: HeLaS3 AGO2KO

city: Berlin

first: Nikolaus

last: Rajewsky

address: Hannoversche Str. 28

country: Germany

institute: Max Delbrück Center for Molecular Medicine

description: PMID 30591524 for description of generation of the monoclonal AGO2dKO cell line

data_processing:
Cell and molecular barcodes were extracted from read1 and added as tags using Drop-seq tools v2.0.0
Sequenced reads were trimmed for polyA stretches, SMART adaptor sequences and low quality filtering using Drop-seq tools v2.0.0
Reads were aligned to the GRCh38 genome using STAR version 2.6.0c with default parameter and sorted using samtools v1.9
Gene annotation tags were added and bead synthesis errors were detected and corrected using Drop-seq tools v2.0.0
Estimated the number of barcodes was determined by a knee point in the cumulative curve using dropbead version 0.25
Expression matrix with only intronic reads was created by specifying the list of functional annotations using Drop-seq tools v2.0.0
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-separated files containing UMI counts per gene and per cell of each sample

source_name: Monoclonal cell line with both AGO2 alleles knock-out (AGO2dKO)

growth_protocol: Cells were grown in DMEM (Invitrogen 61965-026 supplemented with 10% (v/v) fetal bovine serum without antibiotics. Cells were grown to the logarithmic phase - by constant splitting - for the day of fixation.

extract_protocol:
Fixed cells were prepared for the Drop-seq run by centrifugation (1000 g, 5 min) and resuspension in 1 ml of PBS-BSA 0.01% + RiboLock (ThermoFisher) (0.8 U/µl), followed by another centrifugation (1000 g, 5 min) and resuspension in 0.5 ml of PBS-BSA 0.01% + RiboLock (ThermoFisher) (0.8 U/µl). Cells were then passed through a cell strainer (35 µm), counted, diluted with PBS-BSA 0.01% to a final concentration of 100 cells/µl and transferred into a syringe to be loaded on the Drop-seq apparatus.
Alles et al BMC Biol 2017 doi: 10.1186/s12915-017-0383-5.
single-cell RNAseq

treatment_protocol: Cells were dissociated with 0.05% bovine trypsin-EDTA (Invitrogen 25300062), quenched with growth medium and collected, then pelleted by centrifugation (300 g, 5 minutes), fixed with 80% cold methanol while mildly vortexing and kept on ice until the run.


title: EIN2C-EIN3DB/Col-0 4 hour ethylene ChIP-seq input


title: HeLaS3 wild-type

source_name: Wild-type

value: Wild-type


title: F266L_DMSO_Rep3 RNA-Seq


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_E11_AD008


title: EIN2C-EIN3DB/ein3-1eil-1 4 hour air ChIP-seq, rep1


title: EIN2C-EIN3DB/Col-0 4 hour ethylene ChIP-seq

value: EIN2C-EIN3DB in Col-0 background


title: 2015-431

city: PARIS

first: Stephane

last: Le Crom

address: 46 rue Ulm

department: Genomic Core Facility

institute: IBENS

data_processing:
Illumina bcl2fastq v2.17.1.14 software used for basecalling.
RNA-Seq data analysis was done using the Eoulsan software version 2.0-alpha6. Before mapping, reads ≤40 bases were removed, and reads with  quality mean ≤30 were discarded. Reads were then aligned against the Trichoderma reesei genome (from JGI) using the Bowtie mapper (version 0.12.9, parameters -n 2 -l 34 -e 70 -k 2 –best). Alignments from reads matching more than once on the genome were removed. Trichoderma reesei GFF3 genome annotation from JGI was used to compute gene expression. All overlapping regions between alignments and referenced exons were counted with HTSeq-count 0.5.3.
Genome_build: treesei JGI
Supplementary_files_format_and_content: tab-delimited text files include transcripts counting for each Sample

organism: Trichoderma reesei

source_name: T. reseei RUT-C30 (ATCC 56765)_T48h_Fed batch Glucose 75%-lactose 25%

growth_protocol: Fed-ask cultivation was performed according to (Jourdier, E., Cohen, C., Poughon, L., Larroche, C., Monot, F., Chaabane, F.B.: Cellulase activity mapping of Trichoderma reesei cultivated in sugar mixtures under fed-batch conditions. Biotechnol. Biofuels 6(1), 2013) with few modifications, and repeated 2 to 6 times independently to allow for the 2 to 6 biological replicates. For each replicate, a Fernbach flask was prepared with 250mL culture medium and inoculated with around 107 spores/mL. Initial growth phase on glucose lasted around 48 h and resulted in around 7 g/L biomass. Immediately after glucose exhaustion, empty 250mL Erlenmeyer flasks were fillled with 50mL broth per flask then fed at 0:3mL/h (using Dasgip MP8 peristaltic pumps) with different sugar solutions (one ask fed with pure lactose, one ask fed with pure glucose, one ask fed with a mixture of glucose and lactose). Incubation was performed in an Infors rotary shaker at 30 °C and 150 rpm.

extract_protocol:
Frozen mycelia were disrupted and homogenized in Lysis Matrix C (Fast RNA Pro Red Kit, MP Bio) in the presence of 700 µL of Lysis buffer RLT (RNeasy Mini Kit, Qiagen) complemented with 7 µL of β-mercaptoethanol on a rotor-stator homogenizer (FastPrep, MP Bio, Santa Ana, CA, USA). After centrifugation, the lysate was transferred on a Qiashredder spin column (Qiagen) and centrifuged for 2 min to eliminate all cell debris. The flow-through was then mixed with 0.5 volumes of pure ethanol and transferred to an RNeasy spin column. All further steps, including an on-column DNAse digestion, were realized following the manufacturer’s instructions. The quantity and quality of the total RNA were determined using a Nanodrop spectrophotometer (Nanodrop tech- nologies, Wilmington, DE) and the Bioanalyzer 2100 system (Agilent, Santa Clara, CA)
TruSeq Stranded mRNA Illumina

value: T. reseei RUT-C30 (ATCC 56765)

tag: growth

value: T48h_Fed batch Glucose 75%-lactose 25%


title: F266L_DMSO_Rep1 RNA-Seq

value: breast cancer


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_E11_AD006

value: brain

value: VIS

value: SSp


title: F266L_DMSO_Rep2 RNA-Seq


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_E11_AD007

value: Pons


title: HeLaS3 wildtype

source_name: HeLaS3 cells

extract_protocol:
Fixed cells were prepared for the Drop-seq run by centrifugation (1000 g, 5 min) and resuspension in 1 ml of PBS-BSA 0.01% + RiboLock (ThermoFisher) (0.8 U/µl), followed by another centrifugation (1000 g, 5 min) and resuspension in 0.5 ml of PBS-BSA 0.01% + RiboLock (ThermoFisher) (0.8 U/µl). Cells were then passed through a cell strainer (35 µm), counted, diluted with PBS-BSA 0.01% to a final concentration of 100 cells/µl and transferred into a syringe to be loaded on the Drop-seq apparatus (Alles et al BMC Biol 2017 doi: 10.1186/s12915-017-0383-5).
Macosko et al. 2015 Cell; Online-Dropseq-Protocol-v.3.1;
Drop-seq cDNA seuqunced using Illumina sequencing for short reads


title: 2015-429


title: EIN2C-EIN3DB/Col-0 4 hour air ChIP-seq


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_E11_AD004

source_name: C57BL/6J P56 Mouse Brain


title: Kidney, P0

city: Kuamomoto

first: Shunsuke

last: Tanigawa

state: Kumamoto

address: 2-2-1 Chuou-ku honjyo

department: Institute of Molecular Embryology and Genetics

country: Japan

institute: Kumamoto University

data_processing:
Sequencing and making Fastq files by illumina HiSeq X Ten. Read length: Read1:26, Index read 1(i7):8, Read2:98.
Cell Ranger v3.1.0 software was used to perform alignment and gene and UMI counting each cell.
Genome_build: GRCm38_93
Supplementary_files_format_and_content: tab-delimited text files and comma-separated value files

source_name: Kidney

extract_protocol:
Single cells were lysed in droplets using the 10X Chromium. Reverse transcription was performed in droplet.
library construction was performed by using Chromium Single Cell 3ʹ Reagent Kits v2.

value: ICR

value: Kidney

value: Wild type


title: EIN2S645A/ein3-1eil-1 4 hour air RNAseq, rep2

description: E2S645Ainein3vsCol_gene_exp.diff.FC2.RPKM1.xls.rmdup.xls

value: whole seedling

value: EIN2S6345A in ein3-1eil-1 background


title: 2015-425


title: EIN2S645A/ein3-1eil-1 4 hour air RNAseq, rep1


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_E11_AD002

value: female


title: F266L_E2_Rep1 RNA-Seq


title: Kidney, E17.5


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_E11_AD010


title: 2015-421

source_name: T. reseei RUT-C30 (ATCC 56765)_T48h_Fed batch Glucose 90%-lactose 10%

value: T48h_Fed batch Glucose 90%-lactose 10%


title: 2015-423


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_E11_AD001

value: male


title: Kidney, E15.5


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_E10_AD012


title: EIN2C-EIN3DBK245N/ein3-1eil-1 4 hour air RNAseq, rep1

description: E2E3mAinein3.vs.Col_gene_exp.diff.FC2.RPKM1.xls.rmdup.xls

value: air treated for 4 hours

value: EIN2C-EIN3DBK245N in ein3-1eil-1 background


title: EIN2C-EIN3DBK245N/ein3-1eil-1 4 hour air RNAseq, rep2


title: EIN2C-EIN3DB/Col-0 4 hour air ChIP-seq input

value: ethylene treated for 4 hours

value: EIN2C-EIN3DB in Col-0 background


title: 2015-430

source_name: T. reseei RUT-C30 (ATCC 56765)_T24h_Fed batch Glucose 75%-lactose 25%

value: T. reseei RUT-C30 (ATCC 56765)

value: T24h_Fed batch Glucose 75%-lactose 25%


title: 31-3R

city: Cologne

first: Stanislav

last: Kopriva

address: Zülpicher Str. 47 B

department: Institute for Plant Sciences

institute: University of Cologne

data_processing:
Illumina TruSeq mRNA stranded protocoll and Illumina Hiseq4000 with PE75 read length
Sequenced reads were processed with trimmomatic v.0.36 trimming tool to remove adapters and low-quality reads (http://www.usadellab.org/cms/?page=trimmomatic) (Bolger et al., 2014). Trimmed, paired files underwent a second quality control via FastQC.
FastQ files were further processed with kallisto v.0.43.1 (Bray et al., 2016) to quantify transcript abundances in pseudo-alignment to the Arabidopsis reference transcriptome as TPM (Transcripts Per Kilobase Million).
Genome_build: TAIR10_seq_20110103_representative_gene_model_updated.fas
Supplementary_files_format_and_content: Excel table with est_count and tpm for each samle and transcript

source_name: Root

growth_protocol: Arabidopsis thaliana plants of the ecotype Col-0 and the T-DNA insertion lines eil1 (AT2G27050; SALK_042113), eil3 (AT1G73730; SALK_089129), and their double mutant eil3 eil1 were grown on modified Long Ashton Medium agarose plates with either full sulfur supply (+S; 0.75 mM MgSO4) or low sulfur supply (-S; 0.75 mM MgCl2 + 0.015 mM MgSO4) for 18 days at 22°C in long-day conditions with a 16/8 h light cycle and 100 µmol photons m-2s-1. Leaf and root samples of 3 biological replicates were collected.

extract_protocol:
Total RNA was isolated by phenol-chlorophorm-isoamylalcohol extraction and LiCl precipitation. RNA samples were further purified with TURBO DNA-freeTM Kit (Thermo Fisher Scientific, Waltham, Massachusetts, USA) according to the manufacturer’s instruction. RNA integrity number (RINe) of samples (2 µg; 50-200 ng/µl; OD260/280 = 1.8-2.1; OD260/230 > 1.5) were determined in a pre-control of RNA quality.
TruSeq Stranded mRNA Library Prep assay

value: eil3 eil1

tag: treatment

value: -S

value: 18 days


title: 31-2R


title: 2015-428


title: 2015-427

value: T48h_Fed batch Glucose 75%-lactose 25%


title: EIN2C-EIN3DB/ein3-1eil-1 4 hour air RNAseq, rep2

description: E2E3Ainein3vsCol_gene_exp.diff.FC2.RPKM1.xls.rmdup.xls

value: EIN2C-EIN3DB in ein3-1eil-1 background


title: 31-1R


title: EIN2C-EIN3DB/ein3-1eil-1 4 hour air RNAseq, rep1


title: 2015-426


title: 31+3R

value: +S


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_E10_AD007

extract_protocol:
Approximately two weeks after the AAVretro injection, brains were extracted from the 56-63 day old INTACT mice, immediately submerged in ice-cold slicing buffer (2.5mM KCl, 0.5mM CaCl2, 7mM MgCl2, 1.25mM NaH2PO4, 110mM sucrose, 10mM glucose and 25mM NaHCO3) that was bubbled with carbogen, and sliced into 0.6 mm coronal sections starting from the frontal pole. From each AAVretro-injected brain, the slices were kept in the ice-cold dissection buffer from which selected brain regions (Supplementary Table 1) were manually dissected under a fluorescent dissecting microscope (Olympus SZX16), following the Allen Mouse Common Coordinate Framework (CCF), Reference Atlas, Version 3 (2015) (Extended Data Fig. 1). The dissected brain tissues were transferred to prelabeled microcentrifuge tubes, immediately frozen in dry ice, and subsequently stored at -80oC.   For each dissected brain region, samples from 2 males and 2 females were pooled separately as biological replicates for nuclei preparation. The 2-mL glass tissue dounce homogenizer and pestles (Sigma-Aldrich D8938-1SET) were pre-chilled on ice. Nuclei were prepared using a modified protocol as reported by Lacar et al., 201622. In summary, the frozen brain tissues were transferred to the dounce homogenizer with 1 mL ice-cold NIM buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT (Sigma 646563), 10μl of protease inhibitor (Sigma P8340)), with 0.1% Triton X-100 and 5μM Hoechst 33342 (Invitrogen H3570), and gently homogenized on ice with the pestle 10-15 times. The homogenate was transferred to pre-chilled microcentrifuge tubes and centrifuged at 1000 rcf for 8 min at 4oC to pellet the nuclei. The pellet was resuspended in 1 mL ice-cold NIM buffer, and again centrifuged at 1000 rcf for 8 min at 4oC. The pellet was then resuspended in 450 μL of ice-cold NSB buffer (0.25M sucrose, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT, 9ul of Protease inhibitor), and filtered through 40μM cell strainer. The filtered nuclei suspension was incubated on ice for at least 30 minutes with 50μl of nuclease-free BSA for at least 10 minutes, then incubated with GFP antibody, Alexa Fluor 488 (Invitrogen, A-21311) and anti-NeuN antibody (EMD Millipore MAB377) conjugated with Alexa Fluor 647 (Invitrogen A20173). GFP+/NeuN+ single nuclei were isolated using fluorescence-activated nuclei sorting (FANS) on a BD Influx sorter with 100μm nozzle, and sorted into 384-well plates preloaded with 2μl of digestion buffer for snmC-seq215 (20 mL digestion buffer consists of 10 mL M-digestion buffer (2×, Zymo D5021-9), 1 ml Proteinase K (20 mg, Zymo D3001-2-20), 9 mL water, and 10 µL unmethylated lambda DNA (100 pg/µL, Promega, D1521)). The collected plates were incubated at 50oC for 20 minutes then stored at -20 oC.
The bisulfite conversion and library preparation were performed following the detailed snmC-seq2 protocol as previously described (Luo, C. et al., Nat. Commun. 2018, 9(1):3824.). The snmC-Seq2 libraries were sequenced on Illumina Novaseq 6000 using the S4 flow cell 2 x 150 bp mode.

value: brain

value: VIS

value: Pons


title: 31+2R


title: 31+1R


title: 2015-424


title: 2015-420

source_name: T. reseei RUT-C30 (ATCC 56765)_T24h_Fed batch Glucose 90%-lactose 10%

value: T24h_Fed batch Glucose 90%-lactose 10%


title: 2015-422


title: 16006-0009_nas-38(ok3407)_3

city: Marburg

first: Marina

middle: Patricia

last: Sinner

state: Hessen

address: Karl-von-Frisch-Str. 8

department: Biology

institute: University of Marburg

data_processing:
RNA-Seq analysis was performed with the CLC genomics workbench 'RNA-Seq analysis' tool. It maps the NGS reads against the C. elegans genome NC_001328 from NCBI. Following mapping parameters were applied: mismatch  cost: 2, insertion/deletion cost: 3, length fraction: 0.8, similarity fraction: 0.8, local alignment,maximum number of hits per read: 5
The expression values were normalized to reads per kilobase of exon model per million mapped reads (RPKM)
The differentially expressed transcripts were  calculated. The comparisons were based on the “total exon reads” expression values to allow subsequent statistical analysis by “empirical analysis of DGE”. To analyze significant expression, the exact test for two-group comparisons was used. The dispersion of the data was chosen to be tag wise and the total count filter cutoff  threshold was set to 100. To control the false discovery rate (FDR), FDR corrected p-values were calculated and stringent filtering was used.
A feature was classified “upregulated” if its  FDR-corrected p-value was ≤ 0.05 and fold change was ≥ 2. Analogously, a gene was classified “downregulated” if its FDR-corrected p-value was ≤ 0.05 and fold change was ≤ -2. By using stringent filtering, all features outside of these thresholds were filtered out of the data.
Genome_build: C. elegans genome NC_001328 from NCBI
Supplementary_files_format_and_content: nas-38_transcriptome_all_mapped_data_per_sample: includes the following information about mapped data: Name, Chromosome, Region, Expression Value, Gene length, RPKM, Unique gene reads, Total gene reads, Transcripts annotated, detected transcripts, Exon length, Exons, Unique exon reads, total exon reads, Ratio of unique to total exon reads, unique exon-exon reads, total exon-exon reads, unique intron reads, total intron reads, ratio of intron to total gene reads for all individual samples
Supplementary_files_format_and_content: nas-38_transcriptome_fold_change_analysis: includes the following information : all total gene reads, all expression values, differential expression analysis nas-38(ok3407) vs wt and nas-38(tm2655) vs wt

organism: Caenorhabditis elegans

source_name: whole organism

growth_protocol: grown on E. coli OP50 at 20°C

extract_protocol:
RNA was isolated using the Rneasy lipid tissue kit (Qiagen)
library preparation was performed with the TruSeq Stranded mRNA HT technology and created cDNA strands using reverse transcription
Sequencing was performed at a final concentration of 1.8pM and with a 1% PhiX v3 control library spike-in(Illumina) on the NextSeq500 sequencing system (Illumina). 75 cycles of paired-end runs were done with the final library and sequencing was performed using NextSeq Control software.

treatment_protocol: Worm populations were synchronized using a standard bleaching protocol and sleeping L4 larvae were collected manually in TRIzol.

tag: developmental stage

value: L4 lethargus

value: whole organism


title: 16006-0008_nas-38(ok3407)_2


title: 16006-0007_nas-38(ok3407)_1


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_E10_AD002

tag: age

value: SSp

value: female


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_E10_AD010

tag: source


title: 3-2R


title: 3-3R


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_D9_AD008

tag: target

value: male


title: 16006-0006_wild_type_3


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_D9_AD006

tag: gender


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_E10_AD001


title: 16006-0005_wild_type_2


title: 3-1R


title: 2014_275

source_name: T. reseei RUT-C30 (ATCC 56765)_T48h_Fed batch Lactose 100%

value: T. reseei RUT-C30 (ATCC 56765)

value: T48h_Fed batch Lactose 100%


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_D9_AD002


title: 16006-0004_wild_type_1


title: 3+3R


title: 2014_276


title: 3+2R


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_E10_AD008


title: 2014_274


title: 16006-0003_nas-38(tm2655)_3


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_D9_AD001


title: 2014_273


title: 16006-0002_nas-38(tm2655)_2


title: 2014_277


title: 16006-0001_nas-38(tm2655)_1


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_D8_AD012


title: 1-3R


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_D8_AD008


title: 1-2R


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_D8_AD007


title: 1-1R


title: Frozen CD138negative sample for patient 6

city: Indianapolis

first: Duojiao

last: Chen

state: INDIANA

address: 410 W. 10th Street

department: Departments of Medical and Molecular Genetics

institute: Indiana University

data_processing:
cellranger mkfastq was used for extracting fastq files
cellranger count was used for sequence alignment and UMI counting
Genome_build: hg38
Supplementary_files_format_and_content: cellranger filtered gene barcode matrices

source_name: Bone Marrow

extract_protocol:
Chromium Single Cell 3′ Library & Gel Bead Kit v3
Single-cell 3’ gene expression libraries were prepared for each sample from 5,000-10,000 cells using the Chromium Single Cell 3’ Reagent Kits v2 User Guide, CG00052 Ver B (10x Genomics, Inc) and the Chromium single-cell system (10x Genomics, Inc). The resulting library was sequenced using a custom program for 26b plus 98b paired-end sequencing on a Illumina NovaSeq 6000 sequencer (Illumina, Inc, San Diego, CA). Depending on targeted cell recovery, about 50K reads per cell were generated and 91% of the sequencing reads reached Q30 (99.9% base call accuracy). A Phred quality score (Q score) was used to measure the quality of sequencing.

tag: disease state

value: multiple myeloma

value: Bone Marrow

tag: condition

value: frozen

tag: cell population


title: Frozen CD138negative sample for patient 5


title: 2014_259

source_name: T. reseei RUT-C30 (ATCC 56765)_T24h_Fed batch Lactose 100%

value: T24h_Fed batch Lactose 100%


title: Frozen CD138negative sample for patient 4


title: 2014_258


title: 1+3R

tag: genotype

value: 18 days


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_D8_AD002


title: 2014_257


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_D8_AD006


title: Frozen CD138negative sample for patient 3


title: Fresh CD138negative sample for patient 6

value: fresh


title: 2014_256


title: 1+2R

value: +S


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_D8_AD001

value: brain

value: VIS


title: 1+1R


title: 2014_255


title: 2014_272


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_D7_AD012

value: Pons


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_E10_AD006


title: Fresh CD138negative sample for patient 5


title: 3+1R


title: 2014_254


title: C-3R

value: -S


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_D7_AD008


title: 2014_271

source_name: T. reseei RUT-C30 (ATCC 56765)_T48h_Fed batch Glucose 100%

value: T48h_Fed batch Glucose 100%


title: C-2R


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_D7_AD007


title: C-1R


title: Frozen CD138positive sample for patient 6


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_D7_AD006

value: SSp


title: C+3R


title: Fresh CD138negative sample for patient 3


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_D7_AD002

value: female


title: 2014_268


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_D7_AD001

value: male


title: 2014_269

value: T. reseei RUT-C30 (ATCC 56765)


title: C+2R


title: Frozen CD138positive sample for patient 5


title: Frozen CD138positive sample for patient 4


title: C+1R


title: 2014_267


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_D6_AD010


title: 2014_266


title: 31-4S

source_name: Shoot

value: eil3 eil1


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_D6_AD006


title: 31-2S


title: Frozen CD138positive sample for patient 3

value: multiple myeloma


title: Frozen CD138positive sample for patient 2

value: Bone Marrow


title: Fresh CD138negative sample for patient 4


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_D6_AD004


title: 31-1S


title: 2014_252

source_name: T. reseei RUT-C30 (ATCC 56765)_T24h_Fed batch Glucose 100%

value: T24h_Fed batch Glucose 100%


title: 2014_270


title: 2014_253


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_D6_AD001


title: Frozen CD138positive sample for patient 1

value: frozen


title: 31+4S

value: 18 days


title: 2014_251


title: 2014_250


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_D5_AD010


title: Fresh CD138positive sample for patient 5

value: fresh


title: Fresh CD138positive sample for patient 6


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_D5_AD008


title: 31+3S

value: +S


title: Fresh CD138positive sample for patient 4


title: 2014_248


title: Fresh CD138positive sample for patient 3


title: 3-3S


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_D5_AD007

value: brain


title: Fresh CD138positive sample for patient 2


title: Adenovirus-GFP #2

city: Daegu

first: Dipanjan

last: Chanda

address: Chilgok

country: South Korea

institute: Kyungpook National University Hospital

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 whole genome using Bowtie2
Read count extraction and nomalization were performed using edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: primary acinar cells

growth_protocol: Primary acinar cells were maintained in Waymouth's media supplemented with  2.5 % FBS, 1 % Penicillin-Streptomycin mixture (PS), 0.25 mg/ml of trypsin inhibitor, and 25 ng/ml of recombinant human Epidermal Growth Factor (EGF)

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#015.96) standard protocols.

treatment_protocol: Primary acinar cells were transduced with Adenovirus-GFP (100 MOI) or Adenovirus-ERRgamma (100 MOI) for 36 hours prior to cell harvesting.

value: pancreas

tag: cell type

value: primary acinar cells

value: GFP overexpression


title: 3-2S

value: -S


title: Fresh CD138positive sample for patient 1


title: 3-1S


title: Adenovirus-GFP #1


title: Transplanted embryonic kidney

description: E12.5 embryonic kidneys were tramsplanted into the epididymis fat of host mice for 12 days

source_name: E12.5 embryonic kidneys transplanted for 12 days

value: Wild type

value: Kidney

tag: host strain


title: Adenovirus-ERRgamma #2

value: ERR gamma overexpression


title: LNCaP_shMAOA

city: Spokane

first: Boyang

state: Washington

address: 412 E. Spokane Falls Blvd

institute: Washington State University

data_processing:
Bowtie2 version 2.1.0 was used for mapping to the human genome hg19 transcript set.
RSEM v1.2.15 was used to calculate the count and estimate the gene expression level.
Trimmed Mean of M-values (TMM) method in the edgeR package was used for gene  expression normalization.
Genome_build: hg19
Supplementary_files_format_and_content: TMM normalized RPM

source_name: LNCaP

growth_protocol:
C4-2B ENZR cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS), 1% penicillin/streptomycin and 20 µM ENZ. LNCaP cells were cultured in RPMI 1640 medium supplemented with 10% FBS and 1% penicillin/streptomycin. Both cells were maintained at 37°C in a humidified atmosphere containing 5% CO2 (v/v).
LNCaP cells were maintained in RPMI 1640 medium [supplemented with 10% fetal bovine serum (FBS), 1% penicillin/streptomycin], and at 37°C in a humidified atmosphere containing 5% CO2 (v/v).

extract_protocol:
The total RNA was extracted by RNeasy Mini Kit (Qiagen) following the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols
RNA-Seq was performed on an Illumina HiSeq 3000 for a single read 50 run. Data quality check was done on Illumina SAV. Demultiplexing was performed with Illumina Bcl2fastq2 v 2.17 program.

treatment_protocol: Stable knockdown of MAOA in C4-2B ENZR and LNCaP cells were achieved by infection of lentivirus expressing a shRNA targeting the MAOA coding region, with a non-targeting shRNA as control, followed by antibiotic selection.

tag: cell line

value: LNCaP

value: Human prostate cancer cell line

tag: genotype/variation

value: shRNA-based MAOA stable knockdown

tag: sample type

value: Cell culture


title: 3+4S


title: Adenovirus-ERRgamma #1

tag: strain

tag: tissue


title: LNCaP_shCon

value: Control


title: C42B_ENZR_shMAOA

source_name: C4-2B ENZR

value: C4-2B ENZR


title: 2014_249

value: T. reseei RUT-C30 (ATCC 56765)

tag: growth

value: T24h_Fed batch Glucose 100%


title: 31+1S

value: eil3 eil1

tag: treatment

value: +S

value: 18 days


title: 3+1S

tag: age


title: I+T6

city: Praha 4

first: Petra

last: Hruba

address: Videnska 1958

department: Transplant Laboratory

country: Czech Republic

institute: Institute for Clinical and Experimental Medicine

description: I+T

data_processing:
High throughput sequencing of final pool was performed using NovaSeq6000 S4 system (Illumina) with following instrument settings: single-end, 100 b, 300-400 million reads per lane.
Raw data were automatically processed by Basespace cloud interface (Illumina) in default settings.
The basecalling, adapter clipping, and quality filtering were carried out using bcl2fastq v2.20.0.422 Conversion Software (Illumina).
The quality of raw reads was evaluated using FastQC (v0.11.8) and MultiQC (v1.7).
Clipping adaptor sequences was carried out using cutadapt (v1.18). The trimmed reads were aligned to the human transcriptome reference (GRCh38) using bowtie2 (v2.3.4.3).
The alignments were evaluated using qualimap2 (v2.2.2). The counts of reads mapped to the reference were extracted and used for differential gene expression analysis using SAMtools (v1.9).
Genome_build: human transcriptome reference (GRCh38)
Supplementary_files_format_and_content: Matrix table with raw transcript counts for every transcript and every sample

source_name: kidney allograft biopsy

extract_protocol:
To perform RNA sequencing in 8 ISO-T and 8 I+T biopsies, total RNA was isolated from biopsy specimens stored at -80°C in RNAlater™ (Qiagen) using the RNeasy Micro Kit (Qiagen, Hilden, Germany). RNA concentration was measured by Qubit fluorimetr and RNA integrity number was checked using Agilent Bioanalyzer 2100.
From 400 ng of total RNA was isolated mRNA using poly (A) magnetic selection NEBNext® Poly (A) mRNA magnetic isolation module (New England, BioLabs, Inc). Transcriptome libraries for differential gene expression were prepared using the NEBNext® Ultra™ II Directional RNA Library Prep with Sample Purification Beads according to the manufacturer’s protocol (New England, BioLabs, Inc). In brief, mRNA was randomly sheared by heat digestion in the presence of a divalent metal cation (Mg2+). Sheared RNA was reversibly transcribed making 1st strand of cDNA using random hexamers as primers and reverse transcriptase. The second strand was created using dUTPs and after purification with Sample Purification Beads, NEBNext adapters were ligated. After removal of 2nd strand by uracil-DNA-dependent glycosylase, final amplification of adaptor ligated DNA using NEBNext® Multiplex Oligos for Illumina® was done. Library quality was assessed on a Bioanalyzer 2100 using Agilent High Sensitivity DNA 1000 assay. Libraries from all 16 samples were pooled to a final concentration of 50 nmol and the quality of pooling was assessed by sequencing using MiSeq.

value: kidney allograft biopsy

tag: biopsy post operative day

tag: creatinine at biopsy (umol/l)

tag: histological diagnosis

value: tubulitis with interstitial inflammation


title: I+T8

description: I+T


title: I+T7

description: I+T


title: I+T5

description: I+T


title: 3+2S


title: C42B_ENZR_shCon


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P5_180419_P6_D5_AD006

first: Joseph

institute: HHMI-Salk-Institute

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 INTACT reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10 INTACT
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

source_name: C57BL/6J P56 Mouse Brain

value: brain

tag: source

value: VIS

tag: target

value: SSp

tag: gender

value: female


title: Reactivated KPR cells, replicate 1

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

description: Reactivated KPR cells, replicate 1

data_processing:
RNA-seq data was aligned using bowtie2 against mm10 version of the human genome and RSEM v1.2.31 software was used to estimate raw read counts using transcriptome information from Ensemble v84 set
DESeq2 was used to estimate significance of differential expression between groups
Genome_build: mm10
Supplementary_files_format_and_content: Prosessed files contains the raw counts for each gene as estimated by RSEM

source_name: KrasG12D/+;Trp53LSL/LSL;Rosa26Cre-ER/CreER (KPr) lung cancer cell lines

extract_protocol:
Total RNA was extracted from cell pellets using the Direct-zol RNA Miniprep (Zymo Research). RNA quality was validated using the TapeStation RNA ScreenTape (Agilent).
100 ng of total RNA was used to prepare library for Illumina Sequencing using the Quant-Seq 3’mRNA-Seq Library Preparation Kit (Lexogen). Library quantity was determined using qPCR (KAPA Biosystem).

tag: reactivation

value: reactivated


title: I+T4

description: I+T


title: amygdala3-3

city: shanghai

first: yanyong

last: cheng

address: 639 Zhizaoju Road

department: Department of Anesthesiology

institute: Shanghai Ninth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

description:
Rhesus macaques
Nuclear RNA
snRNA-Seq
S011_3-3
processed data file: RDS.RawData.txt

data_processing:
We applied fastp with default parameter filtering the adaptor sequence and removed the low-quality reads to achieve clean data. Feature-barcode matrices were obtained by aligning reads to the rhesus monkey genome (Version: Mmul 10, Ensembl) using CellRanger v3.0.0. In order to minimize the sample batch, we applied the down sample analysis among samples sequenced according to the mapped barcoded reads per cell of each sample and achieved the aggregated matrix eventually. Nucleus contained over 200 expressed genes and mitochondria UMI rate below 20% passed the quality filtering and mitochondria genes were removed in the expression table but used for nucleus expression regression to avoid the effect of the nucleus status for clustering analysis and marker analysis of each cluster.
Genome_build: GRCH38 (Ensembl Version91)
Supplementary_files_format_and_content: RDS.RawData.txt includes counts.

organism: Macaca mulatta

source_name: nucleus

growth_protocol: The tissues samples of amygdala were surgically removed and the frozen tissue was used to intact nucleus isolation. The nucleus was isolated and purified as previously described with some modifications.

extract_protocol:
The scRNA-Seq libraries were generated using the 10X Genomics Chromium Controller Instrument and Chromium Single Cell 3’ V2 Reagent Kits (10X Genomics, Pleasanton, USA). Briefly, cells nuclei were concentrated to 1000 nuclei/μL and approximately 15000 nuclei were loaded into each channel to generate single-cell Gel Bead-In-Emulsions (GEMs), which results into expected mRNA barcoding of 9000 single nucleus for each sample. After the RT step, GEMs were broken and barcoded-cDNA was purified and amplified.
The amplified barcoded cDNA was fragmented, A-tailed, ligated with adaptors and index PCR amplified. The final libraries were quantified using the Qubit High Sensitivity DNA assay (Thermo Fisher Scientific, USA) and the size distribution of the libraries were determined using a High Sensitivity DNA chip on a Bioanalyzer 2200 (Agilent, USA). All libraries were sequenced by HiSeq Xten (Illumina, USA) on a 150 bp paired-end run.

value: amygdala

tag: passage


title: amygdala3-4

description:
Rhesus macaques
Nuclear RNA
snRNA-Seq
S012_3-4
processed data file: RDS.RawData.txt


title: 1-2S

tag: genotype

value: -S


title: Parental KPR cells, replicate 3

description: Parental KPR cells, replicate 3

value: not


title: I+T3

description: I+T


title: 1-1S


title: Parental KPR cells, replicate 2

description: Parental KPR cells, replicate 2


title: amygdala3-2

description:
Rhesus macaques
Nuclear RNA
snRNA-Seq
S010_3-2
processed data file: RDS.RawData.txt


title: I+T2

description: I+T


title: 1+3S


title: Parental KPR cells, replicate 1

description: Parental KPR cells, replicate 1


title: amygdala3-1

description:
Rhesus macaques
Nuclear RNA
snRNA-Seq
S009_3-1
processed data file: RDS.RawData.txt


title: Reactivated KPR cells, replicate 3

description: Reactivated KPR cells, replicate 3


title: 1+2S


title: ISOT-8

description: ISO-T

value: isolated tubulitis without interstitial inflammation


title: 1+1S


title: Reactivated KPR cells, replicate 2

description: Reactivated KPR cells, replicate 2


title: C-4S


title: ISOT-7

description: ISO-T


title: amygdala2-4

description:
Rhesus macaques
Nuclear RNA
snRNA-Seq
S008_2-4
processed data file: RDS.RawData.txt


title: amygdala2-2

description:
Rhesus macaques
Nuclear RNA
snRNA-Seq
S006_2-2
processed data file: RDS.RawData.txt


title: 1-4S


title: amygdala2-3

description:
Rhesus macaques
Nuclear RNA
snRNA-Seq
S007_2-3
processed data file: RDS.RawData.txt


title: amygdala2-1

description:
Rhesus macaques
Nuclear RNA
snRNA-Seq
S005_2-1
processed data file: RDS.RawData.txt


title: C-3S


title: ISOT-6

description: ISO-T


title: C-2S


title: ISOT-5

description: ISO-T


title: amygdala1-4

description:
Rhesus macaques
Nuclear RNA
snRNA-Seq
S004_1-4
processed data file: RDS.RawData.txt


title: ISOT-4

description: ISO-T


title: ISOT-3

description: ISO-T


title: I+T1

description: I+T


title: C+3S


title: amygdala1-3

description:
Rhesus macaques
Nuclear RNA
snRNA-Seq
S003_1-3
processed data file: RDS.RawData.txt


title: ISOT-2

description: ISO-T


title: C+4S


title: ISOT-1

description: ISO-T


title: C+2S


title: Cerebral cortex and Striatum_BT_mouse4

type: RNA

city: Noda

first: Shota

last: Mizuno

state: Chiba

address: 2641 Yamazaki

department: Department of Applied Biological Science

institute: Tokyo University of Science

description: Gene expression in whole cerebral cortex and striatum of BTBRTF/ArtRbrc

hyb_protocol: The Cy3-labelled cRNA was hybridized to SurePrint G3 Mouse GE v2 8x60K Microarray (Agilent-074809; Agilent) for 17 hours according to the manufacturer's instructions.

scan_protocol: The hybridization images were acquired using the DNA Microarray Scanner (Agilent) according to manufacturer's instructions.

data_processing: The scanned images were analyzed with Feature Extraction Software version 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 074809_D_F_20150624) to obtain background subtracted and spatially detrended Processed Signal intensities. Intensity values were processed with GeneSpring GX (Agilent). In data processing, “75 percentile shift“ and “baseline to median of control samples” were selected as normalization and preprocess baseline options, respectively.

source_name: cerebral cortex and striatum, BTBRTF/ArtRbrc

label_protocol: The cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the Low Input Quick Amp Labeling Kit, One-Color (Agilent) according to the manufacturer's instructions.

extract_protocol: The dissected brain tissue (cerebral cortex and striatum) were treated in an RNA-stabilizing reagent (RNAlater, Qiagen, Hilden, Germany). The total RNA was extracted with the RNeasy Plus Universal Mini Kit (Qiagen) and RNA quality was analyzed using the 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA) and the NanoDrop (Thermo Fisher Scientific, Waltham, MA, USA). Only RNA with a high (>8) RNA integrity number was selected and used for subsequent labeling, and array hybridization according to manufacturer's instructions.

value: whole cerebral cortex and striatum

value: male

value: BTBRTF/ArtRbrc

value: 4 month


title: Cerebral cortex and Striatum_BT_mouse2


title: amygdala1-2

description:
Rhesus macaques
Nuclear RNA
snRNA-Seq
S002_1-2
processed data file: RDS.RawData.txt


title: Cerebral cortex and Striatum_BT_mouse3


title: Cerebral cortex and Striatum_BT_mouse1

value: 6 month


title: Control3 mRNAseq

status: Public on Nov 18 2020

city: 苏州

first: haifang

last: zhang

address: 苏州

institute: 苏州大学附属二院

data_processing:
Paired-end reads were harvested from Illumina HiSeq 4000 sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3). The high quality trimmed reads were used to analyse circRNAs, LncRNAs and mRNAs.
The high quality reads were aligned to the reference genome/transcriptome with STAR software (v2.5.1b) and circRNAs were detected and identified with DCC software (v0.4.4). edgeR software (v3.16.5) was used to normalized the data and perform differentially expressed circRNA analysis. GO and KEGG analysis were performed for the differentially expressed circRNA-associated genes.
The high quality reads were aligned to the Mouse reference genome (UCSC MM10) with hisat2 software (v2.0.4). Then, guided by the Ensembl gtf gene annotation file, cuffdiff software (v2.2.1, part of cufflinks) was used to get the FPKM as the expression profiles of LncRNA and mRNA, and fold change and p-value were calculated based on FPKM, differentially expressed LncRNA and mRNA were identified. LncRNA target genes were predicted by the locations to nearby genes. And GO and Pathway analysis were performed on these target genes. GO and Pathway enrichment analysis were also performed based on the differentially expressed mRNAs.
Genome_build: MM 10
Supplementary_files_format_and_content: excel format

source_name: osteoclasts

growth_protocol: RAW264.7 cells were seeded in a 6-well plate with 2.5 × 105 cells per well in α-MEM medium (HyClone, USA) containing 10% FBS, 100 ng/mL soluble RNAKL (sRNAKL, R&D Systems, USA), 0.002 mol/L L-glutamine, 100 units/mL penicillin, and 100 µg/mL streptomycin. The cell culture medium was changed every other day and osteoclast induction was completed after 5 days of culture

extract_protocol:
Total RNA was isolated using trizol.Total RNA (1 μg) was used for removing the rRNAs using NEBNext rRNA Depletion Kit (New England Biolabs, Inc., Massachusetts, USA)  following the manufacturer's instructions
RNA libraries were constructed by using rRNA-depleted RNAs with NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England Biolabs, Inc., Massachusetts,USA) according to the manufacturer’s instructions.
Libraries were controlled for quality and quantified using the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA). Library sequencing was performed on an illumina Hiseq instrument with 150bp paired end reads.

treatment_protocol: Osteoclasts induced by RAW264.7 cells were infected with S. aureus at a ratio of 1:10. Following incubation at 37°C for 2 h, cells were incubated with 100 µg/mL gentamicin for 1 h to kill extracellular bacteria

value: osteoclasts of staphylococcus aureus infection

tag: cell type

value: RAW264.7 cell


title: Control2 mRNAseq


title: mepic EV 2

city: Madrid

first: Cristina

middle: Villa

last: del Campo

state: Madrid

address: Melchor Fernandez Almagro, 3 Pabellon 18, CNIC

institute: CNIC

description:
p312sMedicExD1a_Zimmermann_S45_L006
Medic ExD1a
The processed data file contains miRNAs counts present in the mouse epicardial Evs. Combination of two sequencing runs (mepic EV 1 and mepic EV 2 samples)

data_processing:
Sequence reads were pre-processed to remove adapters and retain only 16-30 base pair- length reads
The reads aligning to each known mature miRNA were counted using Bioconductor packages for next-generation sequencing data analysis based on miRNA definitions in miRBase database
The differential expression analysis between different sample types was performed using the negative binomial statistical model of read counts as implemented in the DESeqBioconductor package
The statistical significance of differential expression is established based on the FDR-adjusted p-values. The cluster analysis of all differentially expressed miRNA was performed using the Bayesian infinite mixture model. Pathway enrichment analysis was conducted with Gene Ontology (GO)
Enrichment p-values were corrected for false discovery rate (FDR) and were considered significant when adjusted p ≤ 0.05.
Supplementary_files_format_and_content: Counts for miRNAs

source_name: Evs from mouse epicardial cells

growth_protocol: Cells were grown in standard culture conditions

extract_protocol:
AllPrep DNA/RNA Mini Kit
Library preparation was performed using TrueSeq Kit (TruSeq Small RNA Library Prep Kit Illumina Cat N° RS-200-0012) with modifications on gel size selection (30-300bp fragments).

value: mouse epicardial cells

value: extracellular vesicles (Evs)

tag: molecule subtype

value: miRNA


title: Control mRNAseq


title: Cerebral cortex and Striatum_B6_mouse3

description: Gene expression in whole cerebral cortex and striatum of C57BL/6J

source_name: cerebral cortex and striatum, C57BL/6J


title: Treat3 mRNAseq

value: osteoclasts of normal


title: Cerebral cortex and Striatum_B6_mouse1


title: Cerebral cortex and Striatum_B6_mouse2


title: Cerebral cortex and Striatum_B6_mouse4


title: Treat2 mRNAseq


title: MCF-7, biological rep1 [lncRNA and mRNA]

city: Suzhou

first: Min

last: Jiang

state: Jiangsu

address: No. 188, Shi Zi Road

institute: The First Affiliated Hospital of Soochow University

description:
S-1
LncRNA and mRNA expression data from MCF-7 cells.

hyb_protocol: DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm at 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: Scanned on an Agilent G2565CA scanner.

data_processing: Feature Extraction v10.7 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and GeneSpring software was used to analyze the raw data, which are normalized by quantile normalization.

source_name: MCF-7 cell

label_protocol: cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. This procedure has been previously described, and the procedure has been improved by using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio) for producing higher yields of labeled cDNA.

growth_protocol: MCF-7, LCC2 and LCC9 cells were grown in phenol red free IMEM supplemented with 5% charcoal-stripped FBS and 1% penicillin/streptomycin in a cell culture incubator at 37 ℃ and 5% CO2.

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: MCF-7, LCC2 or LCC9 cells were resuspended with phenol red free IMEM supplemented with 5% charcoal-stripped FBS and 1% penicillin/streptomycin and seeded in T75 flasks. Culture medium was changed once on day 2. Cells were washed with normal saline twice and harvested on day 4.

tag: cell line

tag: tamoxifen resistance

value: No

tag: fulvestrant resistance


title: LCC9, biological rep3 [lncRNA and mRNA]

description:
FUL-5
LncRNA and mRNA expression data from LCC9 cells.

source_name: LCC9 cell

value: tamoxifen-resistant

value: fulvestrant-resistant


title: amygdala1-1

description:
Rhesus macaques
Nuclear RNA
snRNA-Seq
S001_1-1
processed data file: RDS.RawData.txt

tag: tissue

value: amygdala


title: MCF-7, biological rep2 [lncRNA and mRNA]

description:
S-5
LncRNA and mRNA expression data from MCF-7 cells.


title: Treat mRNAseq

tag: treatment


title: MCF-7, biological rep3 [lncRNA and mRNA]

description:
S-6
LncRNA and mRNA expression data from MCF-7 cells.


title: LCC2, biological rep3 [lncRNA and mRNA]

description:
TAM-4
LncRNA and mRNA expression data from LCC2 cells.

source_name: LCC2 cell


title: LCC2, biological rep2 [lncRNA and mRNA]

description:
TAM-3
LncRNA and mRNA expression data from LCC2 cells.


title: LCC9, biological rep2 [lncRNA and mRNA]

description:
FUL-4
LncRNA and mRNA expression data from LCC9 cells.


title: siPTBP1+siPTBP2 CY Replicate 1

city: LOS ANGELES

first: Chia-ho

last: Lin

address: 6577 MRL. 675 CHARLES E YOUNG DR. SOUTH

institute: UCLA

description: siPTBP1+siPTBP2 CY Replicate 1

data_processing:
Sequencing reads were mapped to the mm10 genome using STAR. Intron retention analysis was conducted using SQUID that was developed from the Xing lab.
gene expression estimation with Kallisto
Genome_build: mm10

source_name: E14 mESCs

growth_protocol: E14 mESCs were cultured on gelatin, supplemented by LIF+ mESC media to inhibit spontaneous differentiation of the cells.

extract_protocol:
Trizol was used to extract total RNA from the samples.
Sequencing libraries were constructed using the Illumina TruSeq Stranded mRNA kit. PolyA+ RNA was selected using poly-T oligo beads.

treatment_protocol: The cells were reverse-transfected with 20 uM of either eGFP, PTBP1 or PTBP1+PTBP2 siRNAs. After 24 hours, the attached cells were transfected again with the same amount of siRNAs for another 24 hours.

tag: fraction

value: CY

tag: molecule

value: polyA+ cytoplasmic RNA


title: siPTBP1 CY Replicate 2

description: siPTBP1 CY Replicate 2


title: siPTBP1+siPTBP2 CH Replicate 1

description: siPTBP1+siPTBP2 CH Replicate 1

value: CH

value: polyA+ chromatin-associated RNA


title: siPTBP1+siPTBP2 NP Replicate 1

description: siPTBP1+siPTBP2 NP Replicate 1

value: NP

value: polyA+ nucleoplasm RNA


title: siPTBP1+siPTBP2 NP Replicate 3

description: siPTBP1+siPTBP2 NP Replicate 3


title: siPTBP1 NP Replicate 2

description: siPTBP1 NP Replicate 2


title: siPTBP1 CY Replicate 1

description: siPTBP1 CY Replicate 1


title: siPTBP1 CY Replicate 3

description: siPTBP1 CY Replicate 3


title: siPTBP1 CH Replicate 3

description: siPTBP1 CH Replicate 3


title: siPTBP1 CH Replicate 2

description: siPTBP1 CH Replicate 2


title: siPTBP1 CH Replicate 1

description: siPTBP1 CH Replicate 1


title: siGFP NP Replicate 3

description: siGFP NP Replicate 3

value: siGFP


title: siGFP NP Replicate 1

description: siGFP NP Replicate 1


title: siGFP NP Replicate 2

description: siGFP NP Replicate 2


title: siGFP CY Replicate 3

description: siGFP CY Replicate 3


title: siGFP CY Replicate 1

description: siGFP CY Replicate 1


title: siGFP CY Replicate 2

description: siGFP CY Replicate 2


title: siGFP CH Replicate 1

description: siGFP CH Replicate 1


title: LCC2, biological rep1 [lncRNA and mRNA]

description:
TAM-2
LncRNA and mRNA expression data from LCC2 cells.


title: siGFP CH Replicate 2

description: siGFP CH Replicate 2


title: siPTBP1+siPTBP2 CY Replicate 3

description: siPTBP1+siPTBP2 CY Replicate 3


title: Lmna-/-:AAV9 Lmna WT 2

city: Houaton

first: Ali

last: Marian

state: Texas

address: 6770 Bertner Ave DAC C900a

department: Centre for Cardiovascular Genetics

institute: UTHSC, Houston

data_processing:
Mapping of sequencing reads to the mouse genome GRCm38.91 (Ensembl) was performed using Tophat2  using mm10 mouse genome as reference.
Read quantitation on a per-gene basis was performed with HTSeq  and the default gene annotation file (gtf) provided with the GRCm38.91 Ensembl genome distribution. Calculation of fold-change and FDR for differentially expressed RNAs used the R/Bioconductor packages limma and edgeR/voom.A batch correction was performed through by including batch as a blocking factor in the linear model used by limma.
Differential gene expression was determined using EdgeR.
Supplementary_files_format_and_content: xlsx file contains the cpm for the Samples and the calculated log2ratio for the KO and AAV9 samples  along with the FDR and pvalue for the comparison.

source_name: Heart

extract_protocol:
A miRNeasy Mini Kit  (Qiagen, Cat:217004) was used to isolate the RNA following the manufacturer's guidelines
A Illumina TruSeq kit was used in library preparation following the manufacturer's guidelines.

value: Heart

tag: strain

value: Mixed

tag: age

value: 2 week

value: AV9 mediated re-introduction of WT LMNA in the Lmna knockout


title: Lmna-/-:AAV9 Lmna WT 3


title: Lmna-/-:AAV9 Lmna WT 5


title: Lmna-/-:AAV9 Lmna WT 4


title: Lmna-/-:AAV9 Lmna WT 1

value: AAV9 mediated re-introduction of WT LMNA in the Lmna knockout


title: siPTBP1+siPTBP2 NP Replicate 2

description: siPTBP1+siPTBP2 NP Replicate 2


title: Lmna-/- 8

value: Lmna knockout


title: Lmna-/- 6


title: siPTBP1 NP Replicate 1

description: siPTBP1 NP Replicate 1


title: siGFP CH Replicate 3

description: siGFP CH Replicate 3