title: TLE3 ChIP-seq, iWAT adipocytes

city: Odense M

first: Anne

last: Loft

address: Campusvej 55

department: Biochemistry & Molecular Biology

country: Denmark

institute: University of Southern Denmark

data_processing:
ChIP-seq data sets were mapped to the mm9 genome with STAR (Dobin et al., 2013) set to not map across splice junctions, and tag directory generation, peak calling/annotations and motif analyses were performed with HOMER (Heinz et al., 2010).
TLE3 binding sites were called using ”-style factor” and ”-F 10” settings with all other parameters set at default in eWAT-derived, iWAT-derived and BAT-derived adipocytes, and overlapping peaks were merged into one master peak file. Subsequently, TLE3 peaks in each condition were identified as having >15 normalized tags/peak in a 230bp window and 10-fold more tags relative to the input control.
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph, peaks.txt

source_name: iWAT-derived primary adipocytes

growth_protocol: Brown adipose tissue (pooled interscapular, cervical, and axillary depots) as well as the epididymal (eWAT) and inguinal (iWAT) adipose tissue were optained from 4-5wk old male NMRI mice.  Adipose tissues pooled from 10-15 mice were carefully minced and treated with collagenase (type II; Sigma) to separate the SVF from mature adipocytes.

extract_protocol:
For preparation of material for TLE3 ChIP-seq, eWAT-, iWAT-, and BAT-derived adipocytes were treated with 2 mM disuccinimidyl glutarate (DSG) (Proteochem) for 15 min followed by cross-linking with 1% formaldehyde for 30 min. Crosslinking was stopped by addition of glycine. Nuclei isolation, chromatin preparation and chromatin IP was performed as described previously (Siersbæk et al., 2012, MCB, 32: 3452-3463)).
ChIP-seq libraries were constructed according to the manufacturer's instructions (Illumina) as described in (Nielsen R, Mandrup S, 2014 Genome-Wide Profiling of Transcription Factor Binding and Epigenetic Marks in Adipocytes by ChIP-seq. Methods in Enzymology 2014, Vol. 537, pp. 261-279).

treatment_protocol: The isolated SVF cells were cultured under differentiation-inducing conditions in a medium consisting of DMEM (Sigma), 10% newborn calf serum (NCS) (HyClone), 30 nM insulin, 25 μg/ml sodium ascorbate, 10 mM HEPES, pH 7.4, at 37°C, 4 mM l-glutamine (Invitrogen), 100 μg/ml streptomycin, 62.5 μg/ml penicillin, and 1 μM rosiglitazone (Novo Nordisk). The cultures were harvested 8 days after plating and for comparison between the in vitro differentiated adipocytes, only cultures with a >50% degree of differentiation were used.

value: iWAT

value: Primary in vitro differentiated SVF cells

tag: chip-antibody

value: anti-TLE3 (Proteintech 11372-1-AP)


title: Input ChIP-seq, iWAt adipocytes

status: Public on May 23 2019

type: SRA

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: tissue

tag: cell type


title: TLE3 ChIP-seq, eWAT adipocytes

source_name: eWAT-derived primary adipocytes

value: eWAT


title: TLE3 ChIP-seq, BAT adipocytes

source_name: BAT-derived primary adipocytes

value: BAT


title: E. cyaneus, control, 3 hours, sample 4

city: Irkutsk

first: Polina

last: Drozdova

state: Irkutsk region

address: Lenin str. 3

department: Institute of Biology

country: Russia

institute: Irkutsk State University

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 3 days and kept at 6 degrees C for 3 hours (parallel control).
EcyB3_4
differential expression file:
EcyCd3_annot.csv
Ecy10LT3_annot.csv
EcyPB3_annot.csv

library_source: transcriptomic

data_processing:
Raw reads were mapped onto transcriptome assemblies with salmon v0.9.1.
DESeq2 abundance estimation was performed with an in-house R script, which can be found at https://github.com/drozdovapb/EveEcyGlaDE.
Transcript abundances were merged with transcript annotation for selection of Metazoa-related contigs if necessary.
Genome_build: de novo transcriptome assembly of the corresponding species (FASTA files are available on series record).
Supplementary_files_format_and_content: Salmon output files as TPM (transcript per million counts, *sf.txt files) and DESeq2 output files with custom annotation (*annot.csv)

molecule: total RNA

organism: Eulimnogammarus cyaneus

source_name: whole body

extract_protocol:
Total RNA for RNA sequencing was extracted from either a single individual or from a pool of up to 5 individuals (see individual BioSample description). Amphipods were homogenized in 1 ml of Qiazol Reagent (Qiagen) with MM400 homogenizer (Retsch). RNA isolation from the aqueous phases was performed with a Qiacube (Qiagen) and miRNeasy kit (Qiagen).
mRNA was isolated from the total RNA sample using Oligotex mRNA Mini Kit (Qiagen). The quality of RNA was checked with RNA 6000 Nano Kit on the Agilent Bioanalyzer 2100. mRNA libraries were prepared with ScriptSeq v2 RNA-Seq Library Preparation Kit (Epicentre, # SSV21124).

treatment_protocol: Animals were acclimated at 6 degrees C for 3-5 days before the experiment. Please refer to description of individual samples for species- and sample-specific details

value: whole body

value: rocky littoral zone

value: Russia:Irkutsk region, Lake Baikal, Bolshie Koty village

value: Till Luckenbach, Daria Bedulina

tag: depth

value: adult

value: littoral zone

value: Maxim Timofeyev, Daria Bedulina

tag: condition


title: hcr1-delta DY114F

city: Bethesda

first: Nicholas

middle: R

last: Guydosh

state: MD

address: 8 Center Dr, Bldg 8, 220

department: NIDDK

country: USA

institute: National Institutes of Health

description:
hcr1-delta
Ribosome-protected RNA 25-34 nt
Biological replicate of DY115F. Wig files composed of combination of two biological replicates (DY114F and DY115F).

data_processing:
Base calling and demultiplexing was performed at the NIDDK Genomics Core at the NIH Intramural program, Bethesda, MD.
Files were demultiplexed and filtered to remove low-quality reads. They were then trimmed to the start of the linker sequence. Contaminating sequences that corresponded to gel markers were eliminated.
Reads were aligned to a library of RNA genes and those not matching were retained.
Reads were then aligned to the genome and those not matching to a custom library of splice junctions by using Bowtie (Langmead et al., 2009). For footprints, reads that did not match in these steps were trimmed of consecutive 3' As and realigned. The aligned reads from all alignment rounds were pooled and normalized to units of reads per million (rpm) (by dividing by the total number of million mapped reads in a sample) to generate wig files.
Replicates or multiple sequencing lanes for a given sample were pooled together to create a single wig file for each condition to be used in downstream analysis.
Genome_build: R64-1-1
Supplementary_files_format_and_content: All files are fixedStep wig files (text format, each line representing one position in the genome).

organism: Saccharomyces cerevisiae

source_name: Whole cells

growth_protocol: Cells were generally grown to an OD of ~0.6 and harvested.

extract_protocol:
Ribosome profiling lysates were clarified, RNase treated, and run over sucrose gradients to extract the monosome peak. RNA was then extracted using SDS/hot phenol/chloroform and footprints of the specified size were retained by gel purification.
Briefly, RNAs were ligated to a universal DNA linker followed by reverse transcription. cDNAs were then circularized and PCR amplified. Ribosome profiling circularized cDNA was subject to ribosomal RNA subtraction using custom biotinylated oligos in some cases. In others, Ribo-Zero was used. RNA-Seq samples were prepared with the Illumina Truseq Stranded ribo-zero kit.

treatment_protocol: Cells were rapidly vacuum filtered and flash frozen. Ribosome profiling samples were lysed in a freezer mill with lysis buffer. Total RNA for mRNA-Seq was extracted from whole cells.

tag: strain


title: E. cyaneus, control, 3 hours, sample 2

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 3 days and kept at 6 degrees C for 3 hours (parallel control).
EcyB3_2
differential expression file:
EcyCd3_annot.csv
Ecy10LT3_annot.csv
EcyPB3_annot.csv


title: S08-LLC-SH21-GFP-1

city: Aurora

first: Joanna

last: Poczobutt

department: Medicine

institute: University of Colorado Denver

data_processing:
Read quality was checked using FastQC (http://www.bioinformatics. bbsrc.ac.uk/projects/fastqc).
Reads were trimmed to 125 bp using FASTQ Toolkit v2.2.0 application on Basespace Illumina analysis website (https://basespace.illumina.com/apps/3122120/FASTQ-Toolkit?preferredversion).
Samples were mapped to mouse genome and quantified using RNA-Seq Alignment v1.1.0 application on Basespace Illumina analysis website. The aligner software: STAR_2.5.0b with default parameters. Quantification: Cufflinks v.2.2.1 and Cuffnorm.(https://basespace.illumina.com/apps/3086084/RNA-Seq-Alignment?preferredversion)
Differential expression analysis was preformed using the Cufflinks Assembly & DE v 2.1.0 application on Basespace Illumina analysis website  using standard FPKM normalization. (https://basespace.illumina.com/apps/3088085/Cufflinks-Assembly-DE?preferredversion)
Genome_build: mm10
Supplementary_files_format_and_content: Excel spreadsheet containing matrix with normalized abundance measurements (FPKM)

source_name: lung tumor

growth_protocol: LLC-sh21 In Vivo samples: LLC-sh21 cells (1x10^5 in 40 µl per injection) were suspended in HBSS containing 15% Growth Factor Reduced Matrigel (BD Biosciences, cat# 354230) and injected into the parenchyma of the left lung lobe of mice, as previously described (Poczobutt et al., J Immunol. 2016 Jan 15;196(2):891-901). Cells were injected into 8-12 week old C57BL/6J male and female mice, which expressed green fluorescent protein (C57BL/6-Tg(UBC-GFP)30Scha/J, Jackson Laboratory, Bar Harbor, ME). Mice were sacrificed 3 weeks after injection, tumors were harvested and processed into single cell suspension as described (Poczobutt et al., J Immunol. 2016 Jan 15;196(2):891-901). Cell sorting was performed at the University of Colorado Cancer Center Flow Cytometry Shared Resource using an XDP-100 cell sorter (Beckman Coulter). The sorting strategy excluded debris and cell doublets by light scatter and dead cells by DAPI. LLC-sh21 cells were separated from murine host cells by sorting for GFP-negative cells. Cells were pelleted and RNA was extracted. Animals were bred and maintained in the Center for Comparative Medicine at the University of Colorado Denver, Anschutz Medical Campus. All procedures were performed under protocols approved by the Institutional Animal Care and Use Committee at the University of Colorado Denver.

extract_protocol:
Total RNA was extracted from cells using RNeasy Plus Mini Kit (Qiagen), which includes a step to eliminate genomic DNA.
RNA libraries were constructed using an Illumina TruSEQ stranded mRNA Sample Prep Kit (Cat# RS-122-2101). Total RNA was combined with RNA purification beads to bind PolyA RNA to oligodT magnetic beads. mRNA was eluted and converted to double stranded DNA. A-tailing, adapter ligation, and PCR amplification using 15 cycles was performed to complete the library construction.

tag: strain background

tag: sample group

value: LLC-sh21 In Vivo

value: Lewis Lung carcinoma (LLC)


title: S07-LLC-NTC-GFP-2

growth_protocol: LLC-NT In Vivo samples: LLC-NT cells (1x10^5 in 40 µl per injection) were suspended in HBSS containing 15% Growth Factor Reduced Matrigel (BD Biosciences, cat# 354230) and injected into the parenchyma of the left lung lobe of mice, as previously described (Poczobutt et al., J Immunol. 2016 Jan 15;196(2):891-901). Cells were injected into 8-12 week old C57BL/6J male and female mice, which expressed green fluorescent protein (C57BL/6-Tg(UBC-GFP)30Scha/J, Jackson Laboratory, Bar Harbor, ME). Mice were sacrificed 3 weeks after injection, tumors were harvested and processed into single cell suspension as described (Poczobutt et al., J Immunol. 2016 Jan 15;196(2):891-901). Cell sorting was performed at the University of Colorado Cancer Center Flow Cytometry Shared Resource using an XDP-100 cell sorter (Beckman Coulter). The sorting strategy excluded debris and cell doublets by light scatter and dead cells by DAPI. LLC-NT cells were separated from murine host cells by sorting for GFP-negative cells. Cells were pelleted and RNA was extracted. Animals were bred and maintained in the Center for Comparative Medicine at the University of Colorado Denver, Anschutz Medical Campus. All procedures were performed under protocols approved by the Institutional Animal Care and Use Committee at the University of Colorado Denver.

value: LLC-NT In Vivo


title: S03-LLC-SH21-GFP-2


title: S09-LLC-SH21-GFP-3


title: E. cyaneus, control, 24 hours, sample 3

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 3 days and kept at 6 degrees C for 24 hours (parallel control).
EcyB24_3
differential expression file:
EcyCd24_annot.csv
Ecy10LT24_annot.csv
EcyPB24_annot.csv


title: E. cyaneus, LC10 cadmium, 3 hours, sample 1

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 3 days and subjected to LC10 (3.7 uM) cadmium chloride for 3 hours.
EcyCd3_1
differential expression file:
EcyCd3_annot.csv


title: Refed_11

type: RNA

city: Tallahassee

first: gang

last: wang

state: Florida

address: 319 Stadium Dr

department: The Center for Genomics and Personalized Medicine

institute: Florida State University

description: Gene expression data from Tibialis Anterior of Refed Mouse

hyb_protocol: Following fragmentation, 5.5 ug of single stranded cDNA was hybridized for 16 hr at 45 degrees C on GeneChip Mouse Gene 2.0 ST Arrays.  The staining and washing of the arrays were conducted using an Affymetrix Fluidics 450 Station.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Command Console Sofware and GeneChip Scanner 3000 7G according to manufacturer's instructions.

data_processing: Raw data files were imported into Partek's Genomic Software.  The Robust Microarray Average method was used for data processing which included background correction, quantile normalization, and median polish corrections.  Signals for probes were Log2 transformed to create data sets closer to the normal distruibution.

label: biotin

source_name: Tibialis Anterior from Refed Mouse

label_protocol: 300 ng of total RNA was labeled according to the Whole Transcript Sense Target Labeling Assay protocol using Affymetrix's GeneChip WT PLUS Reagent kit (cat. #902281)

growth_protocol: Mice were bred and housed in a temperature (25 degree C) and light controlled environment (12hr:12hr light:dark) on corn cob bedding.  Mice were provided rodent chow (irradiated PicoLab 5053; LabDiet, St. Louis, MO) and water ad libitum until the experimental treatment.

extract_protocol: Tibialis Anterior muscle samples (~25 mg) were homogenized in Tri Reagent (Zymo, Irvine, CA).  Total RNA was then extracted using Zymo Direct-zol RNA Miniprep kit with on column DNase treatment according to manufacturer's instructions (cat. #R2051).   Samples were eluted from the columns with 25 ul of water.

treatment_protocol: Mice were fasted beginning at 1800 hr.  The next morning (~0800 hr), mice were randomized to remain fasted or were allowed to refeed for 30 minutes.  Following the refeeding, all mice were fasted for an additional 4 hr until sacrifice.  Those mice not refed also remained fasted until sacrifice at the same time of day as those mice that were refed.  At sacrifice, all mice were anesthetized with isoflurane, and the tibialis anterior muscle was extracted and flash frozen in liquid nitrogen, and stored at -80 degree C until analysis.

value: Tibialis Anterior muscle

tag: gender

value: Male

tag: age

value: 18 weeks

tag: stress

value: Refed


title: Refed_7


title: Refed_9


title: Fasted_3

description: Gene expression data from Tibialis Anterior of Fasted Mouse

source_name: Tibialis Anterior from Fasted Mouse

value: Fasted


title: S10-In-Vitro-NTC-1

growth_protocol: LLC-NT In Vitro samples: Lewis lung carcinoma cells stably expressing luciferase (LLC) were obtained from Caliper and maintained in 4.5 g/L glucose DMEM (Corning CellGro #19-017-CV) containing 10% fetal bovine serum, penicillin/streptomycin and G418 (500 ug/ml) and 2ug/ml puromycin for stable selection of cells harboring the non-targeting control shRNA plasmid.

value: LLC-NT In Vitro


title: S05-In-Vitro-sh21-1

growth_protocol: LLC-sh21 In Vitro samples: Lewis lung carcinoma cells stably expressing luciferase (LLC) were obtained from Caliper and maintained in 4.5 g/L glucose DMEM (Corning CellGro #19-017-CV) containing 10% fetal bovine serum, penicillin/streptomycin, G418 (500 ug/ml) and 2ug/ml puromycin for stable selection of cells harboring the Socs1 knockdown shRNA plasmid.

value: LLC-sh21 In Vitro


title: S02-LLC-NTC-GFP-3


title: S01-LLC-NTC-GFP-1


title: S12-In-Vitro-sh21-2


title: S11-In-Vitro-NTC-3

growth_protocol: LLC-NT In Vitro samples: Lewis lung carcinoma cells stably expressing luciferase (LLC) were obtained from Caliper and maintained in 4.5 g/L glucose DMEM (Corning CellGro #19-017-CV) containing 10% fetal bovine serum, penicillin/streptomycin, G418 (500 ug/ml) and 2ug/ml puromycin for stable selection of cells harboring the non-targeting control shRNA plasmid.


title: S06-In-Vitro-sh21-3


title: Control_2

city: Salt Lake City

first: Stephanie

last: Pearson

state: UT

address: 15 N Medical Drive East, Rm 4100

department: Biochemistry

institute: University of Utah

data_processing:
Fastq sequences were aligned with Novoalign (v. 2.8) against the mouse genome (UCSC release mm9) with splice junctions. Alignments to splice junctions were converted to genomic coordinates with USeq SamTranscriptomeParser (version 8.8.8).
RNASeq quality was evaluated by running Picard CollectRnaSeqMetrics.
Differential gene expression was identified using the USeq application DefinedRegionDifferentialSeq (version 8.8.8), which counts alignment tags over collapsed Ensembl gene annotation, executes the R DESeq2 application, filters the gene results at log2 ratio of 1.0 and -10log10(adjusted P) of 20, and reports the results.
Genome_build: Genome Build: mm9, M_musculus_Jul_2007, NCBI Build 37.
Supplementary_files_format_and_content: tab-delimited text files including counts and FPKM values

source_name: iWAT SVF

growth_protocol: TLE3F/F CreERT2 preadipocytes isolated from the inguinal white adipose tissue and immortalized with the Large T antigen were plated in a 12-well dish in DMEM, 10% FBS, 20 nM insulin, 1nM T3, with a seeding density of 0.1 x 106 cells per well. Upon confluence, cells were differentiated using DMEM media containing 10% FBS, 20nM insulin, 1nM T3, 0.5 mM isobutylmethylxanthine, 0.5 uM dexamethasone, 0.125 mM indomethacin and 1 uM rosiglitazone. After two days the media was changed to DMEM, 10% FBS, 20 nM insulin, 1nM T3 and 1 uM rosiglitazone. On the fourth day cells were treated with 4-hydroxytamoxifen or ethanol for 24 hours. Cells were harvested on the tenth day.

extract_protocol:
Cells were scraped and collected and RNA harvested using TRIzol standard protocol. RNA was further purified using QIAGEN RNeasy kit.
Intact poly(A) RNA was purified from total RNA samples (100-500 ng) with oligo(dT) magnetic beads and stranded mRNA sequencing libraries were prepared as described using the Illumina TruSeq Stranded mRNA Library Preparation Kit (RS-122-2101, RS-122-2102).

treatment_protocol: On the fourth day cells were either given 500 nM Tamoxifen to induce knockout of TLE3, or an equivalent volume of ethanol as a control, for 24 hours.

tag: background strain

tag: source tissue

value: inguinal white adipose tissue

tag: differentiation state

value: beige adipocytes

tag: genotype

value: TLE3F/F CreERT2

tag: treatment

value: EtOH


title: Fasted_1


title: S04-In-Vitro-NTC-2


title: TLE3 KO_1


title: Control _3


title: TLE3 KO_2


title: CMT_Pass_3

data_processing:
Read quality was checked using FastQC (http://www.bioinformatics. bbsrc.ac.uk/projects/fastqc).
Reads were trimmed to 95 bp using FASTQ Toolkit v2.2.0 application on Basespace Illumina analysis website (https://basespace.illumina.com/apps/3122120/FASTQ-Toolkit?preferredversion).
Samples were mapped to mouse genome and quantified using RNA-Seq Alignment v1.1.0 application on Basespace Illumina analysis website. The aligner software: STAR_2.5.0b with default parameters. Quantification: Cufflinks v.2.2.1 and Cuffnorm.(https://basespace.illumina.com/apps/3086084/RNA-Seq-Alignment?preferredversion)
Differential expression analysis was preformed using the Cufflinks Assembly & DE v 2.1.0 application on Basespace Illumina analysis website  using standard FPKM normalization. (https://basespace.illumina.com/apps/3088085/Cufflinks-Assembly-DE?preferredversion)
Genome_build: mm10
Supplementary_files_format_and_content: Matrix with normalized abundance measurements (FPKM)

growth_protocol: CMT Pass samples: CMT cells isolated from tumors as described above (CMT In Vivo samples) were replated and cultured in vitro under standard conditions (as described in CMT in Vitro).

treatment_protocol: not applicable

tag: cell line

value: CMT167 (CMT)

tag: protocol

value: Pass


title: CMT_Pass_2


title: CMT_Pass_1


title: Fasted_5

tag: tissue


title: CMT_InVivo_3

growth_protocol: CMT In Vivo samples: CMT cells (1x10^5 in 40 µl per injection) were suspended in PBS containing 15% Growth Factor Reduced Matrigel (BD Biosciences, cat# 354230) and injected into the parenchyma of the left lung lobe of mice, as described (Poczobutt et al., J Immunol. 2016 Jan 15;196(2):891-901). Cells were injected into 8-12 week old C57BL/6 male mice, which expressed green fluorescent protein (C57BL/6-Tg(UBC-GFP)30Scha/J, Jackson Laboratory, Bar Harbor, ME). Mice were sacrificed 4 weeks after injection, tumors were harvested and processed into single cell suspension as described (ref macrophage paper). Cell sorting was performed at the University of Colorado Cancer Center Flow Cytometry Shared Resource using an XDP-100 cell sorter (Beckman Coulter). The sorting strategy excluded debris and cell doublets by light scatter and dead cells by DAPI. CMT cells were separated from murine host cells by sorting for GFP-negative cells. Cells were pelleted and RNA was extracted. Animals were bred and maintained in the Center for Comparative Medicine at the University of Colorado Denver, Anschutz Medical Campus. All procedures were performed under protocols approved by the Institutional Animal Care and Use Committee at the University of Colorado Denver.

value: InVivo


title: CMT_InVivo_2


title: CMT_InVivo_1


title: CMT_InVitro_1

growth_protocol: CMT In Vitro samples: CMT167 cells (CMT) that were expressing luciferase (Weiser-Evans, et al., Cancer Res. 2009 Mar 1;69(5):1733-8) were cultured in 1 g/L DMEM containing 10% FBS, penicillin/streptomycin, MEM Non-Essential Amino Acids, 10 mM HEPES, and 500 ug/mL G418.

value: InVitro


title: CMT_InVitro_2


title: Control_1


title: CMT_InVitro_3


title: LLC_Pass_5

growth_protocol: LLC Pass samples: LLC cells isolated from tumors as described above (LLC In Vivo samples) were replated and cultured in vitro under standard conditions (as described in LLC in Vitro).

value: Lewis Lung carcinoma (LLC)


title: TLE3 KO_3


title: E. cyaneus, control, 24 hours, sample 1

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 3 days and kept at 6 degrees C for 24 hours (parallel control).
EcyB24_1
differential expression file:
EcyCd24_annot.csv
Ecy10LT24_annot.csv
EcyPB24_annot.csv

value: whole body

value: rocky littoral zone

value: Russia:Irkutsk region, Lake Baikal, Bolshie Koty village

value: Till Luckenbach, Daria Bedulina

value: adult

value: littoral zone

value: Maxim Timofeyev, Daria Bedulina


title: LLC_Pass_3


title: LLC_Pass_1


title: LLC_Pass_2


title: LLC_InVivo_5

growth_protocol: LLC In Vivo samples: LLC cells (1x10^5 in 40 µl per injection) were suspended in PBS containing 15% Growth Factor Reduced Matrigel (BD Biosciences, cat# 354230) and injected into the parenchyma of the left lung lobe of mice, as previously described (Poczobutt et al., J Immunol. 2016 Jan 15;196(2):891-901). Cells were injected into 8-12 week old C57BL/6 male mice, which expressed green fluorescent protein (C57BL/6-Tg(UBC-GFP)30Scha/J, Jackson Laboratory, Bar Harbor, ME). Mice were sacrificed 3 weeks after injection, tumors were harvested and processed into single cell suspension as described (Poczobutt et al., J Immunol. 2016 Jan 15;196(2):891-901). Cell sorting was performed at the University of Colorado Cancer Center Flow Cytometry Shared Resource using an XDP-100 cell sorter (Beckman Coulter). The sorting strategy excluded debris and cell doublets by light scatter and dead cells by DAPI. LLC cells were separated from murine host cells by sorting for GFP-negative cells. Cells were pelleted and RNA was extracted. Animals were bred and maintained in the Center for Comparative Medicine at the University of Colorado Denver, Anschutz Medical Campus. All procedures were performed under protocols approved by the Institutional Animal Care and Use Committee at the University of Colorado Denver.


title: LLC_InVivo_4


title: HeLa, GFP+fed16

first: Rytis

last: Prekeris

state: CO

address: 12801 East 17th Ave, Bldg RC1 S, Room L18-12402C, None

description:
scRNAseq grouped FDR .01 ALL GENES
4_Hela_GFPplus_4

data_processing:
For all data files: FASTQ files were then mapped to Human Genome Sequence using the Tophat aligner algorithm (Trapnell, Pachter and Salzberg, 2009) under the single-end read setting.  The count table was generated using Bioconductor package; GenomicAlignments 49. The resulting SAM/BAM files were processed, filtered and eventually perform differentially expression analysis using the Ritchie al.et algorithm 50.  We used statistical programming packages from the Bioconductor consortium (www.bioconductor.org) for downstream data analysis, annotation and visualization. Briefly, count data were filtered to remove genes with zero count. The data were further normalized with the "edgeR" package, followed by the "limma" package with its "voom" method, linear modeling and empirical Bayes moderation to assess differential expression.  Genes annotation were perform using the "AnnotationDbi" package. The Principal Component Analysis (PCA) visualization was perform using the "ggplot2" package.  The heatmaps were generated using the "Heatplus" package. For annotation cluster analysis, all genes were assessed by the DAVID Bioinformatics tool for clustering.
Genome_build: GrCh38
Supplementary_files_format_and_content: Spreadsheet format representing read counts

organism: Homo sapiens

source_name: HeLa

extract_protocol:
HeLa MKLP1-GFP cells were sorted into low GFP or high GFP populations and processed using TriZOL or Qiagen RNeasy micro
RNA libraries were prepared for sequencing using standard Illumina protocols (TruSeq kit)

value: HeLa MKLP1-GFP

tag: gfp-sorted cells

value: GFP+fed

value: +fed


title: HeLa, GFP+fed12

description:
scRNAseq grouped FDR .01 ALL GENES
4_Hela_GFPplus_3


title: HeLa, GFP+fed13


title: HeLa, GFP+fed14


title: LLC_InVitro_1

growth_protocol: LLC In Vitro samples: Lewis lung carcinoma cells stably expressing luciferase (LLC) were obtained from Caliper and maintained in 4.5 g/L glucose DMEM (Corning CellGro #19-017-CV) containing 10% fetal bovine serum, penicillin/streptomycin and G418 (500 ug/ml).


title: LLC_InVitro_5


title: LLC_InVitro_2


title: LLC_InVitro_3


title: LLC_InVitro_4


title: LLC_InVivo_1


title: HeLa, GFP+fed11


title: HeLa, GFP+fed10


title: HeLa, GFP+fed9


title: HeLa, GFP+fed8

description:
scRNAseq grouped FDR .01 ALL GENES
4_Hela_GFPplus_2


title: LLC_Pass_4


title: HeLa, GFP+fed6


title: HeLa, GFP+fed7


title: HeLa, GFP+fed5


title: HeLa, GFP+fed4

description:
scRNAseq grouped FDR .01 ALL GENES
4_Hela_GFPplus_1


title: LLC_InVivo_2


title: HeLa, GFP+fed2


title: HeLa, GFP+fed3


title: HeLa, GFP+fed1


title: E. verrucosus, gradual temperature increase, 24 degrees C, sample 4

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 5 days, kept at rising (0.8 degrees C per day) temperature and fixed after 23 days at 24.4 degrees C.
EveT24_4
differential expression file:
EveT24annot.csv

organism: Eulimnogammarus verrucosus

tag: depth


title: E. verrucosus, gradual temperature increase, 24 degrees C, sample 3

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 5 days, kept at rising (0.8 degrees C per day) temperature and fixed after 23 days at 24.4 degrees C.
EveT24_3
differential expression file:
EveT24annot.csv

tag: condition


title: G. lacustris, gradual temperature increase, 24 degrees C, sample 2

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 5 days, kept at rising (0.8 degrees C per day) temperature and fixed after 23 days at 24.4 degrees C.
GlaT24_3
differential expression file:
GlaT24annot.csv

organism: Gammarus lacustris

value: Russia:Irkutsk region, Bolshie Koty village, Lake No14


title: HeLa, GFP-fed13

description:
scRNAseq grouped FDR .01 ALL GENES
3_Hela_GFPminus_4

value: GFP-fed

value: -fed


title: HeLa, GFP-fed15


title: HeLa, GFP-fed10

description:
scRNAseq grouped FDR .01 ALL GENES
3_Hela_GFPminus_3


title: HeLa, GFP-fed11


title: HeLa, GFP-fed12


title: G. lacustris, gradual temperature increase, 24 degrees C, sample 1

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 5 days, kept at rising (0.8 degrees C per day) temperature and fixed after 23 days at 24.4 degrees C.
GlaT24_2
differential expression file:
GlaT24annot.csv


title: E. verrucosus, gradual temperature increase, 24 degrees C, sample 2

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 5 days, kept at rising (0.8 degrees C per day) temperature and fixed after 23 days at 24.4 degrees C.
EveT24_2
differential expression file:
EveT24annot.csv


title: E. verrucosus, gradual temperature increase, 18 degrees C, sample 4

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 5 days, kept at rising (0.8 degrees C per day) temperature and fixed after 15 days at 18 degrees C.
EveT18_4
differential expression file:
EveT18annot.csv


title: E. verrucosus, gradual temperature increase, 24 degrees C, sample 1

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 5 days, kept at rising (0.8 degrees C per day) temperature and fixed after 23 days at 24.4 degrees C.
EveT24_1
differential expression file:
EveT24annot.csv


title: G. lacustris, gradual temperature increase, 18 degrees C, sample 4

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 5 days, kept at rising (0.8 degrees C per day) temperature and fixed after 15 days at 18 degrees C.
GlaT18_4
differential expression file:
GlaT18annot.csv


title: E. verrucosus, gradual temperature increase, 18 degrees C, sample 3

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 5 days, kept at rising (0.8 degrees C per day) temperature and fixed after 15 days at 18 degrees C.
EveT18_3
differential expression file:
EveT18annot.csv


title: G. lacustris, gradual temperature increase, 24 degrees C, sample 3

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 5 days, kept at rising (0.8 degrees C per day) temperature and fixed after 23 days at 24.4 degrees C.
GlaT24_4
differential expression file:
GlaT24annot.csv


title: HeLa, GFP-fed9


title: U251-TRPV2-KD-PL_Replica3

city: Homburg (Saar)

first: Marc

last: Remke

state: Saarland

address: Kirrberger Straße 100, Gebäude 9

department: Pediatric Translational Oncology Lab

country: Germany

institute: Universitätsklinikum des Saarlandes

description:
48 hours post treatment
Picard_22_05_2019_processed_matrix.txt

data_processing:
Fastq files were imported into Partek Flow (Partek Incorporated, Missouri, USA).
Quality analysis and quality control were performed on all reads to assess read quality and to determine the amount of trimming required (both ends: 13 bases 5´and 1 base 3´).
Trimmed reads were aligned against the hg38 genome using the STAR v2.4.1d aligner. Unaligned reads were further processed using Bowtie 2 v2.2.5 aligner.
Aligned reads were combined before quantifying the expression against the ENSEMBL (release 84) database by the Partek Expectation-Maximization algorithm using the counts per million normalization.
Genes with missing values and with a mean expression less than one were filtered out
Genome_build: hg38
Supplementary_files_format_and_content: txt

extract_protocol:
500 ng total RNA was processed using the TruSeq RNA Sample Preparation v2 Kit (low-throughput protocol; Illumina, San Diego, USA) to prepare the barcoded libraries.
Libraries were validated and quantified using DNA 1000 and high-sensitivity chips on a Bioanalyzer (Agilent, Böblingen, Germany); 7.5 pM denatured libraries were used as input into cBot (Illumina), followed by deep sequencing using HiSeq 2500 (Illumina) for 101 cycles, with an additional seven cycles for index reading.

treatment_protocol: samples were treated with either DMSO or Piperlongumine and extracted 48 hours post-treatment

tag: modification

value: TRPV2 CRISPRi KD

value: Piperlongumine

tag: replica


title: HeLa, GFP+fed15

description:
scRNAseq grouped FDR .01 ALL GENES
4_Hela_GFPplus_4


title: LLC_InVivo_3

tag: strain

value: InVivo


title: G. lacustris, gradual temperature increase, 18 degrees C, sample 3

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 5 days, kept at rising (0.8 degrees C per day) temperature and fixed after 15 days at 18 degrees C.
GlaT18_3
differential expression file:
GlaT18annot.csv


title: E. verrucosus, gradual temperature increase, 18 degrees C, sample 2

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 5 days, kept at rising (0.8 degrees C per day) temperature and fixed after 15 days at 18 degrees C.
EveT18_2
differential expression file:
EveT18annot.csv


title: HeLa, GFP-fed16


title: HeLa, GFP-fed8

description:
scRNAseq grouped FDR .01 ALL GENES
3_Hela_GFPminus_2


title: U251-TRPV2-KD-PL_Replica2


title: G. lacustris, gradual temperature increase, 18 degrees C, sample 2

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 5 days, kept at rising (0.8 degrees C per day) temperature and fixed after 15 days at 18 degrees C.
GlaT18_2
differential expression file:
GlaT18annot.csv


title: HeLa, GFP-fed14


title: U251-TRPV2-KD-PL_Replica1


title: E. verrucosus, gradual temperature increase, 18 degrees C, sample 1

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 5 days, kept at rising (0.8 degrees C per day) temperature and fixed after 15 days at 18 degrees C.
EveT18_1
differential expression file:
EveT18annot.csv


title: G. lacustris, gradual temperature increase, 18 degrees C, sample 1

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 5 days, kept at rising (0.8 degrees C per day) temperature and fixed after 15 days at 18 degrees C.
GlaT18_1
differential expression file:
GlaT18annot.csv


title: HeLa, GFP-fed6


title: E. verrucosus, gradual temperature increase, 12 degrees C, sample 3

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 5 days, kept at rising (0.8 degrees C per day) temperature and fixed after 8 days at 12.4 degrees C.
EveT12_3
differential expression file:
EveT12annot.csv


title: U251-TRPV2-KD_Replica2

value: DMSO


title: E. verrucosus, gradual temperature increase, 12 degrees C, sample 2

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 5 days, kept at rising (0.8 degrees C per day) temperature and fixed after 8 days at 12.4 degrees C.
EveT12_2
differential expression file:
EveT12annot.csv

value: whole body


title: U251-TRPV2-KD_Replica3


title: HeLa, GFP-fed5


title: G. lacustris, gradual temperature increase, 12 degrees C, sample 4

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 5 days, kept at rising (0.8 degrees C per day) temperature and fixed after 8 days at 12.4 degrees C.
GlaT12_4
differential expression file:
GlaT12annot.csv

value: rocky littoral zone


title: E. verrucosus, gradual temperature increase, 12 degrees C, sample 1

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 5 days, kept at rising (0.8 degrees C per day) temperature and fixed after 8 days at 12.4 degrees C.
EveT12_1
differential expression file:
EveT12annot.csv

value: Russia:Irkutsk region, Lake Baikal, Bolshie Koty village


title: G. lacustris, gradual temperature increase, 12 degrees C, sample 3

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 5 days, kept at rising (0.8 degrees C per day) temperature and fixed after 8 days at 12.4 degrees C.
GlaT12_3
differential expression file:
GlaT12annot.csv

value: Till Luckenbach, Daria Bedulina


title: U251-PL_Replica3

value: wt


title: HeLa, GFP-fed3

description:
scRNAseq grouped FDR .01 ALL GENES
3_Hela_GFPminus_1


title: G. lacustris, gradual temperature increase, 12 degrees C, sample 2

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 5 days, kept at rising (0.8 degrees C per day) temperature and fixed after 8 days at 12.4 degrees C.
GlaT12_2
differential expression file:
GlaT12annot.csv

value: adult

value: littoral zone


title: E. verrucosus, parallel control for EveT24, sample 4

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 5 days and kept at 6 degrees C for 23 days (parallel control for gradual temperature rise).
EveB24_4
differential expression file:
EveT24annot.csv

value: Maxim Timofeyev, Daria Bedulina


title: G. lacustris, gradual temperature increase, 12 degrees C, sample 1

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 5 days, kept at rising (0.8 degrees C per day) temperature and fixed after 8 days at 12.4 degrees C.
GlaT12_1
differential expression file:
GlaT12annot.csv


title: U251-PL_Replica2

description:
48 hours post treatment
Picard_22_05_2019_processed_matrix.txt


title: HeLa, GFP-fed2

value: HeLa MKLP1-GFP


title: U251-PL_Replica1


title: HeLa, GFP-fed1


title: G. lacustris, parallel control for GlaT24, sample 4

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 5 days and kept at 6 degrees C for 23 days (parallel control for gradual temperature rise).
GlaB24_4_7
differential expression file:
GlaT24annot.csv


title: E. verrucosus, parallel control for EveT24, sample 1

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 5 days and kept at 6 degrees C for 23 days (parallel control for gradual temperature rise).
EveB24_1_6
differential expression file:
EveT24annot.csv


title: HeLa, GFP-fed7


title: E. verrucosus, parallel control for EveT24, sample 3

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 5 days and kept at 6 degrees C for 23 days (parallel control for gradual temperature rise).
EveB247
differential expression file:
EveT24annot.csv


title: HeLa, GFP high 3

description:
GFP lo vs GFP hi original.xls
H3_GCCAAT

value: GFP high


title: E. verrucosus, parallel control for EveT18, sample 4

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 5 days and kept at 6 degrees C for 15 days (parallel control for gradual temperature rise).
EveB18_4
differential expression file:
EveT18annot.csv


title: G. lacustris, parallel control for GlaT24, sample 3

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 5 days and kept at 6 degrees C for 23 days (parallel control for gradual temperature rise).
GlaB247
differential expression file:
GlaT24annot.csv

value: Russia:Irkutsk region, Bolshie Koty village, Lake No14


title: U251-TRPV2-KD_Replica1


title: U251_Replica3


title: G. lacustris, parallel control for GlaT24, sample 2

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 5 days and kept at 6 degrees C for 23 days (parallel control for gradual temperature rise).
GlaB24_2_6
differential expression file:
GlaT24annot.csv


title: U251_Replica2


title: HeLa, GFP-fed4

value: GFP-fed


title: E. verrucosus, parallel control for EveT18, sample 3

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 5 days and kept at 6 degrees C for 15 days (parallel control for gradual temperature rise).
EveB18_3
differential expression file:
EveT18annot.csv


title: U251_Replica1


title: G. lacustris, parallel control for GlaT24, sample 1

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 5 days and kept at 6 degrees C for 23 days (parallel control for gradual temperature rise).
GlaB24_1_6
differential expression file:
GlaT24annot.csv


title: HeLa, GFP high 2

description:
GFP lo vs GFP hi original.xls
H2_ACAGTG


title: E. verrucosus, parallel control for EveT18, sample 2

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 5 days and kept at 6 degrees C for 15 days (parallel control for gradual temperature rise).
EveB18_2
differential expression file:
EveT18annot.csv


title: G. lacustris, parallel control for GlaT18, sample 3

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 5 days and kept at 6 degrees C for 15 days (parallel control for gradual temperature rise).
GlaB18_3
differential expression file:
GlaT18annot.csv


title: E. verrucosus, parallel control for EveT18, sample 1

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 5 days and kept at 6 degrees C for 15 days (parallel control for gradual temperature rise).
EveB18_1
differential expression file:
EveT18annot.csv


title: HeLa, GFP low 3

description:
GFP lo vs GFP hi original.xls
L3_CAGATC

value: GFP low


title: chr5

city: Ithaca

first: Jian

last: Hua

state: NY

address: 158 Emerson Hall

department: Plant Biology

institute: Cornell University

description: Nucleosome occupied DNA

data_processing:
Using BWA aln (0.7.5a) to align reads to Arabidopsis thaliana reference genome v10 with default setting
BEDtools coverage (2.19.1) was used to count read coveage in a 10kb sliding window, with output in a bed file.
Genome_build: Arabidopsis thaliana reference genome v10
Supplementary_files_format_and_content: The bed files were generated wtth bedtools coverage. The  numbers are read counts in the 10kb sliding windows.

organism: Arabidopsis thaliana

source_name: leaf

growth_protocol: 22C, on plate

extract_protocol:
Mnase digest
standard genomic DNA library construction

treatment_protocol: no treatment

tag: genotype/variation


title: G. lacustris, parallel control for GlaT18, sample 2

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 5 days and kept at 6 degrees C for 15 days (parallel control for gradual temperature rise).
GlaB18_2
differential expression file:
GlaT18annot.csv


title: wild type

description: Nucleosome occupied DNA

value: wild type


title: HeLa, GFP low 2

description:
GFP lo vs GFP hi original.xls
L2_TGACCA


title: G. lacustris, parallel control for GlaT18, sample 1

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 5 days and kept at 6 degrees C for 15 days (parallel control for gradual temperature rise).
GlaB18_1
differential expression file:
GlaT18annot.csv


title: E. verrucosus, parallel control for EveT12, sample 4

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 5 days and kept at 6 degrees C for 8 days (parallel control for gradual temperature rise).
EveB12_4
differential expression file:
EveT12annot.csv


title: G. lacustris, parallel control for GlaT12, sample 4

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 5 days and kept at 6 degrees C for 8 days (parallel control for gradual temperature rise).
GlaB12_4
differential expression file:
GlaT12annot.csv


title: E. verrucosus, parallel control for EveT12, sample 2

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 5 days and kept at 6 degrees C for 8 days (parallel control for gradual temperature rise).
EveB12_2
differential expression file:
EveT12annot.csv


title: G. lacustris, parallel control for GlaT12, sample 3

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 5 days and kept at 6 degrees C for 8 days (parallel control for gradual temperature rise).
GlaB12_3
differential expression file:
GlaT12annot.csv


title: E. verrucosus, parallel control for EveT12, sample 1

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 5 days and kept at 6 degrees C for 8 days (parallel control for gradual temperature rise).
EveB12_1
differential expression file:
EveT12annot.csv


title: HeLa, GFP low 1

description:
GFP lo vs GFP hi original.xls
L1_CGATGT


title: G. lacustris, parallel control for GlaT12, sample 2

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 5 days and kept at 6 degrees C for 8 days (parallel control for gradual temperature rise).
GlaB12_2
differential expression file:
GlaT12annot.csv


title: HeLa, GFP high 1

description:
GFP lo vs GFP hi original.xls
H1_CCGTCC


title: CNV 1

city: Changsha

first: Yedi

last: Zhou

state: Hunan

address: No. 139, Middle Renmin Road

department: Department of Ophthalmology

country: China

institute: The Second Xiangya Hospital, Central South University

description: miRNAs and tsRNAs expression data from samples of laser-induced CNV mice

data_processing:
Raw sequencing data generated form Illumina NextSeq 500 system that pass the Illumina chastity filter are used for the following sequence analysis.
Trimmed reads (trimmed 5’, 3’-adaptor bases) are aligned allowing for 1 mismatch only to the mature tRNA sequences, then reads that do not map are aligned allowing for 1 mismatch only to precursor tRNA sequences with bowtie software.
The remaining reads are aligned allowing for 1 mismatch only to miRNA reference sequences with miRDeep2.
Based on alignment statistical analysis (mapping ratio,read length,fragment sequence bias),we determine whether the results can be used for subsequent data analysis. If so, the expression profiling and differentially expressed tRFs & tiRNAs and miRNAs are calculated.
Principal Component Analysis (PCA), Correlation Analysis, Pie plots, Vennplots, Hierarchical clustering, Scatter plots and Volcano plots are performed for the expressed tRF & tiRNA in R or perl environment for statistical computing and graphics.
Genome_build: The mature tRNA libraries and precursor tRNA libraries： tRNA sequences of cytoplasmic were downloaded from GtRNAdb.tRNA sequences of mitochondrial were predicted with tRNAscan-SE software. miRNA:miRbase
Supplementary_files_format_and_content: txt file includes CPM

source_name: RPE-choroid-sclera complexes

growth_protocol: The animals were maintained in cages in temperature-controlled rooms featuring a 12-h light/12-h dark cycle.

extract_protocol:
RNA was isolated from the RPE-choroid-sclera complexes following instructions of the manufacturer using Trizol RNA extraction kit (Invitrogen,Carlsbad,CA,USA). RPE-choroid-sclera complexes from 4 eyes were pooled as one sample.
For each sample, the total RNA was sequentially ligated to 3’ and 5’ small RNA adapters.cDNA synthesis and library PCR amplification were then performed by Illumina’s proprietary RT primers and amplification primers. Subsequently, ~134-160 bp PCR amplified fragments (corresponding to 14∼40nt small RNA size range) were extracted and purified from the PAGE gel.
The prepared tsRNAs-seq libraries are finally quantified by Agilent BioAnalyzer 2100 (Agilent Technologies,Santa Clara,CA,USA).The diluted libraries were loaded onto reagent cartridge and forwarded to the sequencing run by using Illumina NextSeq 500 system (Illumina, San Diego, CA,USA) with NextSeq 500/550 V2 kit (Illumina).

treatment_protocol: The photocoagulation was applied in eyes of mice around the optic disc using a 532-nm diode laser (100 mW, 0.1 s duration, 50 μm).  Twenty-five spots were burned on each eye, and the eyes were enucleated at 7 days after the laser photocoagulation. Age-matched mice without laser photocoagulation treatment were used as controls.

value: RPE-choroid-sclera complexes

tag: disease state

value: laser-induced CNV eye (7 days after the laser photocoagulation)

tag: age

value: Seven to eight-week-old

tag: Sex

value: male


title: CNV 3


title: CNV 2


title: E. verrucosus, parallel control for EveT12, sample 3

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 5 days and kept at 6 degrees C for 8 days (parallel control for gradual temperature rise).
EveB12_3
differential expression file:
EveT12annot.csv

value: whole body

value: rocky littoral zone


title: E. verrucosus, initial control for EveT, sample 3

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 5 days (initial control).
EveB6_3
differential expression file:

value: Russia:Irkutsk region, Lake Baikal, Bolshie Koty village

value: Till Luckenbach, Daria Bedulina


title: comp2

city: Cambridge

first: Murray

last: Tipping

state: MA

address: 16 Divinity Ave

department: MCB

institute: Harvard University

description:
processed mRNA
TippingGibbs2019.xlsx

data_processing:
Basecalling done in Bauer core with Illumina CASAVA 1.8
Sequences were matched to BB2000 reference genome PMID: 24009111 using TopHat2, default arguments
mRNA abundance data were generated using Cufflinks 2.1.1, max-multiread-fraction 0.9, -multi-read-correct
Samples combined using cuffmerge, default arguments
Differential expression data were generated using Cuffdiff 2.1.1, total-hits-norm
Genome_build: PMID: 24009111
Supplementary_files_format_and_content: 1 xlsx file containing complete Cuffdiff output, including differential expression data

molecule: polyA RNA

organism: Proteus mirabilis

source_name: CCS01 consolidator cells

growth_protocol: Samples were grown on CM55 swarming agar and harvested by scraping into RNA-Protect solution

extract_protocol:
Lysates were prepared from RNA-protect cell suspension using RNEasy minikit. rRNA was digested with terminator 5' phosphate dependent exonuclease according to manufacturer's instructions.
Libraries were constructed using NEBNext Ultra library prep kit.

value: delta_ids complemented by a vector containing the ids operon


title: G. lacustirs, initial control for GlaT, sample 4

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 5 days (initial control).
GlaB6_4
differential expression file:

value: adult

value: littoral zone


title: comp1

description:
processed mRNA
TippingGibbs2019.xlsx


title: E. verrucosus, initial control for EveT, sample 4

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 5 days (initial control).
EveB6_4
differential expression file:

value: Maxim Timofeyev, Daria Bedulina


title: E. verrucosus, initial control for EveT, sample 2

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 5 days (initial control).
EveB6_2
differential expression file:


title: G. lacustirs, initial control for GlaT, sample 3

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 5 days (initial control).
GlaB6_3
differential expression file:


title: E. verrucosus, initial control for EveT, sample 1

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 5 days (initial control).
EveB6_1
differential expression file:


title: Control 2

description: miRNAs and tsRNAs expression data from samples of normal mice

value: normal eye


title: 966-1

description:
processed mRNA
TippingGibbs2019.xlsx

source_name: Sorted ∆ids consolidator cells from coswarms

value: delta_ids strain constitutively expressing GFPmut2


title: Control 1


title: G. lacustirs, initial control for GlaT, sample 2

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 5 days (initial control).
GlaB6_2
differential expression file:

value: Russia:Irkutsk region, Bolshie Koty village, Lake No14


title: G. lacustris, parallel control for GlaT12, sample 1

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 5 days and kept at 6 degrees C for 8 days (parallel control for gradual temperature rise).
GlaB12_1
differential expression file:
GlaT12annot.csv


title: E. verrucosus, 1 mg/L phenanthrene, 24 hours, sample 4

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 3 days and subjected to 1 mg/L phenanthrene for 24 hours.
EveP24_4
differential expression file:
EvePh24_annot.csv


title: G. lacustirs, initial control for GlaT, sample 1

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 5 days (initial control).
GlaB6_1
differential expression file:


title: B lymphoblastoid cells (from patient with multiple myeloma) 1

type: genomic

city: Madrid

first: Inmaculada

last: Rapado

address: Avenida Cordoba s/n

country: Spain

institute: Hospital Universitario 12 de Octubre

description:
ACC 117-DSMZ
Test sample: 15 days 0.01 µM folate + 15 days normal medium; Control sample: 30 days normal medium

hyb_protocol: Hybridization and washing was done according to Agilent protocol (65ºC 24h, 20rpm in hyb chambers)

scan_protocol: Scanned on an Agilent G2565C scanner (3um and Cy5/Cy3 analysis). Images were quantified using Agilent Feature Extraction Software (version 10.7.1).

data_processing: Agilent Genomic Workbench using HMM algorithm (state copy number = 7, FDRQ < 0.01) for aberration detection

label_protocol: 500 ng were labeled using Agilent CGH enzymatic protocol 7.2 (Agilent Technologies)

growth_protocol: Cell lines were cultured in 2 mL RPMI 1640 supplemented with 10% foetal bovine serum, 100 U/mL penicillin G and 100 mg/mL streptomycin (Life Technologies, Carlsbad, CA, and were incubated at 37ºC and 5% CO2. Folate depletion studies were conducted while maintaining the cells in RPMI without folate and supplementing with 0, 0.01, or 1 µM of folic acid (Sigma Aldrich, St. Louis, MO).

extract_protocol: Genomic DNA was extracted using AllPrep DNA/RNA Micro Kit (Qiagen, Venlo, The Netherlands)

tag: growth protocol

value: 0.01 µM folate medium

source_name: pooled IM9 normal folate medium

value: 30 days normal medium


title: 17-dids

description:
processed mRNA
TippingGibbs2019.xlsx

source_name: ∆ids consolidator cells

value: BB2000 with ids locus deleted


title: E. verrucosus, 1 mg/L phenanthrene, 24 hours, sample 3

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 3 days and subjected to 1 mg/L phenanthrene for 24 hours.
EveP24_3
differential expression file:
EvePh24_annot.csv


title: G. lacustris, 1 mg/L phenanthrene, 24 hours, sample 4

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 3 days and  subjected to 1 mg/L phenanthrene for 24 hours.
GlaP24_4
differential expression file:
GlaPh24_annot.csv


title: Control 3

value: RPE-choroid-sclera complexes


title: G. lacustris, 1 mg/L phenanthrene, 24 hours, sample 3

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 3 days and  subjected to 1 mg/L phenanthrene for 24 hours.
GlaP24_3
differential expression file:
GlaPh24_annot.csv


title: 966-2

description:
processed mRNA
TippingGibbs2019.xlsx


title: E. verrucosus, 1 mg/L phenanthrene, 24 hours, sample 1

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 3 days and subjected to 1 mg/L phenanthrene for 24 hours.
EveP24_1
differential expression file:
EvePh24_annot.csv


title: G. lacustris, 1 mg/L phenanthrene, 24 hours, sample 2

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 3 days and  subjected to 1 mg/L phenanthrene for 24 hours.
GlaP24_2
differential expression file:
GlaPh24_annot.csv


title: 15-dids

description:
processed mRNA
TippingGibbs2019.xlsx


title: Dex-2

description:
processed mRNA
TippingGibbs2019.xlsx

source_name: CCS02 consolidator cells

value: delta_ids complemented by a vector containing the ids operon, where the variable region of idsD was replaced with that of the variable region of P. mirabilis strain HI4320


title: E. verrucosus, 1 mg/L phenanthrene, 3 hours, sample 4

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 3 days and subjected to 1 mg/L phenanthrene for 3 hours.
EveP3_4
differential expression file:
EvePh3_annot.csv


title: E. verrucosus, 1 mg/L phenanthrene, 24 hours, sample 2

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 3 days and subjected to 1 mg/L phenanthrene for 24 hours.
EveP24_2
differential expression file:
EvePh24_annot.csv


title: 17-didsE

description:
processed mRNA
TippingGibbs2019.xlsx

source_name: CCS06 consolidator cells

value: delta_ids partially complemented with plasmid carrying idsabcdf


title: G. lacustris, 1 mg/L phenanthrene, 24 hours, sample 1

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 3 days and  subjected to 1 mg/L phenanthrene for 24 hours.
GlaP24_1
differential expression file:
GlaPh24_annot.csv

value: whole body


title: B cell lymphoma 1

description:
ACC 47-DSMZ
Test sample: 15 days without folate + 15 days normal medium; Control sample: 30 days normal medium

value: medium without folate

source_name: pooled DOHH2 normal folate medium


title: Dex-1

description:
processed mRNA
TippingGibbs2019.xlsx


title: 10_me3BKO (replicate of 09)

city: San Diego

first: Brian

middle: Patrick

last: James

state: CA

address: 10901 North Torrey Pines Road

department: Genomics

institute: Sanford Burnham Prebys Medical Discovery Institute

data_processing:
Adapter remnants of sequencing reads were removed using cutadapt v1.18 (Martin, 2011).
ChIP-Seq sequencing reads were aligned using STAR aligner version 2.7 to Mouse genome version 38 (Dobin et al., 2013).
Homer v4.10 (Heinz et al., 2010) was used to call peaks from ChIP-Seq samples by comparing the ChIP samples with matching input samples. Homer v4.10 was used to annotate peaks to mouse genes, and quantify reads count to peaks.
The raw reads count for different peaks were compared using DESeq2 (Love et al., 2014). P values from DESeq2 was corrected using Benjamini & Hochberg (BH) method for multiple testing errors (Benjamini and Hochberg, 1995).
Genome_build: Mouse genome version 38
Supplementary_files_format_and_content: Big Wig files

source_name: dissected embryonic trunk tissue

growth_protocol: Mice were maintained on normal chow.

extract_protocol:
Total genomic DNA for all samples (except input) were extracted following immunoprecipitation using the Pierce Magnetic ChIP Kit (Thermo Scientific, Cat# 26157) following the manufacturer’s instructions. Antibodies used were specific for either H3K27ac or H3K27me3 (Active Motif). Genomic DNA for input samples were prepared using the same protocol but without immunoprecipitation.
Libraries were prepared according to NEB's instructions accompanying the NEBNext DNA Ultra II kit (catalog # E7645S).  Libraries were sequenced on the NextSeq 500 following the manufacturer's protocols.

value: Raldh2 (Aldh1a2) knockout

value: outbred

value: stage E8.5 embryo

tag: chip antibody

value: H3K27me3 (Active Motif, Cat#39155)


title: 07_acAKO

tag: genotype

value: H3K27ac (Active Motif, Cat#39133)


title: 06_inputKO


title: 08_acBKO (replicate of 07)


title: 09_me3AKO


title: B lymphoblastoid cells (from patient with multiple myeloma) 2

description:
ACC 117-DSMZ
Test sample: 15 days without folate + 15 days normal medium; Control sample: 30 days normal medium


title: E. verrucosus, 1 mg/L phenanthrene, 3 hours, sample 3

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 3 days and subjected to 1 mg/L phenanthrene for 3 hours.
EveP3_3
differential expression file:
EvePh3_annot.csv

source_name: whole body

value: rocky littoral zone

value: Russia:Irkutsk region, Lake Baikal, Bolshie Koty village

value: Till Luckenbach, Daria Bedulina

value: adult

value: littoral zone

value: Maxim Timofeyev, Daria Bedulina


title: B cell lymphoma 2

description:
ACC 47-DSMZ
Test sample: 15 days 0.01 µM folate + 15 days normal medium; Control sample: 30 days normal medium

value: 0.01 µM folate medium

value: 30 days normal medium


title: 15-didsE

description:
processed mRNA
TippingGibbs2019.xlsx


title: G. lacustris, 1 mg/L phenanthrene, 3 hours, sample 4

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 3 days and subjected to 1 mg/L phenanthrene for 3 hours.
GlaP3_4
differential expression file:
GlaPh3_annot.csv

value: Russia:Irkutsk region, Bolshie Koty village, Lake No14


title: E. verrucosus, 1 mg/L phenanthrene, 3 hours, sample 2

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 3 days and subjected to 1 mg/L phenanthrene for 3 hours.
EveP3_2
differential expression file:
EvePh3_annot.csv


title: 04_me3AWT

value: wild-type


title: 17-BB

description:
processed mRNA
TippingGibbs2019.xlsx

source_name: Wildtype consolidator cells

value: wildtype


title: E. verrucosus, 1 mg/L phenanthrene, 3 hours, sample 1

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 3 days and subjected to 1 mg/L phenanthrene for 3 hours.
EveP3_1
differential expression file:
EvePh3_annot.csv

value: whole body


title: G. lacustris, 1 mg/L phenanthrene, 3 hours, sample 3

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 3 days and subjected to 1 mg/L phenanthrene for 3 hours.
GlaP3_3
differential expression file:
GlaPh3_annot.csv


title: 03_acBWT (replicate of 02)


title: G. lacustris, 1 mg/L phenanthrene, 3 hours, sample 2

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 3 days and subjected to 1 mg/L phenanthrene for 3 hours.
GlaP3_2
differential expression file:
GlaPh3_annot.csv


title: 15-BB

description:
processed mRNA
TippingGibbs2019.xlsx


title: 02_acAWT


title: 01_inputWT


title: E. verrucosus, 0.1% acetone, 24 hours, sample 3

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 3 days and subjected to 0.1% acetone (phenanthrene solvent) for 24 hours.
EvePB24_3
differential expression file:
EvePB24_annot.csv


title: G. lacustris, 0.1% acetone, 24 hours, sample 3

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 3 days and subjected to 0.1% acetone (phenanthrene solvent) for 24 hours.
GlaPB24_3
differential expression file:
GlaPB24_annot.csv


title: E. verrucosus, 0.1% acetone, 24 hours, sample 2

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 3 days and subjected to 0.1% acetone (phenanthrene solvent) for 24 hours.
EvePB24_2
differential expression file:
EvePB24_annot.csv


title: 05_me3BWT (replicate of 04)


title: E. verrucosus, 0.1% acetone, 3 hours, sample 2

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 3 days and subjected to 0.1% acetone (phenanthrene solvent) for 3 hours.
EvePB3_2
differential expression file:
EvePB3_annot.csv


title: G. lacustris, 0.1% acetone, 24 hours, sample 2

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 3 days and subjected to 0.1% acetone (phenanthrene solvent) for 24 hours.
GlaPB24_2
differential expression file:
GlaPB24_annot.csv


title: E. verrucosus, 0.1% acetone, 3 hours, sample 1

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 3 days and subjected to 0.1% acetone (phenanthrene solvent) for 3 hours.
EvePB3_1
differential expression file:
EvePB3_annot.csv


title: G. lacustris, 0.1% acetone, 24 hours, sample 1

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 3 days and subjected to 0.1% acetone (phenanthrene solvent) for 24 hours.
GlaPB24_1
differential expression file:
GlaPB24_annot.csv


title: G. lacustris, 0.1% acetone, 3 hours, sample 2

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 3 days and subjected to 0.1% acetone (phenanthrene solvent) for 3 hours.
GlaPB3_2
differential expression file:
GlaPB3_annot.csv


title: E. verrucosus, LT10, 24 hours, sample 3

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 5 days and subjected to LT10 (24.9 degrees C) for 24 hours.
Eve10LT24_3
differential expression file:
Eve10LT24_annot.csv


title: E. verrucosus, LT10, 24 hours, sample 2

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 5 days and subjected to LT10 (24.9 degrees C) for 24 hours.
Eve10LT24_2
differential expression file:
Eve10LT24_annot.csv


title: E. verrucosus, LT10, 24 hours, sample 1

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 5 days and subjected to LT10 (24.9 degrees C) for 24 hours.
Eve10LT24_1
differential expression file:
Eve10LT24_annot.csv


title: bm1

first: Aviv

last: Regev

address: 415 Main Street

institute: Broad Institute

data_processing:
ScRNA-Seq data were demultiplexed, aligned to the mouse genome, version mm10, and UMI-collapsed with the Cellranger toolkit (version 2.0.1, 10X Genomics).
We excluded cells with fewer than 500 detected genes (where each gene had to have at least one UMI aligned). Gene expression was represented as the fraction of its UMI count with respect to total UMI in the cell and then multiplied by 10,000.
Genome_build: mm10
Supplementary_files_format_and_content: gene-barcode matrices; genes; barcodes

source_name: steady state_bone marrow

extract_protocol:
Bones (femur and tibia) were harvested and placed in Media 199 (ThermoFisher Scientific, Ref#12350039) supplemented with 2% Fetal Bovine Serum (FBS, ThermoFisher Scientific, Ref#10082147). Muscle and tendon tissue was removed and bone marrow was flushed. Niche cells from the bone marrow fraction were isolated by digestion with 1 mg/mL STEMxyme1 (Worthington, Ref#LS004106) and 1 mg/mL Dispase 1 (ThermoFisher Scientific, Ref#17105041), in Media 199 supplemented with 2% FBS for 25 min at 37°C. Niche cells from the bone fraction were isolated by gently crushing and cutting bones (including epiphysis) into small fragments and digested in the same digestion mix as the bone marrow for 25 min, at 37°C with agitation (120 rpm). After digestions, both fractions were filtered through a 70μm filter into a collection tube (Fisher Scientific, Ref#08-771-2), pooled into one sample or run separately (e.g. for bone vs. bone marrow fraction scRNA-seq analysis), and erythrocytes lysed in ACK-lysis buffer (ThermoFisher Scientific, Ref#C1430) for 5 minutes on ice. Cells were then stained in Media 199 supplemented with 2% FBS for FACS cell sorting.
For flow cytometry and FACS, cells were resuspended in Media 199 supplemented with 2% FBS and stained for Ter119-APC (eBioscience, Ref#17-5921-82, clone TER-119), CD71-PECy7 (Biolegend, Ref#113812, clone RI7217), CD45-PE (eBioscience, Ref#12-0451-82, clone 30-F11), CD3-PE (Biolegend, Ref#100206, clone 17A2), B220-PE (Biolegend, Ref#103208, clone RA3-6B2), CD19-PE (Biolegend, Ref#115508, clone 6D5), Gr-1-PE (Biolegend, Ref#108408, clone RB6-8C5), and Cd11b-PE (Biolegend, Ref#101208, clone M1/70) for 30 minutes on ice. Dead cells and debris were excluded by FSC, SSC, DAPI (4',6-diamino-2-phenylindole, Life Technologies, Ref#D3571) and Calcein AM staining profiles and Calcein AM (Life Technologies, Ref#C1430). FACS and cytometry was performed on a BD FACSAria II sorter, and sorted bone marrow niche cells were collected in Media 199 supplemented with 2% FBS and 0.4% UltraPure BSA (Life Technologies, Ref#AM2616). Bone marrow stroma was enriched by sorting of live cells (7-AAD-/Calcein+) negative for erythroid (CD71/Ter119) and immune lineage markers (CD45/CD3/B220/CD19/Gr-1/CD11b). For flow cytometric analysis (e.g. Figure S1K), we used Ly6a/Sca-1 (Biolegend, Ref#108127, clone), CD31 (Pecam1) (BD Bioscience, Ref#565097), Vcam1 (Biolegend, Ref#105710), CD34 (eBioscience, Ref#11-0341-82), Cdh5/CD144 (Biolegend, Ref#138006)
Single cells were encapsulated into emulsion droplets using Chromium Controller (10x Genomics). scRNA-seq libraries were constructed using Chromium Single Cell 3’ v2 Reagent Kit according to the manufacturer’s protocol. Briefly, post sorting sample volume was decreased and cells were examined under a microscope and counted with a hemocytometer. Cells were then loaded in each channel with a target output of ~4,000 cells. Reverse transcription and library preparation were performed on C1000 Touch Thermal cycler with 96-Deep Well Reaction Module (Bio-Rad). Amplified cDNA and final libraries were evaluated on a Agilent BioAnalyzer using a High Sensitivity DNA Kit (Agilent Technologies). Individual libraries were diluted to 4nM and pooled for sequencing. Pools were sequenced with 75 cycle run kits (26bp Read1, 8bp Index1 and 55bp Read2) on the NextSeq 500 Sequencing System (Illumina) to ~70-80% saturation level.

value: steady state

value: bone marrow


title: b3

source_name: steady state_bone

value: bone


title: G. lacustris, LT10, 24 hours, sample 1

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 5 days and subjected to LT10 (24.9 degrees C) for 24 hours.
Gla10LT24_1
differential expression file:
Gla10LT24_annot.csv


title: bm2


title: b4


title: G. lacustris, LT10, 24 hours, sample 2

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 5 days and subjected to LT10 (24.9 degrees C) for 24 hours.
Gla10LT24_3
differential expression file:
Gla10LT24_annot.csv


title: bm3


title: bm4


title: G. lacustris, 1 mg/L phenanthrene, 3 hours, sample 1

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 3 days and subjected to 1 mg/L phenanthrene for 3 hours.
GlaP3_1
differential expression file:
GlaPh3_annot.csv


title: b1


title: E. verrucosus, 0.1% acetone, 24 hours, sample 1

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 3 days and subjected to 0.1% acetone (phenanthrene solvent) for 24 hours.
EvePB24_1
differential expression file:
EvePB24_annot.csv


title: E. verrucosus, LT10, 3 hours, sample 4

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 5 days and subjected to LT10 (24.9 degrees C) for 3 hours.
Eve10LT3_4
differential expression file:
Eve10LT3_annot.csv


title: b2


title: hcr1-deltaski2-delta DY130M

description:
hcr1-deltaski2-delta
Total RNA

data_processing:
Base calling and demultiplexing was performed at the NHLBI DNA Sequencing and Genomics Core at the NIH Intramural program, Bethesda, MD.
Files were demultiplexed and filtered to remove low-quality reads. They were then trimmed to the start of the linker sequence. Contaminating sequences that corresponded to gel markers were eliminated.
Reads were aligned to a library of RNA genes and those not matching were retained.
Reads were then aligned to the genome and those not matching to a custom library of splice junctions by using Bowtie (Langmead et al., 2009). For footprints, reads that did not match in these steps were trimmed of consecutive 3' As and realigned. The aligned reads from all alignment rounds were pooled and normalized to units of reads per million (rpm) (by dividing by the total number of million mapped reads in a sample) to generate wig files.
Replicates or multiple sequencing lanes for a given sample were pooled together to create a single wig file for each condition to be used in downstream analysis.
Genome_build: R64-1-1
Supplementary_files_format_and_content: All files are fixedStep wig files (text format, each line representing one position in the genome).

source_name: Whole cells

growth_protocol: Cells were generally grown to an OD of ~0.6 and harvested.


title: G. lacustris, LT10, 3 hours, sample 4

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 5 days and subjected to LT10 (24.9 degrees C) for 3 hours.
Gla10LT3_4
differential expression file:
Gla10LT3_annot.csv


title: G. lacustris, LT10, 3 hours, sample 3

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 5 days and subjected to LT10 (24.9 degrees C) for 3 hours.
Gla10LT3_3
differential expression file:
Gla10LT3_annot.csv


title: E. verrucosus, LT10, 3 hours, sample 3

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 5 days and subjected to LT10 (24.9 degrees C) for 3 hours.
Eve10LT3_3
differential expression file:
Eve10LT3_annot.csv


title: E. verrucosus, LT10, 3 hours, sample 2

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 5 days and subjected to LT10 (24.9 degrees C) for 3 hours.
Eve10LT3_2
differential expression file:
Eve10LT3_annot.csv


title: E. verrucosus, LT10, 24 hours, sample 4

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 5 days and subjected to LT10 (24.9 degrees C) for 24 hours.
Eve10LT24_4
differential expression file:
Eve10LT24_annot.csv


title: G. lacustris, LT10, 24 hours, sample 3

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 5 days and subjected to LT10 (24.9 degrees C) for 24 hours.
Gla10LT24_4
differential expression file:
Gla10LT24_annot.csv


title: G. lacustris, 0.1% acetone, 3 hours, sample 1

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 3 days and subjected to 0.1% acetone (phenanthrene solvent) for 3 hours.
GlaPB3_1
differential expression file:
GlaPB3_annot.csv


title: MLL_31May

source_name: MLL-AF9 (MLL) mice_bone marrow + bone

value: MLL-AF9 (MLL) mice

value: bone marrow + bone


title: MLL_26May


title: MLL_8May


title: E. verrucosus, LT10, 3 hours, sample 1

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 5 days and subjected to LT10 (24.9 degrees C) for 3 hours.
Eve10LT3_1
differential expression file:
Eve10LT3_annot.csv

value: rocky littoral zone


title: G. lacustris, LT10, 3 hours, sample 1

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 5 days and subjected to LT10 (24.9 degrees C) for 3 hours.
Gla10LT3_1
differential expression file:
Gla10LT3_annot.csv


title: WT DY100M

description:
WT
Total RNA
Biological replicate of DY125M


title: E. verrucosus, LC10 cadmium, 24 hours, sample 4

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 3 days and  subjected to LC10 (2.9 uM) cadmium chloride for 24 hours.
EveCd24_4
differential expression file:
EveCd24_annot.csv

value: Russia:Irkutsk region, Lake Baikal, Bolshie Koty village


title: ctrl_8May

source_name: control transplanted mice _bone marrow + bone

value: control transplanted mice


title: G. lacustris, LC10 cadmium, 24 hours, sample 4

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 3 days and subjected to LC10 (3.2 uM) cadmium chloride for 24 hours.
GlaCd24_4
differential expression file:
GlaCd24_annot.csv

value: Till Luckenbach, Daria Bedulina

value: adult


title: G. lacustris, LC10 cadmium, 24 hours, sample 3

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 3 days and subjected to LC10 (3.2 uM) cadmium chloride for 24 hours.
GlaCd24_3
differential expression file:
GlaCd24_annot.csv

value: littoral zone

value: Maxim Timofeyev, Daria Bedulina


title: G. lacustris, LC10 cadmium, 24 hours, sample 2

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 3 days and subjected to LC10 (3.2 uM) cadmium chloride for 24 hours.
GlaCd24_2
differential expression file:
GlaCd24_annot.csv


title: E. verrucosus, LC10 cadmium, 24 hours, sample 2

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 3 days and  subjected to LC10 (2.9 uM) cadmium chloride for 24 hours.
EveCd24_2
differential expression file:
EveCd24_annot.csv


title: hcr1-delta DY104M

description:
hcr1-delta
Total RNA
Biological replicate of DY115M


title: hcr1-delta  DY115M

description:
hcr1-delta
Total RNA
Biological replicate of DY104M


title: ctrl_7Jun


title: E. verrucosus, LC10 cadmium, 24 hours, sample 1

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 3 days and  subjected to LC10 (2.9 uM) cadmium chloride for 24 hours.
EveCd24_1
differential expression file:
EveCd24_annot.csv


title: ctrl_26May


title: E. verrucosus, LC10 cadmium, 24 hours, sample 3

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 3 days and  subjected to LC10 (2.9 uM) cadmium chloride for 24 hours.
EveCd24_3
differential expression file:
EveCd24_annot.csv


title: E. verrucosus, LC10 cadmium, 3 hours, sample 4

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 3 days and subjected to LC10 (2.9 uM) cadmium chloride for 3 hours.
EveCd3_4
differential expression file:
EveCd3_annot.csv


title: G. lacustris, LC10 cadmium, 24 hours, sample 1

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 3 days and subjected to LC10 (3.2 uM) cadmium chloride for 24 hours.
GlaCd24_1
differential expression file:
GlaCd24_annot.csv


title: G. lacustris, LC10 cadmium, 3 hours, sample 3

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 3 days and subjected to LC10 (3.2 uM) cadmium chloride for 24 hours.
GlaCd3_3
differential expression file:
GlaCd3_annot.csv


title: E. verrucosus, LC10 cadmium, 3 hours, sample 3

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 3 days and subjected to LC10 (2.9 uM) cadmium chloride for 3 hours.
EveCd3_3
differential expression file:
EveCd3_annot.csv


title: G. lacustris, LT10, 3 hours, sample 2

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 5 days and subjected to LT10 (24.9 degrees C) for 3 hours.
Gla10LT3_2
differential expression file:
Gla10LT3_annot.csv


title: G. lacustris, LC10 cadmium, 3 hours, sample 2

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 3 days and subjected to LC10 (3.2 uM) cadmium chloride for 24 hours.
GlaCd3_2
differential expression file:
GlaCd3_annot.csv


title: ctrl_10May


title: E. verrucosus, LC10 cadmium, 3 hours, sample 2

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 3 days and subjected to LC10 (2.9 uM) cadmium chloride for 3 hours.
EveCd3_2
differential expression file:
EveCd3_annot.csv


title: MLL_10May


title: std6

source_name: steady state_bone marrow + bone


title: WT DY125M

description:
WT
Total RNA
Biological replicate of DY100M


title: G. lacustris, LC10 cadmium, 3 hours, sample 1

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 3 days and subjected to LC10 (3.2 uM) cadmium chloride for 24 hours.
GlaCd3_1
differential expression file:
GlaCd3_annot.csv


title: E. verrucosus, LC10 cadmium, 3 hours, sample 1

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 3 days and subjected to LC10 (2.9 uM) cadmium chloride for 3 hours.
EveCd3_1
differential expression file:
EveCd3_annot.csv


title: E. verrucosus, control, 24 hours, sample 3

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 3 days and kept at 6 degrees C for 24 hours (parallel control).
EveB24_3
differential expression file:
EveCd24_annot.csv
Eve10LT24_annot.csv
EvePB24_annot.csv


title: std5


title: std4


title: G. lacustris, control, 24 hours, sample 3

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 3 days and kept at 6 degrees C for 24 hours (parallel control).
GlaB24_3
differential expression file:
GlaCd24_annot.csv
Gla10LT24_annot.csv
GlaPB24_annot.csv


title: ctrl_16May


title: Ctrl Hypoxia [204]

city: Stockholm

first: Paul

last: Petrus

address: Hälsovägen 7

country: Sweden

institute: Karolinska intitute

hyb_protocol: Not provided

scan_protocol: Not provided

data_processing: SST-RMA (TAC)

source_name: Non-targeting siRNA treated and maintained in 1% oxygen

label_protocol: Not provided

growth_protocol: 13 days with adipogenic differentiation cocktail in the media.

extract_protocol: RNA extracted using a column based RNA extraction kit (from Machery-Nagel).

treatment_protocol: 40 nM siRNA delivered with HiperFect. Oxygen levels were reduced in an hypoxic chamber.

tag: cell type

value: hASC differentiated to adipocytes

tag: sirna

value: Non-targeting

value: 1% oxygen


title: G. lacustris, control, 24 hours, sample 4

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 3 days and kept at 6 degrees C for 24 hours (parallel control).
GlaB24_4
differential expression file:
GlaCd24_annot.csv
Gla10LT24_annot.csv
GlaPB24_annot.csv

value: Russia:Irkutsk region, Bolshie Koty village, Lake No14


title: std3


title: siCD248 Hypoxia [209]

source_name: Treated with siRNA targeting CD248 and maintained in 1% oxygen


title: E. verrucosus, control, 24 hours, sample 2

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 3 days and kept at 6 degrees C for 24 hours (parallel control).
EveB24_2
differential expression file:
EveCd24_annot.csv
Eve10LT24_annot.csv
EvePB24_annot.csv

value: whole body


title: G. lacustris, control, 3 hours, sample 4

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 3 days and kept at 6 degrees C for 3 hours (parallel control).
GlaB3_4
differential expression file:
GlaCd3_annot.csv
Gla10LT3_annot.csv
GlaPB3_annot.csv


title: std2

value: steady state


title: G. lacustris, control, 24 hours, sample 2

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 3 days and kept at 6 degrees C for 24 hours (parallel control).
GlaB24_2
differential expression file:
GlaCd24_annot.csv
Gla10LT24_annot.csv
GlaPB24_annot.csv


title: std1


title: siCD248 Hypoxia [208]


title: G. lacustris, control, 3 hours, sample 3

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 3 days and kept at 6 degrees C for 3 hours (parallel control).
GlaB3_3
differential expression file:
GlaCd3_annot.csv
Gla10LT3_annot.csv
GlaPB3_annot.csv


title: siCD248 Hypoxia [210]


title: Ctrl Hypoxia [203]


title: Ctrl Hypoxia [202]


title: E. verrucosus, control, 3 hours, sample 3

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 3 days and kept at 6 degrees C for 3 hours (parallel control).
EveB3_3
differential expression file:
EveCd3_annot.csv
Eve10LT3_annot.csv
EvePB3_annot.csv


title: E. verrucosus, control, 3 hours, sample 4

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 3 days and kept at 6 degrees C for 3 hours (parallel control).
EveB3_4
differential expression file:
EveCd3_annot.csv
Eve10LT3_annot.csv
EvePB3_annot.csv


title: ATAC-Seq_rep2

city: Memphis

first: JIE

last: Lv

state: TN

address: 262 Danny Thomas Place

department: Department of Computational Biology

institute: St Jude Children's Research Hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
Total read numbers of ATAC-Seq samples are normalized to be 25 millions
ATAC-seq reads were aligned to the mm9 genome assembly using bowtie v1.1.2 with parameters -p 8 -m 1 --chunkmbs 512 --best
ATAC-Seq peaks were called using DANPOS2 v2.2.3 with the following parameters: --smooth_width 0  --frsz 200 --extend 200 --pheight 1e-10 -c 25000000.
Genome_build: mm9
Supplementary_files_format_and_content: wig

source_name: C57BL/6J (The Jackson Laboratory)

extract_protocol: The ATAC-Seq was performed using 50,000 c-Kit+CD144+ CD45.2- cells isolated from AGM region of E11.5 wild-type B6 mouse embryos. The Tn5 transposome was purified and assembled following a published protocol (46).  The permeabilization was performed with 50 µl cold ATAC-RSB buffer (0.1% NP40, 0.1% Tween-20, and 0.01% Digitonin) and the transposition was performed with 50 µl transposition mix (10µl 5× HEPES DMF Buffer, 3 µl 5 µM Tn5 transposome, 37 µl PBS, 0.5 µl 10% Tween-20, and 0.5 µl 1% digitonin) and incubated at 37° for 30 min. After transposition, the cleaned-up DNA fragments were pre-amplified for 5 cycles using NEB Q5 master mix. Each reaction contains 2.5 µl of 25 µM i5 primer, 2.5 µl of 25 µM i7 primer, 25 µl 2× NEB Q5 master mix, and 20 µl cleaned up samples.  PCR settings were 5 min at 72°C, 30 sec at 98°C, and followed by additional 5 cycles (98°C for 10 sec, 63°C for 30 sec, 72°C for 1 min). After pre-amplification, 1 µl of the pre-amplified mixture was used to run a 10 µl qPCR test to determine the optimal amplification cycle. The final amplified DNA library was purified using Qiagen DNA purification kit.

value: HEC and hematopoietic precursors

value: E11.5 mouse aorta-gonad-mesonephros (AGM)N/A


title: G. lacustris, control, 3 hours, sample 2

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 3 days and kept at 6 degrees C for 3 hours (parallel control).
GlaB3_2
differential expression file:
GlaCd3_annot.csv
Gla10LT3_annot.csv
GlaPB3_annot.csv

data_processing:
Raw reads were mapped onto transcriptome assemblies with salmon v0.9.1.
DESeq2 abundance estimation was performed with an in-house R script, which can be found at https://github.com/drozdovapb/EveEcyGlaDE.
Transcript abundances were merged with transcript annotation for selection of Metazoa-related contigs if necessary.
Genome_build: de novo transcriptome assembly of the corresponding species (FASTA files are available on series record).
Supplementary_files_format_and_content: Salmon output files as TPM (transcript per million counts, *sf.txt files) and DESeq2 output files with custom annotation (*annot.csv)


title: siCD248 Normoxia [189]

source_name: Treated with siRNA targeting CD248 and maintained in 21% oxygen

value: 21% oxygen


title: E. verrucosus, control, 24 hours, sample 1

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 3 days and kept at 6 degrees C for 24 hours (parallel control).
EveB24_1
differential expression file:
EveCd24_annot.csv
Eve10LT24_annot.csv
EvePB24_annot.csv


title: E. verrucosus, control, 3 hours, sample 1

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 3 days and kept at 6 degrees C for 3 hours (parallel control).
EveB3_1
differential expression file:
EveCd3_annot.csv
Eve10LT3_annot.csv
EvePB3_annot.csv


title: siCD248 Normoxia [187]


title: B16F10_KO_IFNg_plus_11

status: Public on May 22 2019

city: Boston

first: Xintao

last: Qiu

address: 440 brookline ave

institute: Dana Faber Cancer Institute

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were aligned to mm9 using Bowtie.
For peak calling MACS2 was used.
Genome_build: mm9
Supplementary_files_format_and_content: bw files were generated using MACS2 using the chilin pipeline

extract_protocol:
The OMNI-ATAC protoclol (Corces et al Nat . Methods 2017) was used on all samples.
The OMNI-ATAC protoclol (Corces et al Nat . Methods 2017) was used on all samples.

value: Pbrm1 deficient

tag: treatment

value: IFNg for 24 hours


title: B16F10_KO_IFNg_plus_12


title: B16F10_KO_IFNg_minus_7

value: untreated


title: siCD248 Normoxia [188]


title: B16F10_control_IFNg_plus_5

value: control


title: E. verrucosus, control, 3 hours, sample 2

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 3 days and kept at 6 degrees C for 3 hours (parallel control).
EveB3_2
differential expression file:
EveCd3_annot.csv
Eve10LT3_annot.csv
EvePB3_annot.csv

tag: tissue

value: rocky littoral zone

value: Russia:Irkutsk region, Lake Baikal, Bolshie Koty village

value: Till Luckenbach, Daria Bedulina


title: B16F10_KO_IFNg_minus_9


title: B16F10_control_IFNg_minus_3


title: B16F10_control_IFNg_plus_6


title: B16F10_control_IFNg_minus_2


title: B16F10_control_IFNg_minus_1


title: B16F10_control_IFNg_plus_4


title: Ctrl Normoxia [175]

source_name: Non-targeting siRNA treated and maintained in 21% oxygen


title: Ctrl Normoxia [176]


title: ATAC-Seq_rep1


title: Ctrl Normoxia [177]


title: B16F10_KO_IFNg_plus_10


title: G. lacustris, control, 3 hours, sample 1

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 3 days and kept at 6 degrees C for 3 hours (parallel control).
GlaB3_1
differential expression file:
GlaCd3_annot.csv
Gla10LT3_annot.csv
GlaPB3_annot.csv

value: adult

value: littoral zone

value: Maxim Timofeyev, Daria Bedulina


title: dKO-1

city: Los Angeles

first: WEI

last: ZHANG

state: California

address: 2250 Alcazar St

department: CCMB

institute: University of Southern California

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw RNAseq reads in fastq format were passed through FASTQC to verify quality. The low quality reads were removed with Fastx-toolkit
The high quality reads were mapped to the mouse genome (GRCm38/mm10) by TopHat (PMID:19289445) at the optional setting of –G mouse_mRNA.gtf and assembled against mRNA annotation by HTSeq.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: brain

growth_protocol: Two replicates were performed using neural tube tissues from E11.5  embryos with control or Lin28a-/-;b-/- genotypes.

extract_protocol:
RNA was then isolated using standard Trizol extraction
The resulting RNA fractions were subjected to strand-specific library preparation using NEBNext Ultra Directional RNA Library Prep Kit for Illumina

value: brain

tag: developmental stage


title: WT-polysome-1

value: wildtype


title: dKO-2


title: dKO-polysome-1


title: WT-1


title: WT-2


title: B16F10_KO_IFNg_minus_8


title: RT - RNA-seq

data_processing:
Read data was processed in BaseSpace (basespace.illumina.com).
Reads were aligned to to Mus musculus genome (mm10) using STAR aligner (https://code.google.com/p/rna-star/) with default settings.
Differential transcript expression was determined using the Cufflinks Cuffdiff package (https://github.com/cole-trapnell-lab/cufflinks).
Genome_build: Mus musculus genome mm10
Supplementary_files_format_and_content: Read FPKM and Log2 fold differential expression, and FDR corrected Q-values

source_name: trunk tissue

extract_protocol:
RNA was extracted using the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Takara).
PolyA RNA was isolated using the NEBNext® Poly(A) mRNA Magnetic Isolation Module and barcoded libraries were made using the NEBNext® Ultra II™ Directional RNA Library Prep Kit for Illumina®(NEB, Ipswich MA).  Libraries were pooled and single end sequenced (1X75) on the Illumina NextSeq 500 using the High output V2 kit (Illumina Inc., San Diego CA).

value: Raldh2 (Aldh1a2) knockout

value: stage E8.5 embryo

value: dissected embryonic trunk tissue


title: Wt - RNA-seq

value: wild-type


title: WT-polysome-2


title: Nfia_b_x_tCKO_rep1

city: St. Louis

middle: Stewart

last: Clark

state: Missouri

address: 660 S Euclid Ave; Campus Box #8096

department: Ophthalmology and Visual Sciences

institute: Washington University

description:
10x Genomics single cell RNAseq
NFI_aggregate.mtx
NFI_barcodes.tsv
NFI_genes.tsv

data_processing:
Smart-seq: fastq files were aligned to mm10 using Hisat and processed to bam files using samtools; mapped reads were assigned using Cuffquant and libraries normalized using Cuffnorm
10X: Demux and generation of fastq files using default parameters from Cellranger v1.2.1 mkfastq; Alignment of .fastq files using Cellranger v1.2.1 count with refdata-cellranger-mm10 v1.2.0 as a reference index; count matrices were manually aggregated and used as input to Monocle2 single cell RNAseq framework
Genome_build: mm10 (refdata-cellranger-mm10 v1.2.0)
Supplementary_files_format_and_content: Expression Data of aggregate NFI mutant 10x Samples
Supplementary_files_format_and_content: Gene features of aggregate NFI mutant 10x Samples
Supplementary_files_format_and_content: Cell Features of aggregate 10x Samples

source_name: Retinal Cells

extract_protocol:
10x Genomics Chromium single cell system with v2 Chemistry
Adapted Smart-seq2 protocol

treatment_protocol: none - wildtype, Nfia/b/x lox/+ Chx10-Cre-GFP, or Nfia/b/x lox/lox Chx10-Cre-GFP animals

value: P14 Nfia/b/x F/F Chx10:GFP-Cre (triple mutant) mouse single retinal cells from 10x Genomics Chromium Single Cell

value: Mixed CD1/C57Bl6


title: Nfia_b_x_het_rep2

value: P14 Nfia/b/x F/+ Chx10:GFP-Cre mouse single retinal cells from 10x Genomics Chromium Single Cell


title: Nfia_b_x_tCKO_rep3


title: Nfia_b_x_het_rep1


title: P2 Cell 288

description:
P2_C288
Smart-Seq2 Single cell RNAseq
P2 RPC
PolyA RNA
processed data file: Smart_aggregate.mtx
processed data file: Smart_genes.tsv
processed data file: Smart_cells.tsv

data_processing:
Smart-seq: Fastq files were aligned to mm10 using Hisat and processed to bam files using samtools; mapped reads were assigned using Cuffquant and libraries normalized using Cuffnorm.
10x: Demux and generation of fastq files using default parameters from Cellranger v1.2.1 mkfastq; Alignment of .fastq files using Cellranger v1.2.1 count with refdata-cellranger-mm10 v1.2.0 as a reference index; count matrices were manually aggregated and used as input to Monocle2 single cell RNAseq framework.
Genome_build: Smart-seq: mm10 (GRCm38)
Genome_build: 10x: mm10 (refdata-cellranger-mm10 v1.2.0)
Supplementary_files_format_and_content: SmartSeq_aggregate.mtx: Expression Data of aggregate Smart-Seq cells.
Supplementary_files_format_and_content: SmartSeq_genes.tsv: Gene features of aggregate Smart-Seq cells.
Supplementary_files_format_and_content: SmartSeq_cells.tsv: Cell Features of aggregate Smart-Seq cells.
Supplementary_files_format_and_content: 10x_aggregate.mtx: Expression Data of aggregate 10x Samples.
Supplementary_files_format_and_content: genes.tsv: Gene features of aggregate 10x Samples.
Supplementary_files_format_and_content: barcodes.tsv: Cell Features of aggregate 10x Samples.

source_name: Sorted Retinal Progenitor Cell (Chx10-GFP positive)

extract_protocol: Adapted Smart-seq2 protocol or 10x Genomics Chromium single cell system with v2 Chemistry.

treatment_protocol: None - wildtype animals.

value: Retinal progenitor cell

tag: strain/background

value: Wildtype


title: P2 Cell 285

description:
P2_C285
Smart-Seq2 Single cell RNAseq
P2 RPC
PolyA RNA
processed data file: Smart_aggregate.mtx
processed data file: Smart_genes.tsv
processed data file: Smart_cells.tsv


title: P2 Cell 287

description:
P2_C287
Smart-Seq2 Single cell RNAseq
P2 RPC
PolyA RNA
processed data file: Smart_aggregate.mtx
processed data file: Smart_genes.tsv
processed data file: Smart_cells.tsv


title: dKO-polysome-2


title: P2 Cell 280

description:
P2_C280
Smart-Seq2 Single cell RNAseq
P2 RPC
PolyA RNA
processed data file: Smart_aggregate.mtx
processed data file: Smart_genes.tsv
processed data file: Smart_cells.tsv


title: P2 Cell 281

description:
P2_C281
Smart-Seq2 Single cell RNAseq
P2 RPC
PolyA RNA
processed data file: Smart_aggregate.mtx
processed data file: Smart_genes.tsv
processed data file: Smart_cells.tsv


title: P2 Cell 282

description:
P2_C282
Smart-Seq2 Single cell RNAseq
P2 RPC
PolyA RNA
processed data file: Smart_aggregate.mtx
processed data file: Smart_genes.tsv
processed data file: Smart_cells.tsv


title: P2 Cell 283

description:
P2_C283
Smart-Seq2 Single cell RNAseq
P2 RPC
PolyA RNA
processed data file: Smart_aggregate.mtx
processed data file: Smart_genes.tsv
processed data file: Smart_cells.tsv


title: P2 Cell 284

description:
P2_C284
Smart-Seq2 Single cell RNAseq
P2 RPC
PolyA RNA
processed data file: Smart_aggregate.mtx
processed data file: Smart_genes.tsv
processed data file: Smart_cells.tsv


title: P2 Cell 278

description:
P2_C278
Smart-Seq2 Single cell RNAseq
P2 RPC
PolyA RNA
processed data file: Smart_aggregate.mtx
processed data file: Smart_genes.tsv
processed data file: Smart_cells.tsv


title: P2 Cell 276

description:
P2_C276
Smart-Seq2 Single cell RNAseq
P2 RPC
PolyA RNA
processed data file: Smart_aggregate.mtx
processed data file: Smart_genes.tsv
processed data file: Smart_cells.tsv


title: P2 Cell 277

description:
P2_C277
Smart-Seq2 Single cell RNAseq
P2 RPC
PolyA RNA
processed data file: Smart_aggregate.mtx
processed data file: Smart_genes.tsv
processed data file: Smart_cells.tsv


title: P2 Cell 275

description:
P2_C275
Smart-Seq2 Single cell RNAseq
P2 RPC
PolyA RNA
processed data file: Smart_aggregate.mtx
processed data file: Smart_genes.tsv
processed data file: Smart_cells.tsv


title: P2 Cell 274

description:
P2_C274
Smart-Seq2 Single cell RNAseq
P2 RPC
PolyA RNA
processed data file: Smart_aggregate.mtx
processed data file: Smart_genes.tsv
processed data file: Smart_cells.tsv


title: P2 Cell 273

description:
P2_C273
Smart-Seq2 Single cell RNAseq
P2 RPC
PolyA RNA
processed data file: Smart_aggregate.mtx
processed data file: Smart_genes.tsv
processed data file: Smart_cells.tsv


title: P2 Cell 270

description:
P2_C270
Smart-Seq2 Single cell RNAseq
P2 RPC
PolyA RNA
processed data file: Smart_aggregate.mtx
processed data file: Smart_genes.tsv
processed data file: Smart_cells.tsv


title: P2 Cell 272

description:
P2_C272
Smart-Seq2 Single cell RNAseq
P2 RPC
PolyA RNA
processed data file: Smart_aggregate.mtx
processed data file: Smart_genes.tsv
processed data file: Smart_cells.tsv


title: P2 Cell 267

description:
P2_C267
Smart-Seq2 Single cell RNAseq
P2 RPC
PolyA RNA
processed data file: Smart_aggregate.mtx
processed data file: Smart_genes.tsv
processed data file: Smart_cells.tsv


title: P2 Cell 265

description:
P2_C265
Smart-Seq2 Single cell RNAseq
P2 RPC
PolyA RNA
processed data file: Smart_aggregate.mtx
processed data file: Smart_genes.tsv
processed data file: Smart_cells.tsv