title: MNase_fpa

data_processing:
Trimming : Trimmomatic (v0.33, Bolger, Lohse & Usabel, Bioinformatics, 2014 ; btu170) in paired end mode
Alignment : Bowtie2 (v 2.2.6, Langmead & Salzberg, Nature Methods, 2012 ; 9:357-59) with --dovetail option and a maximum insert size of 1Kb
Filtering : Duplicate reads were identified with Picard (v. 2.2.4) MarkDuplicates and removed. Samtools v 1.3 was used to keep only reads mapped in proper pairs with mapping quality (MapQ) above 2. Using samtools and awk (as in www.biostars.org/p/114183/) we further removed the reads corresponding to fragments of size below 70bp or above 250bp.
Coverage and normalization: Aligned reads were imported in R (v.3.3.2) to obtain coverages using Bioconductor (v3.4). Coverages were normalized as fragments per 10 million (FP10M) and exported to bigWig files with the rtracklayer package.
Peak calling: for each histone mark, peaks were called using MACS2 on pooled data from the 3 genotypes (WT, fpa, bdrs), using H3 ChIP-seq as control and following the Encode IDR pipeline (Landt et al., Genome Research, 2012 ; 22 :1813-1831). Irreproducible Discovery Rate (IDR) is described in Li et al., Ann Appl. Stat., 2011 ; 5(3):1752-79. The optimal set of peaks was defined using an IDR threshold of 0.01.
Genome_build: TAIR10
Supplementary_files_format_and_content: bigWig files contain the normalized coverage (FP10M : fragments per 10 million), i.e. the normalized number of fragments covering each base
Supplementary_files_format_and_content: regionPeak files contain the location of peaks detected using MACS2 and the IDR pipeline. Format is similar to the UCSC/Encode narrowPeak format (http://genome.ucsc.edu/FAQ/FAQformat.html#format12). Columns are : Chromosome, Start, End, Peak name, Score, SignalValue, Fold-change, log10(p-value), log10(q-value), summit location

extract_protocol:
The seedlings were ground into fine powder in liquid nitrogen, incubated for 15 min at 4°C in extraction buffer (25mM Tris-HCl, pH=8.0, 0.44M sucrose, 10mM MgCl2, 0.1 % Triton X-100, 2mM spermine, 10mM beta-mercaptoethanol, 1 mM PMSF, 1 % plant protease inhibitor cocktail), filtered through 2 layers of Miracloth and centrifuged at 2000g for 13 min at 4°C. Nuclei were prepared by 2 rounds of resuspension in extraction buffer (without spermine, once with 0.2 % Triton X-100 and once with 0.1 % Triton X-100), incubation 6 min on ice and centrifugation at 1,000g for 12 min at 4°C. The nuclei suspension was stored in 20 % glycerol at -70°C until used. After thawing on ice, the nuclei were centrifuged for 10 min at 11,000g at 4°C and resuspended in MNase digestion buffer (10 mM Tris-HCl, pH=8.0, 1.5mM NaCl, 3mM CaCl2, 1mM MgCl2 , 1mM PMSF). Chromatin was digested with 400U MNase/mL (Thermo Fisher 88216) for 15min at 37°C. MNase digestion was stopped by adding EDTA/EGTA (25mM each final). Nuclei were centrifuged at 10,000g for 10 min at 4°C, the supernatant was kept and added to the soluble chromatin fraction following needle extraction. The pellet was resuspended in ChIP buffer (20mM Tris-HCl, pH=7.6, 50mM NaCl, 10mM EDTA, 0.1 % Triton X-100, 1mM PMSF, 1 % plant protease inhibitor cocktail) and soluble chromatin was recovered in ChIP buffer by 2 rounds of needle extraction (8 passage through 27.2G needle), incubation at 4°C for 20 min and centrifugation at 10,000g for 10 min.
Libraries were prepared using NEBNext Ultra II DNA library prep kits (NEB E7645) following the manufacturer's instructions. Libraries were sequenced on a NextSeq 500 instrument at Indiana University Center for Genomics and Bioinformatics.

value: 8-day old


title: Sample 1: wt control 156 cervical

status: Public on Aug 08 2019

type: SRA

city: La Jolla

first: Samuel

middle: L

last: Pfaff

state: CA

address: 10010 N Torrey Pines Rd

country: USA

institute: Salk Institute for Biological Studies

library_source: transcriptomic

data_processing:
FASTQ files were filtered for reads with a minimum average base quality greater than or equal to 15 and known Illumina adapters were trimmed using tools from the BBMap package.
Isoform expression was quantified with kallisto and the M17 gencode annotation for the mm10 mouse genome.
Isoform expressions were summed into gene level expression based on gencode gene id.
Genome_build: mm10
Supplementary_files_format_and_content: gene level unnormalized counts are provided for all samples in a CSV format file

molecule: total RNA

organism: Mus musculus

source_name: spinal cord (cervical)

extract_protocol:
Qiagen RNeasy Plus Mini kit was used to extract RNA from flash frozen cervical and lumbar spinal cords.  RNA was extracted following manufacturer's protocol.  RNA quality was assayed using Agilent Tapestation analysis.
Illumina TruSeq stranded mRNA kit, following by single-end 75bp sequencing on Illumina HiSeq4000 machine.

treatment_protocol: SOD1 G37R mice were treated with shRNA-SOD1 at either ~120d (presymptomatic) or ~348d (mid-onset disease).  End-stage control animals were ~390d at the time of tissue harvesting, whereas shRNA-treated animals treated presymptomatically were ~470d at the time of tissue harvesting.  shRNA-treated animals that were treated after disease onset survived for three additional months after treatment without progression of disease before tissue harvesting.

tag: tissue

value: spinal cord (cervical)

tag: sequencing batch

value: Batch 1

tag: treatment

tag: age euthanized (days)

tag: genotype

value: Wild Type


title: Stage E7.0 endoderm single cell plate 1D1 cell (E7.0SCVE1-D1)

city: Guangzhou

first: Guangdun

last: Peng

address: 190 Kaiyuan Road

department: Guangzhou Institutes of Biomedicine and Health

country: China

institute: Chinese Academy of Sciences

description: processed data file: E7.0SingleCell.tpm.txt

data_processing:
The reads for all samples are mapped to the mm10 using Tophat v2.0.8b with parameter: -p 20 -g 1 -N 4 --read-edit-dist 4 --microexon-search
The mapped reads were used to estimate transcriptomic alignment rates, and were also used as input in Cufflinks v2.1.1 (Trapnell et al., 2013) to quantify gene expression levels (fragment per kilobase per million, FPKM) with the default parameters
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each embryo

source_name: Mouse embryonic cells

growth_protocol: Embryos from pre-gastrulation to late-gastrulation mouse were embedded with OCT and subjected to cryosection.

extract_protocol:
According to Geo-seq (Chen et al., 2017), RNA from LCM samples were extracted by 5M GuSCN (Invitrogen, # 20012-043), then RNA was precipitated by ethanol with the help of RNA carrier.
Libraries were constructed using illumina Nextera XT DNA sample preparation kit

treatment_protocol: Sample from sections were laser-microdissected and collected for single-cell based RNA sequencing.

tag: developmental stage

value: Mid-gastrulation embryo (E7.0)

tag: tag

tag: cell type

value: Mouse embryonic cells


title: Sample 2: wt control 156 lumbar

source_name: spinal cord (lumbar)

value: spinal cord (lumbar)


title: ARTERIES Sample S84

city: Barcelona

first: Lars

last: Velten

address: C. Dr. Aiguader 88, P05

department: Bioinformatics and Genomics

country: Spain

institute: CRG

data_processing:
Alignment, STAR 2.6.0
Count tables, htseq-count 0.7.2
Filtering for 1 million reads per sample, R-3.5.0
Removal of outlier samples on PC 1 and 2, using PCA of variance stabilizing transformed counts, R-3.5.0, DESeq 1.20.0
Genome_build: Mus Musculus mm10, ENSEMBL release 38.73
Supplementary_files_format_and_content: Raw counts per gene, tab-separated values

source_name: Bone Marrow

extract_protocol:
Mouse femurs were fixed in 4% PFA and cryosectioned at 12 um thickness. Sections were stained using fluorescently labelled antibodies against Sca-1 and EMCN, and Hoechst 33342 was used as a counterstain. Samples were imaged and collected using the Zeiss PALM MicroBeam Axio Observer Z1 (Zeiss). Areas of 14500 µm2 on average, corresponding to around 250-300 cells, were isolated in proteinase K solution. Reverse crosslinked RNA was extracted with 100µl TRI Reagent (Sigma-Aldrich) following manufacturer instructions and cDNA synthesized following the SMARTER stranded Total RNA-Seq Kit v2 – Pico Input Mammalian (Takara Bio, Japan) protocol.
SMARTER stranded Total RNA-Seq Kit v2 – Pico Input Mammalian (Takara Bio, Japan)

value: bone marrow

tag: strain

tag: slide id

tag: area (micrometer2)

tag: niche

value: ARTERIES

tag: distance from endosteum

tag: filter

value: OK


title: Stage E7.0 endoderm single cell plate 1D12 cell (E7.0SCVE1-D12)


title: H3K36me3_bdrs

city: Villenave d'Ornon

first: Pascal

middle: GP

last: Martin

address: 71 avenue Edouard Bourlaux

department: UMR1332 BFP

country: France

institute: INRAE

library_source: genomic

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: seedlings, 8-day-old

growth_protocol: Seeds were sown on MS plates and stratified for 4 days at 4°C in the dark. Plates were transfered to a growth chamber at 21°C and grown for 8 days under long day conditions (16h light/8h dark).

tag: ecotype

value: bdrs triple mutant

tag: age

tag: chip antibody

value: anti-H3K36me3 (abcam ab9050, lot GR288636-2)


title: SINUSOIDS Sample S83

tag: tissue

value: SINUSOIDS


title: MP-3LY49N

city: Stanford

first: Michael

last: Sikora

address: 450 Serra Mall

department: Genetics

institute: Stanford University

description:
count_matrix.txt.gz
tpm_matrix.txt.gz

data_processing:
Read quality was determined with FastQC 0.11.4
Using TopHat v2.0.13, we aligned the reads to the mouse reference genome (NCBI/ assembly GRCm38).
One MOG + PPT sample was removed from downstream analysis as an identified outlier. (not shown)
TPM values were calculated with RSEM v1.3.0
Genome_build: GRCm38
Supplementary_files_format_and_content: count_matrix and tpm_matrix are matrices with expression values for each gene in each cell. count_matrix is the raw counts for reads aligning to each gene. tpm_matrix is identically structured, but values are transcripts per million (TPM).

molecule: polyA RNA

source_name: Ly49-CD8+ T cells

extract_protocol:
Cells were bulk sorted and RNA was harvested using Trizol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Tetramer postive cells, Ly49+, Ly49- cells were obtained from 10 days post MOG, MOG+SP immunized mice

value: CD8+ T cells

tag: mouse strain

value: MOG+SP


title: MP-3LY49P

description:
count_matrix.txt.gz
tpm_matrix.txt.gz

source_name: Ly49+CD8+ T cells

tag: treatment


title: Stage E7.0 endoderm single cell plate 1D11 cell (E7.0SCVE1-D11)


title: MNase_WT

value: wild-type


title: Stage E7.0 endoderm single cell plate 1D10 cell (E7.0SCVE1-D10)


title: MP-2LY49N

description:
count_matrix.txt.gz
tpm_matrix.txt.gz


title: MNase_bdrs

source_name: seedlings, 7-day-old


title: ARTERIES Sample S82


title: H3K4me3_bdrs

value: anti-H3K4me3 (Millipore 17-614, lot 2769057)


title: H3K4me2_bdrs

value: 8-day old

value: anti-H3K4me2 (Millipore 17-677, lot 2865656)


title: ARTERIES Sample S81


title: H3_bdrs

value: anti-histone H3 (abcam ab1791, lot GR312884-1)


title: MP-1LY49P

description:
count_matrix.txt.gz
tpm_matrix.txt.gz


title: Stage E7.0 endoderm single cell plate 1C9 cell (E7.0SCVE1-C9)


title: SINUSOIDS Sample S80


title: MP-1LY49N

description:
count_matrix.txt.gz
tpm_matrix.txt.gz


title: Stage E7.0 endoderm single cell plate 1C8 cell (E7.0SCVE1-C8)


title: H3K36me3_fpa

value: fpa single mutant (fpa-7)


title: Stage E7.0 endoderm single cell plate 1C7 cell (E7.0SCVE1-C7)

value: Mid-gastrulation embryo (E7.0)


title: 6-M5

description:
count_matrix.txt.gz
tpm_matrix.txt.gz

source_name: SP tetramer+ CD8+ T cels

value: MOG


title: H3K4me3_fpa


title: 5-M4

description:
count_matrix.txt.gz
tpm_matrix.txt.gz


title: Stage E7.0 endoderm single cell plate 1C6 cell (E7.0SCVE1-C6)

value: Mouse embryonic cells


title: ARTERIES Sample S79

value: bone marrow


title: H3K4me2_fpa


title: SINUSOIDS Sample S78


title: MP-2LY49P

description:
count_matrix.txt.gz
tpm_matrix.txt.gz


title: Stage E7.0 endoderm single cell plate 1C5 cell (E7.0SCVE1-C5)


title: 4-M3

description:
count_matrix.txt.gz
tpm_matrix.txt.gz


title: H3_fpa


title: Stage E7.0 endoderm single cell plate 1C4 cell (E7.0SCVE1-C4)


title: 14-MP3

description:
count_matrix.txt.gz
tpm_matrix.txt.gz


title: LOW SINUSOIDS Sample S77

value: LOW SINUSOIDS


title: H3K36me3_WT


title: Stage E7.0 endoderm single cell plate 1C3 cell (E7.0SCVE1-C3)


title: H3K4me3_WT


title: SINUSOIDS Sample S75

value: OK


title: 13-MP2

description:
count_matrix.txt.gz
tpm_matrix.txt.gz


title: Stage E7.0 endoderm single cell plate 1C2 cell (E7.0SCVE1-C2)


title: ARTERIES Sample S8

value: ARTERIES


title: H3K4me2_WT


title: ARTERIES Sample S74


title: Stage E7.0 endoderm single cell plate 1C1 cell (E7.0SCVE1-C1)


title: H3_WT


title: Stage E7.0 endoderm single cell plate 1C12 cell (E7.0SCVE1-C12)


title: Stage E7.0 endoderm single cell plate 1C11 cell (E7.0SCVE1-C11)


title: SUB-ENDOSTEUM Sample S72

value: SUB-ENDOSTEUM


title: FPA

data_processing:
Trimming : Trimmomatic (v0.33, Bolger, Lohse & Usabel, Bioinformatics, 2014 ; btu170) in paired end mode
Alignment : Bowtie2 (v 2.2.6, Langmead & Salzberg, Nature Methods, 2012 ; 9:357-59) with --dovetail option and a maximum insert size of 1Kb
Filtering : Duplicate reads were identified with Picard (v. 2.2.4) MarkDuplicates and removed. Samtools v 1.3 was used to keep only reads mapped in proper pairs with mapping quality (MapQ) above 2.
Coverage and normalization: Aligned reads were imported in R (v.3.3.2) to obtain coverages using Bioconductor (v3.4). Coverages were normalized as fragments per 10 million (FP10M) and exported to bigWig files with the rtracklayer package.
Peak calling : ChIP-seq peaks were detected using MACS2 (v. 2.1.0, Zhang et al., Genome Biology, 2008 ; 9 :R137) in paired-end mode using Myc_WT ( for BDR1 and BDR2) or input DNA (for FPA) as controls. peaks with a p-value<0.01 were kept. Peaks located in blacklisted regions were removed.
Genome_build: TAIR10
Supplementary_files_format_and_content: bigWig files contain the normalized coverage (FP10M : fragments per 10 million), i.e. the normalized number of fragments covering each base
Supplementary_files_format_and_content: bed files contain the location of peaks identified with MACS2

extract_protocol:
The seedlings were crosslinked for 15 min in 1 % formaldehyde under vacuum (5 min vacuum / vacuum release / 10 min vacuum) followed by 6 min quenching with glycine (125mM final concentration, under vacuum), extensive rinsing with ice-cold water and drying. Crosslinked seedlings were ground into fine powder in liquid nitrogen, incubated for 15 min at 4°C in extraction buffer (25mM Tris-HCl, pH=8.0, 0.44M sucrose, 10mM MgCl2, 0.1 % Triton X-100, 2mM spermine, 10mM beta-mercaptoethanol, 1 mM PMSF, 1 % plant protease inhibitor cocktail) and filtered through 2 layers of Miracloth. Nuclei were prepared by 3 rounds of resuspension in extraction buffer (without spermine, twice with 0.25 % Triton X-100 and once with 0.1 % Triton X-100), incubation 12 min on ice and centrifugation at 1,000g for 12 min at 4°C (only 300g for the last centrifugation). The nuclei suspension was stored in 20 % glycerol at -70°C until used. After thawing on ice, nuclei were centrifuged for 10 min at 11,000g at 4°C and resuspended in nuclei lysis buffer (500 mM Tris-HCl, pH=8.0, 10mM EDTA, 1 % SDS, 1mM PMSF, 1 % plant protease inhibitor cocktail). Chromatin was sonicated for 12 min using a Covaris S220 (peak power=150, duty factor=20, cycles/burst=200). Soluble chromatin was recovered by centrifugation at 13,000g for 15 min at 4°C and diluted to (final concentrations): 20mM Tris-HCl, 150mM NaCl, 2mM EDTA, 0.1 % SDS, 1 % Triton X-100, 1mM PMSF, 1 % plant protease inhibitor cocktail.
Libraries were prepared using NEBNext Ultra DNA library prep kits (NEB, E7370 or E7645). Libraries were sequenced on a NextSeq 500 instrument at Indiana University Center for Genomics and Bioinformatics.

value: anti-FPA, polyclonal

tag: library prep kit

value: NEBNext Ultra II DNA library Prep kit (E7645)


title: input_WT

tag: genotype

value: NEBNext Ultra DNA library Prep kit (E7370)


title: SINUSOIDS Sample S73

value: SINUSOIDS


title: Stage E7.0 endoderm single cell plate 1C10 cell (E7.0SCVE1-C10)

tag: developmental stage


title: input_BDR1

value: bdrs expressing Myc tag-BDR1


title: ENDOSTEUM Sample S71

value: ENDOSTEUM


title: E70_nc

city: Copenhagen

first: Tobias

middle: Borgtoft

last: Bergmann

address: Strandboulevarden 32, 2.63

department: Veterinary and Animal Sciecnes

country: Denmark

institute: University of Copenhagen

data_processing:
CellRanger mkfastq (v2.20)
Demultiplexing of raw basecall files from illumina. Creates fastq files provided as RAW FILES
CellRanger count (v2.20)
Aligns generated fastq files (including intronic sequences), filters for empty / low quality cells, counts barcodes and UMIs in count matrix provided as PROCESSED DATA FILES
Genome_build: Sscrofa11.1 release-94
Supplementary_files_format_and_content: Count matrix stored as text file. Rows are genes and colum are cells

organism: Sus scrofa

source_name: Entorhinal cells

growth_protocol: Tissue collected from fetal / adult porcine brains. Optained from local production farm

extract_protocol: Following 10X genomics protocol

treatment_protocol:
whole cell samples: Cells from fresh tissue were dissociated using papain and 10.000-12.000 viable cells were loaded on the 10X genomics platform
isolated nucleus samples: Tissue was snapfrozen, homogenized and dissociated using a pestle. homogenate was filtered and collected nuclei were resuspended in staining buffer including 7-AAD used to later FACS sort the nuclei, befor they were loaded on the 10X genomics chip

tag: cell fraction

value: Isolated nucleus

tag: pooled brains

value: Entorhinal cells


title: E70_2

value: Whole cell

tag: cell type


title: E70_3


title: LOW SINUSOIDS Sample S70

tag: strain

tag: slide id


title: ARTERIES Sample S7

tag: area (micrometer2)

tag: niche


title: Stage E7.0 endoderm single cell plate 1B8 cell (E7.0SCVE1-B8)

value: Mid-gastrulation embryo (E7.0)

tag: tag


title: E70_1


title: LOW SINUSOIDS Sample S76

tag: distance from endosteum

tag: filter


title: ARTERIES Sample S69


title: input_BDR2_lib1_seq2

description: sequencing replicate

tag: ecotype

value: bdrs expressing Myc tag-BDR2

tag: age

value: 8-day old

tag: chip antibody


title: Stage E7.0 endoderm single cell plate 1B7 cell (E7.0SCVE1-B7)

value: Mouse embryonic cells


title: E60_3


title: input_BDR2_lib1_seq1


title: Stage E7.0 endoderm single cell plate 1B6 cell (E7.0SCVE1-B6)


title: ARTERIES Sample S68

tag: tissue

value: bone marrow


title: E60_1


title: Myc_WT

value: wild-type

value: Anti-Myc tag, clone 4A6 (Millipore 05-724, lot 2720363)

tag: library prep kit


title: E60_2


title: Stage E7.0 endoderm single cell plate 1B5 cell (E7.0SCVE1-B5)


title: ARTERIES Sample S66

value: ARTERIES

value: OK


title: Myc_BDR2

tag: genotype


title: Stage E7.0 endoderm single cell plate 1B4 cell (E7.0SCVE1-B4)

tag: developmental stage


title: input_BDR2_lib2

description: library replicate with lower amount of starting DNA


title: ARTERIES Sample S67


title: Myc_BDR1


title: Stage E7.0 endoderm single cell plate 1B9 cell (E7.0SCVE1-B9)


title: E50_1

tag: cell fraction


title: Stage E7.0 endoderm single cell plate 1B2 cell (E7.0SCVE1-B2)


title: ARTERIES Sample S64


title: Adult_1

value: Adult

tag: pooled brains


title: Stage E7.0 endoderm single cell plate 1B1 cell (E7.0SCVE1-B1)

tag: cell type


title: bdrs_HEAT_rep2

description:
processed data file:
GSF1377_RawCounts_heatshock.txt
GSF1377_NormalizedCounts_heatshock.txt
GSF1377-41_S29

data_processing:
Alignment : STAR v2.5.2b (Dobin et al., Bioinformatics, 2013) with default parameters
Filtering : samtools v1.3.1 was used to keep only primary alignments of reads with mapping quality above 10 (MapQ>10)
Counting: featureCounts from the Rsubread package (v 1.24.2) of R (v. 3.3.2) / Bioconductor (v. 3.4) was used to count uniquely mapping read pairs on TAIR10 annotated genes.
DE analysis : Differential expression analysis was performed using the DESeq2 package (v1.14.1) on protein-coding genes (excluding genes with zero counts in all samples or overlapping with blacklisted regions)
Genome_build: TAIR10
Supplementary_files_format_and_content: GSF1238_RawCounts_photomorphogenesis.txt contains the raw counts from featureCounts for the dark/light experiment
Supplementary_files_format_and_content: GSF1238_NormalizedCounts_photomorphogenesis.txt contains the DESeq2-normalized counts for the dark/light experiment
Supplementary_files_format_and_content: GSF1238_RawCounts_heatshock.txt contains the raw counts from featureCounts for the cold vs heat shock experiment
Supplementary_files_format_and_content: GSF1238_NormalizedCounts_heatshock.txt contains the DESeq2-normalized counts for the cold vs heat shock experiment

source_name: bdrs triple mutant_HEAT_seedlings

growth_protocol: Seeds were sown on MS plates and stratified for 4 days at 4°C in the dark. For the photomorphogenesis experiment, plates were grown in the dark for 5 days at 21°C. For th eheat shock experiment, plates were transfered to a growth chamber at 12°C under long day conditions (16h light/8h dark) for 12 days.

extract_protocol:
The seedlings were ground into fine powder in liquid nitrogen. Total RNA was extracted by Spectrum Plant total RNA kit (Sigma) following the manufacturer's instructions
Libraries were prepared from 1.5µg of total RNA using Illumina TruSeq Stranded mRNA Library Prep kit. Libraries were sequenced on a NextSeq500 instrument at Indiana University Center for Genomics and Bioinformatics.

treatment_protocol: For the photomorphogenesis experiment, at the end of the 5 days of growth in the dark, 3 plates were maintained in the dark, 3 plates were exposed to white light for 2h and 3 plates were exposed to white light for 4h. For the heat shock experiment, after the 12 days at 12°C, 3 plates were maintained at 12°C and 3 plates were exposed to 27°C for 4h.

tag: genotype/vaiation

value: bdrs triple mutant

tag: condition

value: HEAT

value: Twelve-day old

tag: growth

value: grown for 12 days in the cold (12°C) and then moved for 4h at 27°C

tag: light cycle

value: long day (16h light / 8h dark)

tag: temperature

value: 12 days at 12°C + 4h at 27°C

value: seedlings


title: ARTERIES Sample S63

tag: strain

tag: slide id

tag: area (micrometer2)

tag: niche

tag: distance from endosteum


title: SINUSOIDS Sample S60

tag: tissue

value: SINUSOIDS

tag: filter


title: bdrs_HEAT_rep1

description:
processed data file:
GSF1377_RawCounts_heatshock.txt
GSF1377_NormalizedCounts_heatshock.txt
GSF1377-40_S28

tag: ecotype

tag: age


title: Stage E7.0 endoderm single cell plate 1B12 cell (E7.0SCVE1-B12)

tag: developmental stage

value: Mid-gastrulation embryo (E7.0)

tag: tag


title: LOW SINUSOIDS Sample S6

value: LOW SINUSOIDS


title: Stage E7.0 endoderm single cell plate 1B11 cell (E7.0SCVE1-B11)

tag: cell type

value: Mouse embryonic cells


title: bdrs_COLD_rep3

description:
processed data file:
GSF1377_RawCounts_heatshock.txt
GSF1377_NormalizedCounts_heatshock.txt
GSF1377-34_S24

source_name: bdrs triple mutant_COLD_seedlings

tag: genotype/vaiation

value: COLD

value: grown for 12 days in the cold (12°C)


title: bdrs_COLD_rep2

description:
processed data file:
GSF1377_RawCounts_heatshock.txt
GSF1377_NormalizedCounts_heatshock.txt
GSF1377-33_S23

tag: condition


title: LOW SINUSOIDS Sample S65

value: bone marrow


title: Adult_nc

tag: cell fraction

value: Isolated nucleus

tag: pooled brains

value: Entorhinal cells


title: bdrs_COLD_rep1

description:
processed data file:
GSF1377_RawCounts_heatshock.txt
GSF1377_NormalizedCounts_heatshock.txt
GSF1377-32_S22

tag: growth

tag: light cycle

tag: temperature


title: SUB-ENDOSTEUM Sample S57

tag: strain

tag: slide id

tag: area (micrometer2)

value: SUB-ENDOSTEUM

value: OK


title: bdrs_HEAT_rep3

description:
processed data file:
GSF1377_RawCounts_heatshock.txt
GSF1377_NormalizedCounts_heatshock.txt
GSF1377-42_S30

value: bdrs triple mutant

value: HEAT

tag: tissue


title: Stage E7.0 endoderm single cell plate 1A9 cell (E7.0SCVE1-A9)


title: Stage E7.0 endoderm single cell plate 1B10 cell (E7.0SCVE1-B10)


title: ENDOSTEUM Sample S56

tag: niche

value: ENDOSTEUM

tag: distance from endosteum

tag: filter


title: WT_HEAT_rep2

description:
processed data file:
GSF1377_RawCounts_heatshock.txt
GSF1377_NormalizedCounts_heatshock.txt
GSF1377-37_S26

tag: ecotype

value: wild-type

tag: age

value: Twelve-day old

value: grown for 12 days in the cold (12°C) and then moved for 4h at 27°C

value: long day (16h light / 8h dark)


title: Stage E7.0 endoderm single cell plate 1B3 cell (E7.0SCVE1-B3)

tag: developmental stage

value: Mid-gastrulation embryo (E7.0)

tag: tag

tag: cell type


title: WT_HEAT_rep3

description:
processed data file:
GSF1377_RawCounts_heatshock.txt
GSF1377_NormalizedCounts_heatshock.txt
GSF1377-38_S27

tag: genotype/vaiation

tag: condition

value: 12 days at 12°C + 4h at 27°C

value: seedlings


title: ENDOSTEUM Sample S58


title: LOW SINUSOIDS Sample S55

value: LOW SINUSOIDS


title: Stage E7.0 endoderm single cell plate 1A7 cell (E7.0SCVE1-A7)

value: Mouse embryonic cells


title: WT_HEAT_rep1

description:
processed data file:
GSF1377_RawCounts_heatshock.txt
GSF1377_NormalizedCounts_heatshock.txt
GSF1377-36_S25

tag: growth


title: Day 9 -1

type: RNA

city: TOKYO

first: Taku

last: Saito

address: 7-3-1 Hongo, Bunkyo-ku

department: Orthopaedic Surgery, Faculty of Medicine

country: Japan

institute: The University of Tokyo

hyb_protocol: 0.6ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE 8x60K Microarray (Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Homo sapiens

source_name: iPS cells during chondrocyte differentiation by the 2C method at day 9

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1ug Total RNA using the Low Input Quick Amp Labeling Kit(Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: Total RNA was extracted from the chondrocytes using RNeasy mini kits (Qiagen) according to manufacturer’s protocol.

treatment_protocol: Human iPS cells were differentiated to chondrocytes by the 2C method for 9 days.

value: iPS

tag: day


title: Stage E7.0 endoderm single cell plate 1A8 cell (E7.0SCVE1-A8)


title: Day 9 -3


title: Day 9 -2


title: Day 5 -3

source_name: iPS cells during chondrocyte differentiation by the 2C method at day 5


title: Stage E7.0 endoderm single cell plate 1A6 cell (E7.0SCVE1-A6)


title: Stage E7.0 endoderm single cell plate 1A5 cell (E7.0SCVE1-A5)


title: WT_COLD_rep3

description:
processed data file:
GSF1377_RawCounts_heatshock.txt
GSF1377_NormalizedCounts_heatshock.txt
GSF1377-30_S21

value: COLD

value: grown for 12 days in the cold (12°C)

tag: light cycle

tag: temperature


title: WT_COLD_rep2

description:
processed data file:
GSF1377_RawCounts_heatshock.txt
GSF1377_NormalizedCounts_heatshock.txt
GSF1377-29_S20


title: Stage E7.0 endoderm single cell plate 1A3 cell (E7.0SCVE1-A3)


title: Stage E7.0 endoderm single cell plate 1A4 cell (E7.0SCVE1-A4)


title: ENDOSTEUM Sample S49

value: bone marrow

tag: strain

tag: slide id


title: Stage E7.0 endoderm single cell plate 1A2 cell (E7.0SCVE1-A2)


title: SUB-ENDOSTEUM Sample S50

tag: tissue

tag: area (micrometer2)

value: SUB-ENDOSTEUM

value: Outlier in PCA


title: SINUSOIDS Sample S54

tag: niche

value: SINUSOIDS

tag: distance from endosteum

value: OK


title: ARTERIES Sample S48

value: ARTERIES

tag: filter


title: WT_COLD_rep1

description:
processed data file:
GSF1377_RawCounts_heatshock.txt
GSF1377_NormalizedCounts_heatshock.txt
GSF1377-28_S19

tag: ecotype

value: wild-type

tag: age

value: Twelve-day old


title: ARTERIES Sample S47


title: Day 5 -1


title: Day 5 -2


title: bdrs_LIGHT4h_rep2

description:
processed data file:
GSF1377_RawCounts_photomorphogenesis.txt
GSF1377_NormalizedCounts_photomorphogenesis.txt
GSF1377-22_S17

source_name: bdrs triple mutant_LIGHT4h_seedlings

value: bdrs triple mutant

value: Five-day old

value: grown for 5 days in the dark and then exposed for 4h to white light

value: 5 days dark + 4h white light


title: Stage E7.0 endoderm single cell plate 1A1 cell (E7.0SCVE1-A1)

tag: developmental stage

value: Mid-gastrulation embryo (E7.0)

tag: tag


title: bdrs_LIGHT4h_rep1

description:
processed data file:
GSF1377_RawCounts_photomorphogenesis.txt
GSF1377_NormalizedCounts_photomorphogenesis.txt
GSF1377-21_S16

tag: genotype/vaiation

value: seedlings


title: Stage E7.0 endoderm single cell plate 1A12 cell (E7.0SCVE1-A12)

tag: cell type

value: Mouse embryonic cells


title: SINUSOIDS Sample S46


title: bdrs_LIGHT2h_rep3

description:
processed data file:
GSF1377_RawCounts_photomorphogenesis.txt
GSF1377_NormalizedCounts_photomorphogenesis.txt
GSF1377-20_S15

source_name: bdrs triple mutant_LIGHT2h_seedlings

tag: condition

tag: growth

value: grown for 5 days in the dark and then exposed for 2h to white light

value: 5 days dark + 2h white light


title: ARTERIES Sample S45

value: bone marrow


title: bdrs_LIGHT4h_rep3

description:
processed data file:
GSF1377_RawCounts_photomorphogenesis.txt
GSF1377_NormalizedCounts_photomorphogenesis.txt
GSF1377-23_S18

tag: light cycle


title: Stage E7.0 endoderm single cell plate 1A11 cell (E7.0SCVE1-A11)

description: processed data file: E7.0SingleCell.tpm.txt


title: Day 4 -3

source_name: iPS cells during chondrocyte differentiation by the 2C method at day 4

value: iPS

tag: day


title: bdrs_LIGHT2h_rep2

description:
processed data file:
GSF1377_RawCounts_photomorphogenesis.txt
GSF1377_NormalizedCounts_photomorphogenesis.txt
GSF1377-19_S14

tag: temperature


title: LOW SINUSOIDS Sample S44

tag: strain

tag: slide id

value: LOW SINUSOIDS


title: Stage E7.0 endoderm single cell plate 1A10 cell (E7.0SCVE1-A10)


title: bdrs_LIGHT2h_rep1

description:
processed data file:
GSF1377_RawCounts_photomorphogenesis.txt
GSF1377_NormalizedCounts_photomorphogenesis.txt
GSF1377-18_S13

tag: tissue


title: SINUSOIDS Sample S43

tag: area (micrometer2)

tag: niche

value: SINUSOIDS


title: veterprofin treated endoderm sample 2 (6PV)

description: processed data file: Invitro.endoderm.cluture.Yap.gene.fpkm.txt


title: veterprofin treated endoderm sample 1 (4PV)


title: bdrs_DARK_rep2

description:
processed data file:
GSF1377_RawCounts_photomorphogenesis.txt
GSF1377_NormalizedCounts_photomorphogenesis.txt
GSF1377-14_S11

source_name: bdrs triple mutant_DARK_seedlings

value: DARK

value: grown for 5 days in the dark

value: dark only


title: bdrs_DARK_rep3

description:
processed data file:
GSF1377_RawCounts_photomorphogenesis.txt
GSF1377_NormalizedCounts_photomorphogenesis.txt
GSF1377-15_S12


title: ENDOSTEUM Sample S41

value: ENDOSTEUM

tag: distance from endosteum

tag: filter

value: OK


title: control endoderm sample 3 (3PC)

source_name: Mouse embryonic cells


title: Day 4 -1


title: SUB-ENDOSTEUM Sample S42

value: SUB-ENDOSTEUM


title: Day 3 -2

source_name: iPS cells during chondrocyte differentiation by the 2C method at day 3


title: bdrs_DARK_rep1

description:
processed data file:
GSF1377_RawCounts_photomorphogenesis.txt
GSF1377_NormalizedCounts_photomorphogenesis.txt
GSF1377-13_S10

tag: ecotype

value: bdrs triple mutant

tag: age

value: Five-day old


title: ARTERIES Sample S53

source_name: Bone Marrow

value: ARTERIES


title: control endoderm sample 2 (2PC)

tag: developmental stage

value: Mid-gastrulation embryo (E7.0)

tag: tag


title: Day 4 -2

tag: cell type


title: KO_Input_Rep2_S6

city: Bethesda

first: David

last: Sturgill

state: MARYLAND

address: Building 41, Rm B622

department: NCI

institute: NIH

data_processing:
ChIP-seq reads were aligned to mm10 using Bowtie version 2.2.9 with default parameters.  Depth normalized read densities were produced with deepTools.
Peak calling was performed with MACS (v 2.2.1), using sonicated chromatin (input) as the control
For RNA-Seq, reads were trimmed, and aligned using Tophat 2.1.1.  Gene expression values were computed with Cufflinks v.2.2.1 using Ensembl rel.83 annotation for mm10
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files include depth normalized read density tracks
Supplementary_files_format_and_content: bed files include peak calling results; text (Cuffdiff output)

growth_protocol: Tdg knockout mouse embryonic stem cells (Tdg KO mESC) and wildtype control mESC were a gift from Dr. Primo Schar. Complete mESC media was composed of KnockOut DMEM (Gibco), supplemented with 2 mM GlutaMAX (Gibco), non-essential amino acids (Gibco), 0.1 mM 2-mercaptoethanol (SIGMA), 1,000 U/ml LIF (Millipore, #ESG1106), and 15% ES-tested FBS (Gibco, #10439-024). mESC were co-cultured with mitotically-arrested mouse embryonic fibroblast (MEF; produced in-house or purchased from Millipore, #PMEF-CF) on gelatin-coated (Millipore, #ES-006-B) dishes. MEF depletion was achieved by three 10-minute rounds of serial-plating onto uncoated tissue culture dishes. Human CD4+ human T lymphocytes were acquired and cultured as described in Marina et al., 2016.

extract_protocol:
Prior to chromatin immunoprecipitation, antibodies (5 μl polyclonal or 5 μg monoclonal) were pre-bound to 200 μl Protein G magnetic beads (Invitrogen, #10004D) by overnight incubation in PBS with 5% BSA; beads were washed and resuspended in PBS with 5% BSA. MEF-depleted mESC were fixed at room temperature with 1% formaldehyde (Sigma-Aldrich, # 252549) for 5 min; fixation was stopped by adding glycine (ICN Biomedical, #ICN808822) to 125 mM. Cell membranes were lysed with cold NP-40 buffer (1% NP40, 150 mM NaCl, 50 mM Tris–HCl; pH 8.0) and nuclei collected by centrifugation at 12,000 × g for 1 min at 4 °C. Nuclear pellets were resuspended at a concentration of 2E8 cells/ml in ChIP sonication buffer (1% SDS, 10 mM EDTA, 50 mM Tris–HCl; pH 8.0) supplemented with protease (Thermo Scientific, #78430) and phosphatase (Calbiochem, #524627) inhibitor cocktails. Chromatin was sheared into 150-400 bp fragments by sonication (Bioruptor Twin, Diagenode). Debris was pelleted by centrifugation and cleared chromatin was diluted 10-fold in ChIP dilution buffer (1.1% Triton X-100, 0.01% SDS, 167 mM NaCl, 1.2 mM EDTA, 16.7 mM Tris–HCl; pH 8.1). The prepared antibody-bound beads were added to 1 ml diluted chromatin containing 2E7 million cell equivalents and incubated overnight with rotation at 4 °C. Immune complexes were washed 5 times with LiCl wash buffer (250 mM LiCl, 1% NP-40, 1% sodium deoxycholate, 100 mM Tris-HCl; pH 7.5) and once with TE (0.1 mM EDTA, 10 mM Tris-HCl; 7.5). Beads were resuspended in IP Elution Buffer (1% SDS, 0.1 M NaHCO3) and crosslinks reversed by overnight incubation at 65 °C. DNA was purified by column purification (QIAGEN, # 28106)
Sequencing libraries were constructed from DNA samples with the Illumina TruSeq V3 library construction protocol.

tag: strain background

tag: genotype/variation

value: TDG KO

value: mESCs

tag: chip antibody


title: control endoderm sample 1 (1PC)

value: Mouse embryonic cells


title: wt_LIGHT4h_rep3

description:
processed data file:
GSF1377_RawCounts_photomorphogenesis.txt
GSF1377_NormalizedCounts_photomorphogenesis.txt
GSF1377-12_S9

tag: genotype/vaiation

value: wild-type

tag: condition

tag: growth

value: grown for 5 days in the dark and then exposed for 4h to white light

tag: light cycle

value: 5 days dark + 4h white light

value: seedlings


title: SUB-ENDOSTEUM Sample S4

tag: tissue

value: bone marrow

tag: strain

tag: slide id


title: KO_Input_Rep1_S5


title: LOW SINUSOIDS Sample S40

tag: area (micrometer2)

tag: niche

value: LOW SINUSOIDS

tag: distance from endosteum


title: wt_LIGHT4h_rep2

description:
processed data file:
GSF1377_RawCounts_photomorphogenesis.txt
GSF1377_NormalizedCounts_photomorphogenesis.txt
GSF1377-11_S8

tag: ecotype

tag: age

tag: temperature


title: KO_IgGr_rep_pooled_S8

tag: cell type

value: anti-IgG (CST, #2729)


title: ARTERIES Sample S39

tag: filter


title: Stage E6.0 embryo 3Reference section 5 region P (E6.0_3Ref_5P)

description: processed data file: E6.0_Embryo3Reference_all.samples.genes.fpkm.txt

tag: developmental stage

value: Pre-gastrulation embryo (E6.0)

tag: tag


title: wt_LIGHT4h_rep1

description:
processed data file:
GSF1377_RawCounts_photomorphogenesis.txt
GSF1377_NormalizedCounts_photomorphogenesis.txt
GSF1377-10_S7

tag: genotype/vaiation


title: Stage E6.0 embryo 3Reference section 5 region EP (E6.0_3Ref_5EP)


title: Day 3 -3

value: iPS

tag: day


title: KO_IgGm_rep_pooled_S7

tag: strain background

tag: genotype/variation

tag: chip antibody

value: anti-IgG (DA1E) (CST, #3900)


title: ENDOSTEUM Sample S37

tag: tissue

tag: strain

value: ENDOSTEUM

value: OK


title: wt_LIGHT2h_rep3

description:
processed data file:
GSF1377_RawCounts_photomorphogenesis.txt
GSF1377_NormalizedCounts_photomorphogenesis.txt
GSF1377-08_S6

tag: condition

value: Five-day old

tag: growth

value: grown for 5 days in the dark and then exposed for 2h to white light

tag: light cycle

value: 5 days dark + 2h white light


title: Day 2 -3

source_name: iPS cells during chondrocyte differentiation by the 2C method at day 2


title: Day 3 -1


title: Day 2 -2


title: Stage E6.0 embryo 3Reference section 5 region EA (E6.0_3Ref_5EA)


title: KO_CTCF_Rep2_S2

value: TDG KO

value: mESCs

value: anti-CTCF (CST, #3418)


title: Day 0 -3

source_name: iPS cells during chondrocyte differentiation by the 2C method at day 0


title: Day 2 -1


title: KO_CTCF_Rep1_S1


title: Day 0 -2


title: wt_LIGHT2h_rep2

description:
processed data file:
GSF1377_RawCounts_photomorphogenesis.txt
GSF1377_NormalizedCounts_photomorphogenesis.txt
GSF1377-07_S5

tag: ecotype

value: wild-type


title: Day 0 -1


title: SINUSOIDS Sample S36

tag: slide id

tag: area (micrometer2)

tag: niche

value: SINUSOIDS

tag: distance from endosteum


title: Stage E6.0 embryo 3Reference section 5 region A (E6.0_3Ref_5A)

tag: developmental stage

tag: cell type

value: Mouse embryonic cells


title: wt_LIGHT2h_rep1

description:
processed data file:
GSF1377_RawCounts_photomorphogenesis.txt
GSF1377_NormalizedCounts_photomorphogenesis.txt
GSF1377-06_S4

tag: genotype/vaiation

tag: age

tag: temperature

value: seedlings


title: KO_4H8_Rep2_S4

tag: strain background

tag: genotype/variation

value: anti-RNA pol II (Millipore, #05-623)


title: ARTERIES Sample S34

tag: tissue

value: bone marrow

value: ARTERIES

tag: filter


title: SUB-ENDOSTEUM Sample S38

tag: strain

value: SUB-ENDOSTEUM


title: ARTERIES Sample S35


title: Stage E6.0 embryo 3Reference section 4 region EP (E6.0_3Ref_4EP)

value: Pre-gastrulation embryo (E6.0)

tag: tag


title: WT_Input_Rep1_S5

value: WT

tag: chip antibody


title: WT_Input_Rep2_S6


title: Stage E6.0 embryo 3Reference section 4 region P (E6.0_3Ref_4P)


title: wt_DARK_rep2

description:
processed data file:
GSF1377_RawCounts_photomorphogenesis.txt
GSF1377_NormalizedCounts_photomorphogenesis.txt
GSF1377-02_S2

tag: ecotype

tag: condition

value: DARK

tag: growth

value: grown for 5 days in the dark

tag: light cycle

value: dark only


title: SINUSOIDS Sample S33

tag: slide id

tag: area (micrometer2)

tag: niche

tag: distance from endosteum

value: OK


title: Stage E6.0 embryo 3Reference section 4 region A (E6.0_3Ref_4A)

tag: developmental stage

tag: cell type


title: wt_DARK_rep1

description:
processed data file:
GSF1377_RawCounts_photomorphogenesis.txt
GSF1377_NormalizedCounts_photomorphogenesis.txt
GSF1377-01_S1

tag: genotype/vaiation

tag: age

value: Five-day old

tag: temperature


title: KO_4H8_Rep1_S3

tag: strain background

tag: genotype/variation

value: TDG KO

value: mESCs


title: WT_IgGr_rep_pooled_S8

value: anti-IgG (CST, #2729)


title: Stage E6.0 embryo 3Reference section 3 region P (E6.0_3Ref_3P)

tag: tag


title: ENDOSTEUM Sample S30

tag: tissue

tag: strain

value: ENDOSTEUM

tag: filter


title: fpa_rep2

data_processing:
Alignment : STAR v2.5.2b (Dobin et al., Bioinformatics, 2013) with default parameters
Filtering : samtools v1.3.1 was used to keep only primary alignments of reads with mapping quality above 10 (MapQ>10)
Counting: featureCounts from the Rsubread package (v 1.24.2) of R (v. 3.3.2) / Bioconductor (v. 3.4) was used to count uniquely mapping read pairs on TAIR10 annotated genes.
DE analysis : Differential expression analysis was performed using the DESeq2 package (v1.14.1) on protein-coding genes (excluding genes with zero counts in all samples or overlapping with blacklisted regions)
Genome_build: TAIR10
Supplementary_files_format_and_content: GSF1238_RawCounts_bdrs.txt contains the raw counts from featureCounts
Supplementary_files_format_and_content: GSF1238_NormalizedCounts_bdrs.txt contains the DESeq2-normalized counts

source_name: fpa single mutant (fpa-7)_seedlings

extract_protocol:
The seedlings were ground into fine powder in liquid nitrogen. Total RNA was extracted using Trizol reagent following the manufacturer's instructions
Libraries were prepared from 1.5µg of total RNA using Illumina TruSeq Stranded mRNA Library Prep kit. Libraries were sequenced on a NextSeq500 instrument at Indiana University Center for Genomics and Bioinformatics.

tag: ecotype

value: fpa single mutant (fpa-7)

value: Eight-day old


title: WT_IgGm_rep_pooled_S7

tag: chip antibody

value: anti-IgG (DA1E) (CST, #3900)


title: wt_DARK_rep3

description:
processed data file:
GSF1377_RawCounts_photomorphogenesis.txt
GSF1377_NormalizedCounts_photomorphogenesis.txt
GSF1377-03_S3

value: wild-type

tag: condition

tag: growth

tag: light cycle

value: seedlings


title: fpa_rep1


title: WT_CTCF_Rep2_S2

value: anti-CTCF (CST, #3418)


title: ENDOSTEUM Sample S3

value: bone marrow

tag: slide id

tag: area (micrometer2)

tag: niche

tag: distance from endosteum


title: Stage E6.0 embryo 3Reference section 3 region EA (E6.0_3Ref_3EA)

tag: developmental stage

value: Pre-gastrulation embryo (E6.0)

tag: cell type

value: Mouse embryonic cells


title: Stage E6.0 embryo 3Reference section 3 region EP (E6.0_3Ref_3EP)


title: LOW SINUSOIDS Sample S29

value: LOW SINUSOIDS


title: Stage E6.0 embryo 3Reference section 4 region EA (E6.0_3Ref_4EA)


title: bdrs_rep2

source_name: bdrs triple mutant_seedlings

value: bdrs triple mutant

tag: age


title: WT_4H8_Rep2_S4

tag: strain background

tag: genotype/variation

value: WT

value: anti-RNA pol II (Millipore, #05-623)


title: WT_CTCF_Rep1_S1


title: ARTERIES Sample S32

tag: tissue

value: ARTERIES

value: OK


title: WT_4H8_Rep1_S3

value: mESCs


title: SINUSOIDS Sample S28

tag: strain

value: SINUSOIDS


title: Stage E6.0 embryo 3Reference section 2 region P (E6.0_3Ref_2P)

tag: tag


title: Stage E6.0 embryo 3Reference section 2 region EP (E6.0_3Ref_2EP)


title: SUB-ENDOSTEUM Sample S31

value: SUB-ENDOSTEUM

tag: filter

value: Outlier in PCA


title: ARTERIES Sample S27


title: Stage E6.0 embryo 3Reference section 2 region EA (E6.0_3Ref_2EA)


title: fpa_rep3

tag: ecotype

value: fpa single mutant (fpa-7)

value: Eight-day old


title: ARTERIES Sample S26


title: Stage E6.0 embryo 3Reference section 2 region A (E6.0_3Ref_2A)


title: SUB-ENDOSTEUM Sample S24


title: bdrs_rep3

value: seedlings


title: Stage E6.0 embryo 3Reference section 3 region A (E6.0_3Ref_3A)


title: Stage E6.0 embryo 3Reference section 1 region EAP (E6.0_3Ref_1EAP)


title: fpa_3

data_processing:
Alignment : Tophat v2.0.8 (Trapnell et al., Bioinformatics, 2009)
Filtering : samtools v1.2 and grep unix command on tag "NH :i :1" were used to keep only uniquely mapped reads
Counting: featureCounts from the Rsubread package (v 1.24.2) of R (v. 3.3.2) / Bioconductor (v. 3.4) was used to count uniquely mapped reads on TAIR10 annotated genes using option strandSpecific=0 (non stranded).
DE analysis : Differential expression analysis was performed using the DESeq2 package (v1.14.1) on protein-coding genes (excluding genes with zero counts in all samples or overlapping with blacklisted regions). Sample WT_12 was removed from the DE analysis because of its low sequencing depth.
Genome_build: TAIR10
Supplementary_files_format_and_content: GSF509_RawCounts.txt contains the raw counts from featureCounts
Supplementary_files_format_and_content: GSF509_NormalizedCounts.txt contains the DESeq2-normalized counts

extract_protocol:
The seedlings were ground into fine powder in liquid nitrogen. Total RNA was extracted with Plant/Fungi Total RNA purification kit (Norgen) following the manufacturer's instructions
Libraries were prepared from 3µg of total RNA using Illumina RNA TruSeq Sample Prep kit. Libraries were sequenced on a HiSeq2000 instrument at the Beijing Genomics Institute.


title: bdrs_7

source_name: bdr triple mutant_seedlings

value: bdr triple mutant


title: fpa_6


title: bdr2_rep3

source_name: bdr2 single mutant (CS852350)_seedlings

value: bdr2 single mutant (CS852350)


title: bdr3_rep1

source_name: bdr3 single mutant (SALK_059905)_seedlings

value: bdr3 single mutant (SALK_059905)


title: bdr3_rep2


title: bdr3_rep3


title: ENDOSTEUM Sample S23

value: bone marrow

value: ENDOSTEUM


title: Stage E6.0 embryo 3Reference section 1 region AP (E6.0_3Ref_1AP)

value: Pre-gastrulation embryo (E6.0)

value: Mouse embryonic cells


title: bdrs_rep1

value: bdrs triple mutant


title: fpa_8


title: ARTERIES Sample S22

value: ARTERIES


title: Stage E5.5 embryo 3Reference section 3 region VE2 (E5.5_3Ref_3EB)

description: processed data file: E5.5_Embryo3Reference_all.samples.genes.fpkm.txt

value: Pre-gastrulation embryo (E5.5)


title: bdrs_2


title: bdr2_rep2


title: bdr2_rep1


title: bdr1_rep3

source_name: bdr1 single mutant (SALK_142108C)_seedlings

value: bdr1 single mutant (SALK_142108C)


title: WT_5

value: wild-type


title: ARTERIES Sample S20

value: OK


title: Stage E5.5 embryo 3Reference section 3 region Epi2 (E5.5_3Ref_3B)


title: ARTERIES Sample S25


title: WT_12


title: bdr1_rep2


title: Stage E5.5 embryo 3Reference section 3 region Epi1 (E5.5_3Ref_3A)


title: LOW SINUSOIDS Sample S19

value: LOW SINUSOIDS


title: WT_1


title: bdrs_4


title: bdr1_rep1


title: SUB-ENDOSTEUM Sample S18

value: SUB-ENDOSTEUM


title: Stage E5.5 embryo 3Reference section 2 region VE1 (E5.5_3Ref_2EA)


title: WT_rep2

value: Eight-day old


title: ENDOSTEUM Sample S17


title: SINUSOIDS Sample S15

value: SINUSOIDS


title: Stage E5.5 embryo 3Reference section 2 region VE2 (E5.5_3Ref_2EB)


title: luh4_4h

city: Qingdao

first: Zhong-Bao

last: Yang

state: Shandong

address: 72# Binhai Road

department: School of Life Science

institute: Shandong University (Qingdao)

data_processing:
By base calling, the original image data produced by the sequencer is transferred into sequences, which are defined as "raw reads"(or "raw data") and saved as ".fastq" files. As the raw reads may contain low quality reads and or adaptor sequences, preprocessing is necessary before starting further analysis. Normally, data cleaning (or data filtering) is performed to obtain "clean reads" (or "clean data") for further analysis.
As there are some adaptor sequences and/or low quality reads present in the raw reads, data filtering is carried out to obtain high quality reads as the clean reads (clean data). The procedure include following steps: 1. Remove reads with adaptor sequences. 2. Remove reads in which the percentage of unknown bases (N) is greater than 10%. 3. Remove low quality reads. If the percentage of the low quality base (base with quality value ≤ 5) is greater than 50% in a read, we define this read as low quality
The gene expression level is calculated by using RPKM[Mortazavi et al. (2008). Nature Methods. 5(7): 621-8] method (Reads Per kb per Million reads),
Clean reads were mapped to reference sequences and/or reference gene set using SOAPaligner/SOAP2[Li R et al. (2009) Bioinformatics, 25 (15). 1966-1967.]. No more than 2 mismatches were allowed in the alignment
Genome_build: TAIR10
Supplementary_files_format_and_content: Excel files include RPKM values for each Sample

source_name: roots_with Al

growth_protocol: The seedlings were pre-grown in nutrient solution for 6 d at pH5.5 in a growth chamber with a 16/8 h light/dark cycle at 22 oC.

extract_protocol:
Total RNA was isolated using the RNeasy® Plant Mini Kit (QIAGEN GmbH, Qiagen, GmbH, Hilden, Germany) following the manufacturer’s protocol.  RNA libraries were prepared for sequencing using standard Illumina protocols
The total RNA samples are first treated with DNase I to degrade any possible DNA contamination. Then the mRNA is enriched by using the oligo(dT) magnetic beads (for eukaryotes). Mixed with the fragmentation buffer, the mRNA is fragmented into short fragments (about 200 bp). Then the first strand of cDNA is synthesized by using random hexamer-primer. Buffer, dNTPs, RNase H and DNA polymerase I are added to synthesize the second strand. The double strand cDNA is purified with magnetic beads. End reparation and 3'-end single nucleotide A (adenine) addition is then performed. Finally, sequencing adaptors are ligated to the fragments. The fragments are enriched by PCR amplification. During the QC step, Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System are used to qualify and quantify of the sample library. The library products are ready for sequencing via Illumina HiSeqTM 2000 or other sequencer when necessary.

treatment_protocol: Approximately 500 seedlings (6-d-old) of both the wild-type Col and luh-4 mutant line were exposed to a nutrient solution containing 0 or 25 μM AlCl3 (pH4.2). After 4 h, the roots were sampled for RNA isolation.

value: root

tag: old of seedlings

value: six-days

tag: time point

value: luh-4 mutant

tag: treament

value: with Al

value: Columbia


title: WT_rep3

value: seedlings


title: Stage E5.5 embryo 3Reference section 3 region VE1 (E5.5_3Ref_3EA)

value: Mouse embryonic cells


title: ARTERIES Sample S21

value: bone marrow

tag: slide id


title: Col_4h

value: wildtype


title: WT_rep1


title: ENDOSTEUM Sample S13

tag: area (micrometer2)

value: ENDOSTEUM


title: Stage E5.5 embryo 3Reference section 2 region Epi2 (E5.5_3Ref_2B)

value: Pre-gastrulation embryo (E5.5)


title: Stage E5.5 embryo 3Reference section 1 region VE (E5.5_3Ref_1EAB)


title: SUB-ENDOSTEUM Sample S14

tag: niche


title: Col_0h

source_name: roots_without Al

value: without Al


title: Stage E5.5 embryo 3Reference section 2 region Epi1 (E5.5_3Ref_2A)


title: SINUSOIDS Sample S12

tag: distance from endosteum

value: OK


title: Stage E5.5 embryo 3Reference section 1 region Epi (E5.5_3Ref_1AB)

tag: developmental stage


title: SUB-ENDOSTEUM Sample S11


title: luh4_0h


title: YY1512_R1

city: Boston

first: Anne

last: Dodson

address: 77 Avenue Louis Pasteur, NRB Room 266

institute: Harvard Medical School

description: total small RNA

data_processing:
Select reads starting with the last 4 nucleotides of the 5’ adapters (either AGCG or CGTC).
Trim the 3’ adapter (cutadapt -a CTGTAGGCACCATCAATAGATCGGAAGAGCAC -m 14 --discard-untrimmed).
Trim the in-line portion of the 5’ adapter (cutadapt -u 4).
Align reads to the C. elegans genome (WS260) using Bowtie
Count reads mapping antisense to each gene (featureCounts -s 2)
Normalize reads using DESeq2
Genome_build: WS260
Supplementary_files_format_and_content: Text file lists the number of reads (normalized using DESeq2) mapping antisense to each gene for each sample.

organism: Caenorhabditis elegans

source_name: population - whole animal

growth_protocol: Synchronous populations of animals were grown on E. coli OP50 at 20˚C.

extract_protocol:
Adult worms were flash-frozen in liquid nitrogen. Total RNA was isolated by TRIzol extraction. RNAs ranging from approximately 15 to 30 nucleotides were gel-purified from total RNA (20 ug) on a 15% polyacrylamide/urea gel.
Small RNA species were ligated to a 3’ adapter (/5rApp/CTGTAGGCACCATCAAT/3ddC/) using T4 RNA ligase 2, truncated (NEB). To enable the cloning of 5’-triphosphorylated RNAs, samples were treated with Antarctic Phosphatase (NEB) followed by treatment with T4 polynucleotide kinase (NEB). Prior to ligation of the 5’ adapter, 3’-ligated small RNAs and any excess 3’ adapter were hybridized to the oligo that would eventually be used as a primer for reverse transcription (5’ GGAGTTCAGACGTGTGCTCTTCCGATCTATTGATGGTGCCTACAG). To help avoid cross-contamination, the 5’ adapter was modified to contain the Illumina genomic sequencing primer annealing site followed by an additional 4 nucleotides at the 3’ end. Two different 5’ adapters (/5AmMC6/ACGCTCTTCCGATCTrArGrCrG and /5AmMC6/ACGCTCTTCCGATCTrCrGrUrC) were mixed in a 1:1 ratio, and the mix was ligated to each sample using T4 RNA ligase I (NEB). Every sample was treated with the same mix of 5’ adapters. Libraries were amplified and multiplexed with a 6-nucleotide 3’ barcode, then pooled for next-generation sequencing on a NextSeq500.

value: whole animal

tag: genotype/generation

value: hrde-1; meg-3 meg-4

value: young adults

tag: biological replicate


title: YY1512_R2

description: total small RNA


title: WT_F25_R2

description: total small RNA

value: wild type descendant (F25)


title: ENDOSTEUM Sample S10


title: WT_F25_R1

description: total small RNA


title: wild-type (Col-0)

city: Athens

first: Polydefkis

last: Hatzopoulos

address: Iera Odos 75

department: Biotechnology

country: Greece

institute: Agricultural University of Athens

data_processing:
Raw reads were filtered into clean reads and aligned to the Arabidopsis genome (TAIR10).
Raw reads were filtered into clean reads and aligned to the Arabidopsis genome (TAIR10).  RNA-seq data were analyzed using the SOAPnuke (version v.1.5.2) with parameters “-l 15 -q 0.2 -n 0.05” and the HISAT2 pipeline (version 2.0.4) with parameters “--phred64 --sensitive --no-discordant --no-mixed -I 1 -X 1000”
Differential alternative splicing events were detected for lefko1 and wild-type using rMATS.
genome build: Arabidopsis genome reference (TAIR10)
processed data files format and content: Excel file with alternative splicing enents (Intron retention, 5’ and 3’ alternative start site, exon skipping) including Gene ID and coordinates.

source_name: Arabidopsis seeds

growth_protocol: Arabidopsis thaliana seeds were surface-sterilized and sown in Petri dishes containing 0.5x Murashige and Skoog (MS) medium (Duchefa) pH 5.7, supplemented with 1% sucrose and solidified with 0.4% phytagel (Sigma). After 24 hr of stratification at 4°C, seedlings were positioned to grow vertically after germination at 22°C in a Fitotron growth chamber under a long photoperiod with 16h of light and 8h of darkness per day and 100 μmol m–2 s–1 light intensity.

extract_protocol:
Total RNA was extracted from lefko1 mutant and wild-type Arabidopsis cotyledons using the NucleoSpin Plant RNA kit (Macherey-Nagel, Düren, Germany) with an on-column DNase treatment according to the manufacturer’s instructions. The quantity and integrity of the RNA were assessed using a NanoDrop 1000 spectrophotometer and agarose gel electrophoresis.
RNA-seq libraries were generated using the TruSeq Low Input kit according to the manufacturer’s instructions (Illumina).


title: ARTERIES Sample S1

value: ARTERIES


title: WT_F15_R2

description: total small RNA

value: wild type descendant (F15)


title: lefko2


title: WT_F15_R1

description: total small RNA


title: TU 2 mvaTU mutant

city: LOWELL

first: GUOQING

last: LI

state: MA

address: 220 Pawtucket St

institute: University of Massachusetts Lowell

description: Gene expression data from Pseudomonas aeruginosa PAO1 mvaT/mvaU knockout mutant.

hyb_protocol: The fragmented cDNA samples were hybridized with the protocol of GeneChip Expression Analysis Technical Manual

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

organism: Pseudomonas aeruginosa PAO1

source_name: Pseudomonas aeruginosa PAO1

label_protocol: Use GeneChip DNA Labeling Reagent (Affymetrix, P/N 900542) to label the 3' termini of the fragmentation products.

growth_protocol: Strains were cultured in 2YT broth at 37°C to OD600=0.6

extract_protocol: Use Qiagen RNeasy Mini Kit to extract total RNA, synthesize and fragement cDNA according to GeneChip Expression Analysis Technical Manual

treatment_protocol: Harvest cells by centrifuging at 5000*g for 5min at 4°C

value: mvaT/mvaU double knockout


title: WT_F10_R2

description: total small RNA

value: wild type descendant (F10)


title: HCV.29.TSC1- 100nm THZ1 Rep2 [100_2_minus_minus]

first: Mahsa

last: Zarei

state: Massachusetts

address: 20 Shattuck Street, Thorn Building (D), 823

department: Medicine

institute: BWH

description: MZ_20170423_100_2_minus_minus_MZ4196-2_S9

data_processing:
Quality trimming on raw reads was performed using Cutadapt prior to sequence mapping (http://journal.embnet.org/index.php/embnetjournal/article/view/200).
Sequence reads were aligned to the hg19 human genome build using the STAR aligning program.
A two-pass alignment was performed and only those reads mapping uniquely to the human genome were maintained for further analysis.
Quantification of all genes and their isoforms was performed using FPKM normalized values using Cufflinks v2.2.1,  differentially expressed genes were identified using the DESeq2 package and manual analysis
Genome_build: hg19
Supplementary_files_format_and_content: Cuff_Gene_Counts.csv file include FPKM normalized values generated by using Cufflinks v2.2.1.

source_name: HCV.29.TSC1- 100nm THZ1

growth_protocol: HCV.29 cells were maintained in high glucose DMEM supplemented with 10% FBS and 1% penicillin/streptomycin (Invitrogen).

extract_protocol:
Total RNA was extracted using the RNeasy mini kit (Qiagen) and analyzed on Agilent 2100 Bioanalyzer for integrity.
RNA Sequencing libraries were constructed by standard methods; 2x75 bp paired-end reads and ~50 million reads were generated for each sample.

treatment_protocol: HCV.29.TSC1- andHCV.29.TSC1+ Cells were plated in 100mm3 dishes in duplicate and treated with DMSO,THZ1 30nM or THZ1 100nM  for 6 hours.

tag: cell line

tag: cell type

value: urothelial cell lines; Bladder Cancer cells

tag: genotype

tag: passages

value: 5 to 8

tag: treatment

value: 100nm THZ1


title: P2 phage KO parental

description: Gene expression data from Pseudomonas aeruginosa PAO1 phage knockout strain.

tag: genotype/variation

value: parental strain


title: TU 1 mvaTU mutant


title: WT_F20_R2

description: total small RNA

tag: tissue

value: wild type descendant (F20)


title: WT_F10_R1

description: total small RNA


title: P1 phage KO parental


title: WT_F20_R1

description: total small RNA


title: HCV.29.TSC1- 30nm THZ1 Rep2 [30_2_minus_minus]

description: MZ_20170423_30_2_minus_minus_MZ4196-2_S7

source_name: HCV.29.TSC1- 30nm THZ1

value: 30nm THZ1


title: HCV.29.TSC1- 100nm THZ1 Rep1 [100_1_minus_minus]

description: MZ_20170423_100_1_minus_minus_MZ4196-2_S8


title: sh-ILF3-1

city: 广州

first: Kai

last: Li

state: 广东

address: 员村二横路26号

department: Guangdong Provincial Key laboratory of Colorectal and Pelvic Floor Disease

institute: Sun Yat-sen University

description: Gene expression data from DLD1 colorectal cancer cell line, i.e. transcription of shRNA targeting ILF3.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: DLD1 cells were obtained from ATCC, and maintained at 37 °C and 5% CO2. Cells were maintained in Dulbecco’s modified Eagle’s medium media supplemented with 10% (v/v) fetal bovine serum (FBS).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: We screened four hairpin shRNAs targeting human ILF3 transcripts and found shILF3-31 that reduced mRNA levels by >70%. The shRNA was in the pLKO.1 vector.Cells were infected twice with culture medium containing 2ml lentivirus expressing shILF3-31, 200μl FBS and 5 mg/ml polybrene (Sigma) at 37℃ for 24 hr and 48 hr. To increase the knockdown efficiency, infected cells were under several days of puromycin selection.

value: colorectal cancer cell line DLD1


title: WT_F7_R2

description: total small RNA

value: wild type descendant (F7)


title: HCV.29.TSC1- 30nm THZ1 Rep1 [30_1_minus_minus]

description: MMZ_20170423_30_1_minus_minus_MZ4196-2_S6


title: LNCaP_EPS-conditioned medium_72h

city: Erlangen

first: Yurdagül

last: Zopf

address: Ulmenweg 18

department: Medicine 1

country: Germany

institute: University Clinic Erlangen

description: After starvation: Treatment with EPS-conditioned myotube medium for 72 h

hyb_protocol: according to manufacturer's protocol

scan_protocol: according to manufacturer's protocol

data_processing: according to manufacturer's protocol

label: Nanostring probes

source_name: metastic prostate cancer tissue

label_protocol: according to manufacturer's protocol

growth_protocol: Normal growth of LNCaP cells in RPMI 1640, 10% FCS, antibiotics until starvation for 24 h in RPMI 1640, 0.1% FCS, antibiotics

extract_protocol: Total RNA isolation using RNeasy Plus Mini Kit (Qiagen, Hilden, Germany)

treatment_protocol: Treatment of LNCaP cells in RPMI 1640 with 10% patient serum pools for 24 h or 72 h; treatment of LNCaP cells with EPS-conditioned human skeletal myotube medium (DMEM + 10% serum) for 24 h or 72 h

value: LNCaP

value: prostate cancer cell line


title: B0568 Healthy

city: Shanghai

first: Yu

last: Zhao

address: NO528 Zhangheng Road, Pudong district

institute: Shuguang Hospital affiliated to Shanghai University of Traditional Chinese Medicine

description: Expression data of peripheral blood leukocytes in patients with Health

hyb_protocol: GeneChips were washed and stained using GeneChip® HT Hybridization, Wash, and Stain Kit (901405 ,Affymetrix)

scan_protocol: GeneChips were scanned using the GeneTitan system.

data_processing: Expression console

source_name: Healthy

label_protocol: Biotinylated cDNA were prepared according to NUGEN Ovation® WB Reagent( 1300, NUGEN )and Encore® Biotin Module( 4200, NUGEN )’s  instructions from 100 ng total RNA

extract_protocol: Total RNA was extracted and purified using QIAamp RNA Blood Mini Kit（Cat#52304, QIAGEN, GmBH, Germany) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

value: peripheral blood leukocytes

tag: diagnosis

value: Healthy


title: LNCaP_medium_72h

description: After starvation: Treatment with control myotube medium for 72 h


title: B0579 Healthy


title: B0574 Healthy


title: B0580 Healthy


title: sh-ILF3-2


title: control HCV.29.TSC1- Rep2 [0_2_minus_minus]

description: MMZ_20170423_0_2_minus_minus_MZ4196-2_S5

source_name: control HCV.29.TSC1-

value: DMSO


title: WT_F6_R2

description: total small RNA

value: whole animal

value: wild type descendant (F6)

value: young adults


title: WT_F7_R1

description: total small RNA


title: LNCaP_WB-EMS serum pool week 12_72h

description: After starvation: Treatment with WB-EMS patient serum from study end for 72 h


title: B0567 Healthy


title: B0570 Healthy


title: control HCV.29.TSC1- Rep1 [0_1_minus_minus]


title: B0581 Healthy


title: LNCaP_WB-EMS serum pool week 0_72h

description: After starvation: Treatment with WB-EMS patient serum from study entry for 72 h


title: WT_F6_R1

description: total small RNA


title: HCV.29.TSC1+ 100nm THZ1 Rep2 [100_2_plus_plus]

source_name: HCV.29.TSC1+ 100nm THZ1


title: Scramble RNA-2

description: Gene expression data from DLD1 colorectal cancer cell line, i.e. transcription of scramble RNA.


title: WT_F5_R2

description: total small RNA

value: wild type descendant (F5)


title: LNCaP_Control serum pool week 12_72h

description: After starvation: Treatment with control patient serum from study end for 72 h


title: HCV.29.TSC1+ 30nm THZ1 Rep1 [30_1plus_plus]

source_name: HCV.29.TSC1+ 30nm THZ1

value: urothelial cell lines; Bladder Cancer cells


title: B0551 Healthy


title: B0557 Healthy


title: WT_F4_R2

description: total small RNA

value: wild type descendant (F4)


title: WT_F5_R1

description: total small RNA


title: LNCaP_medium_24h

description: After starvation: Treatment with control myotube medium for 24 h


title: LNCaP_Control serum pool week 0_72h

description: After starvation: Treatment with control patient serum from study entry for 72 h


title: WT_F4_R1

description: total small RNA


title: control HCV.29.TSC1+ Rep1 [0_1plus_plus]

source_name: control HCV.29.TSC1+

value: 5 to 8


title: Scramble RNA-1


title: control HCV.29.TSC1+ Rep2 [0_2_plus_plus]


title: WT_F3_R2

description: total small RNA

value: wild type descendant (F3)


title: HCV.29.TSC1+ 100nm THZ1 Rep1 [100_1_plus_plus]

value: 100nm THZ1


title: LNCaP_EPS-conditioned medium_24h

description: After starvation: Treatment with EPS-conditioned myotube medium for 24 h


title: B0549 Healthy


title: LNCaP_WB-EMS serum pool week 12_24h

description: After starvation: Treatment with WB-EMS patient serum from study end for 24 h


title: B0544 Healthy


title: WT_F3_R1

description: total small RNA


title: LNCaP_WB-EMS serum pool week 0_24h

description: After starvation: Treatment with WB-EMS patient serum from study entry for 24 h


title: RGLS4326_100nM_3

city: San Diego

first: Sole

last: Gatto

address: 12636 High Bluff Drive, Suite 400

institute: Monoceros Biosystems

data_processing:
Data was collected using the NextSeq 500 sequencer per manufacturer's protocol (Illumina).
Sequencing quality was assessed with the FastQC tool v0.11.2 and trimmed with TrimGalore. Reads were mapped using STAR with samtools v1.1.
HTSeq v0.6.1 was used to generate counts. Map and count quality was assessed by picard tools v1.119 and RSeQC tool.
Genome_build: hg38
Supplementary_files_format_and_content: Raw counts per gene

source_name: Primary human ADPKD cyst cells

growth_protocol: Human primary ADPKD cyst cells were were cultured in DMEM/F12++ (Gibco) supplemented with 5% FBS, 5 mg kg-1 insulin, 5 mg mL-1 transferrin and 5 ng mL-1 sodium selenite and incubated in an atmosphere of 95% air and 5% CO2 at 37°C until 80% confluency.

extract_protocol:
RNA was harvested with Qiagen RNeasy kit
TruSeq Stranded mRNA Library Prep Kit

treatment_protocol: 100,000 human primary ADPKD cyst cells were reverse transfected with Lipofectamine RNAiMAX reagent and RGLS4326 (100 nM) or PBS for 24 hrs.

value: primary kidney cyst cultures

value: ADPKD

tag: dose


title: B0550 Healthy


title: HCV.29.TSC1+ 30nm THZ1 Rep2 [30_2_plus_plus]

value: 30nm THZ1


title: LNCaP_Control serum pool week 12_24h

description: After starvation: Treatment with control patient serum from study end for 24 h

value: LNCaP


title: B0533 CHB WTC

description: Expression data of peripheral blood leukocytes in patients with CHB WTC

source_name: CHB WTC

value: CHB WTC


title: B0541 Healthy

value: peripheral blood leukocytes


title: JH3225_R2

description: total small RNA

value: meg-3 meg-4


title: B0543 Healthy

value: Healthy


title: RGLS4326_100nM_2


title: TP12 48 h Gonadotropin Treatment Ion Torrent small RNASeq

city: Pittsburgh

first: Uma

last: Chandran

state: PA

address: 5150 Center Ave

department: BioMedical Informatics

institute: University of Pittsburgh

description:
TP_smallRNA_rheMac8_HTSeq_counts.txt
TP_miRNA_rheMac2_miRDeep2_counts.txt
TP_miRNA_rheMac2_48GTH_vs_VEH.edgeR_exactTest.txt
TP_smallRNA_rheMac8_48GTH_vs_VEH.edgeR_exactTest.txt

data_processing:
Sequence reads were trimmed using Cutadapt v 1.9.1 (adapter and qual 13, length 18)
Reads of each sample were aligned to reference rheMac8 using Bowtie v 1.1.2 and to reference rheMac2 using miRDeep2 mapper (miRDeep2 v2.0.0.8)
Reads mapped to rheMac8 were annotated (Ensembl database v88) and read counts were generated for smallRNA using HTSeq-counts (HTSeq v 0.6.1p1)
smallRNA of the samples were filtered (raw CPM > 1 for any 3 samples), library normalized (TMM), expression values as normalized CPM calculated and differential expression analyzed (exactTest) using edgeR
Reads mapped to rheMac2 using miRDeep2 mapper were mapped  and annotated to rheMac2 hairpin loop and mature miRNA from miRBase v20 using miRDeep2 module of miRDeep2 v2.0.0.8
Secondary structure prediction of known and novel miRNA was done by miRDeep2 module of miRDeep2 v2.0.0.8
Read counts for known miRNA generated by miRDeep2 module of miRDeep2 v2.0.0.8
mature miRNA of the samples were filtered (raw CPM > 1 for any 3 samples), library normalized (TMM), expression values as normalized CPM calculated and differential expression analyzed (exactTest) using edgeR
Spreadsheet containing rheMac8 containing smallRNA, filtered, normalized and differential expression analyzed were marked for miRNA shared with rheMac2 miRNA  filtered and normalized spreadsheet
Genome_build: rheMac8, rheMac2
Supplementary_files_format_and_content: Bedgraph format: Bowtie mapping output of each sample with rheMac8; tab-delimited text (TP_smallRNA_rheMac8_HTSeq_counts.txt): Raw read counts of non-coding RNA (excluding long non-coding) from HTSeq using reference rheMac8 and databse Ensembl v88; tab-delimited text (TP_miRNA_rheMac2_miRDeep2_counts.txt): Raw read counts of miRNA from miRDeep2 software using rheMac2 reference and miRNA sequences from miRBase v20 database; tab-delimited text (TP_miRNA_rheMac2_48GTH_vs_VEH.edgeR_exactTest.txt): Data normalization, CPM calculation and differential expression analysis of miRNA using edgeR software; tab-delimited text (TP_smallRNA_rheMac8_48GTH_vs_VEH.edgeR_exactTest.txt): Data normalization, CPM calculation and differential expression analysis of non-coding RNA (exlcuding long non-coding) using edgeR software

organism: Macaca mulatta

source_name: 48 h Gonadotropin Treatment

extract_protocol:
The right testis from each animal was rapidly divided into 10 fragments and snap-frozen in liquid nitrogen and stored at -80C until RNA extraction.  Total RNA was isolated from the testes using Trizol reagent. TruSeq Stranded Total RNA library preparation was performed using 1ug total RNA
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Pulsatile gonadotropin (FSH+LH)/vehicle infusion was performed for 48h

value: testis

tag: age

value: 15 months

value: wild type

value: Gonadotropin


title: JH3225_R1

description: total small RNA

value: whole animal

value: young adults


title: B0456 CHB YTC

description: Expression data of peripheral blood leukocytes in patients with CHB YTC

source_name: CHB YTC

value: CHB YTC


title: N2_R2

description: total small RNA

value: wild-type control


title: PBS_3

value: PBS


title: RGLS4326_100nM_1

value: primary kidney cyst cultures


title: TP11 48 h Vehicle Treatment Ion Torrent small RNASeq

source_name: 48 h Vehicle Treatment

value: Vehicle


title: N2_R1

description: total small RNA


title: PBS_1

value: ADPKD


title: B0446 CHB WTC


title: TP10 48 h Gonadotropin Treatment Ion Torrent small RNASeq

value: 14 months


title: TP09 48 h Vehicle Treatment Ion Torrent small RNASeq


title: N2_gfp_elution, replicate 1 [miRNA-seq]

city: Berlin

first: Kathrin

last: Theil

address: Hannoversche Str. 28

institute: BIMSB/MDC

description:
N2_gfp
EN2

data_processing:
de-multiplexing (bcl2fastq Conversion Software v2.18.0.12, Illumina)
adaptor and poly(A) removal with cutadapt (version 1.14) and parameters "--format=fastq --adapter=AAAAAA --error-rate=0.2 --times=3 --overlap=3 --cut=3 --quality-cutoff=20 --quality-base=33 --minimum-length=17 --max-n=0 --discard-untrimmed"
mapping with bowtie2 (version 2.3.3.1) using the parameters “-very-fast-local --phred33 –local” to the E. coli genome (NC_000913.3, K-12, MG1655) for removal of E. coli RNA contamination
miRNA identification with miRDeep2, version 2.0.0.7, with miRBase21 reference
Genome_build: miRBase21
Supplementary_files_format_and_content: comma-separated text files containing three columns: miRNA name, read counts, and precursor (miRNA_expressed.csv output table from miRDeep2)

extract_protocol:
TRIzol
SMARTer smRNA-Seq Kit for Illumina (Clontech)

tag: strain/variation

value: young adult

tag: molecule subtype

value: Pulldown elution; small RNA


title: B0457 CHB YTC

value: peripheral blood leukocytes


title: gfp::lin-41_elution, replicate 1 [miRNA-seq]

description:
DG3913_gfp
EDG


title: TP08 48 h Gonadotropin Treatment Ion Torrent small RNASeq

value: 22 months


title: TP07 48 h Vehicle Treatment Ion Torrent small RNASeq

value: testis

value: 24 months


title: LNCaP_Control serum pool week 0_24h

description: After starvation: Treatment with control patient serum from study entry for 24 h

value: LNCaP

value: prostate cancer cell line


title: gld-1::gfp_elution, replicate 1 [miRNA-seq]

description:
BS1080_gfp
EBS


title: PBS_2


title: B0444 CHB YTC


title: LS1034_DMSO_6hr_C

city: Cambridge

first: Steven

last: Corsello

address: 415 Main Street

institute: Broad Institute

description: 20181003_11_-_LS1034_DMSO_6H_Rep_3_SC6118_S9

data_processing:
Alignment: STAR 2.6.1d
Transcript quantification: RSEM 1.3.1
Genome_build: GRCh38
Supplementary_files_format_and_content: transcript quantification; tab-delimited text files include count, TPM values

growth_protocol: RPMI with 10% FBS and 1% penicillin-streptomycin-glutamine

extract_protocol:
RNeasy Miniprep Kit (Qiagen #74104)
KAPA mRNA HyperPrep Kit (Roche) for RNAseq
mRNA capture using magnetic oligo-dT beads

treatment_protocol: Cells were treated with tepoxalin or DMSO vehicle for 6 hours at the indicated concentration.

value: colon cancer cell line

value: DMSO


title: LS1034_DMSO_6hr_B

description: 20181003_10_-_LS1034_DMSO_6H_Rep_2_SC6118_S8


title: gld-1::gfp_elution_PFA-XL

data_processing:
de-multiplexing (bcl2fastq Conversion Software v2.17.1.14, Illumina)
pseudo-alignment with kallisto (version: 0.43.1; parameters: reads = single end, bootstraps = 100)
Genome_build: C. elegans transcriptome (Caenorhabditis_elegans.WBcel235, Release 81), for pulldown elution samples additionally:  human transcriptome (GENCODE Release 24), if applicable (see description): ERCC spike-in mix 1, transgene sequences (determined by Sanger sequencing)
Supplementary_files_format_and_content: tab-separated text file with five columns: target id, length, effective length, estimated counts, and tpm

source_name: Pulldown elution

extract_protocol:
Ribominus eukaryote kit v2 (Thermo Fisher Scientific)-mediated depletion of human ribosomal RNAs, contains HEK293 RNA and ERCC spike-in mix 1
Trizol
TruSeq Stranded Total LT Sample Prep Kit (Illumina)

tag: strain


title: B0433 CHB YTC

value: CHB YTC


title: B0407 CHB WTC

value: CHB WTC


title: LS1034_DMSO_6hr_A

description: 20181003_9_-_LS1034_DMSO_6H_Rep_1_SC6118_S7


title: LS1034_12uM_Tepoxalin_6hr_C

description: 20181003_15_-_LS1034_tepoxalin_6H_Rep_1_SC6118_S12

value: tepoxalin


title: gld-1::gfp_elution_PAR-XL

extract_protocol:
Ribominus eukaryote kit v2 (Thermo Fisher Scientific)-mediated depletion of human ribosomal RNAs; contains HEK293 RNA and ERCC spike-in mix 1
Trizol
TruSeq Stranded Total LT Sample Prep Kit (Illumina)


title: B0391 CHB YTC


title: gld-1::gfp_input_PAR-XL

source_name: Pulldown input

extract_protocol:
Rnase H-mediated C. elegans ribosomal RNA depletion; contains ERCC spike-in mix 1
Trizol
TruSeq Stranded Total LT Sample Prep Kit (Illumina)


title: LS1034_12uM_Tepoxalin_6hr_B

description: 20181003_14_-_LS1034_tepoxalin_6H_Rep_1_SC6118_S11


title: gld-1::gfp_totalRNA_PAR-XL

source_name: total RNA


title: LS1034_12uM_Tepoxalin_6hr_A

description: 20181003_13_-_LS1034_tepoxalin_6H_Rep_1_SC6118_S10


title: B0408 CHB YTC


title: B0386 CHB YTC


title: SF295_WT_B

extract_protocol:
RNeasy Miniprep Kit (Qiagen)
KAPA mRNA HyperPrep Kit (Roche) for RNAseq
mRNA capture using magnetic oligo-dT beads

treatment_protocol: Cells infected with CRISPR vector were also selected with puromycin.

value: WT


title: WT_RNAseq_rep2

description:
FPKM_TDG_WT_2
processed data file:
TDG_KO_vs_WT_gene_exp_diff.txt, genes.read_group_tracking.asmatrix.txt

extract_protocol:
Total RNA was purified from mESC cells using Trizol (ThermoFisher) followed by treatment with TurboTM DNAse (ThermoFisher).
Sequencing libraries were constructed from RNA samples with the Illumina TruSeq mRNA library construction kit

tag: strain background

value: mESCs

tag: chip antibody


title: KO_RNAseq_rep1

description:
FPKM_TDG_KO_1
processed data file:
TDG_KO_vs_WT_gene_exp_diff.txt, genes.read_group_tracking.asmatrix.txt

value: TDG KO


title: B0389 CHB YTC


title: KO_c_8h [PDK1]

first: Josh

middle: M

last: Brickman

address: 3B Blegdamsvej

department: reNEW

institute: Copenhagen University

description: Gene expression data from Esrrb KO ESCs, treated 8hrs and subsequently 2hrs with Mek inhibitor

hyb_protocol: Samples were then hybridized to the G4852A SurePrint G3 Mouse GE 8x60K Microarray slides (60000 probes, Agilent Technologies).

scan_protocol: Images were scanned using the high sensitivity protocol (AgilentG3_HiSen_GX_1color) on a SureScan microarray scanner (Agilent Technologies) and probe intensities were obtained by taking the gProcessedSignal from the output of Agilent feature extraction software using default settings.

data_processing: Probe intensities were analysed using the NIA Array Analysis tool (http://lgsun.grc.nia.nih.gov/ANOVA/).

label_protocol: RNA was amplified into cRNA and 100ng of total RNA was labeled using the Low Input Quick Amp Labeling Kit (Agilent Technologies- 5190-2305).

growth_protocol: Cell culture using GMEM+serum+lif+250nM PD17 (FGFR inhibitor)

extract_protocol: Total RNA was collected using  the RNeasy Mini Kit (Qiagen). Genomic DNA was eliminated by DNAse treatment (Qiagen).

treatment_protocol: treated with 250mM 4OHT to induce Erk activity

value: ESCs


title: SF295_WT_A


title: SF295_MTF1_sg2_C


title: B0380 CHB YTC


title: KO_c_8h2h [PDK1]

description: Gene expression data from Esrrb KO ESCs, treated 8hrs

source_name: Esrrb KO ESCs, treated 8hrs


title: WT_RNAseq_rep1

description:
FPKM_TDG_WT_1
processed data file:
TDG_KO_vs_WT_gene_exp_diff.txt, genes.read_group_tracking.asmatrix.txt


title: B0374 CHB WTC


title: B0382 CHB YTC


title: KO_c_0h [PDK1]

description: Gene expression data from Esrrb KO ESCs, untreated

source_name: Esrrb KO ESCs, untreated


title: KO_RNAseq_rep2

description:
FPKM_TDG_KO_2
processed data file:
TDG_KO_vs_WT_gene_exp_diff.txt, genes.read_group_tracking.asmatrix.txt


title: SF295_MTF1_sg2_B


title: Barcodes identifying perturbations (gemgroup 8)

city: San Francisco

first: Thomas

last: Norman

address: Biochemistry Box 2542, 1700 4th St QB3 Rm 404

department: CMP

institute: University of California, San Francisco

description:
amplicon sequencing from poly A RNA
sgRNA barcode reads

data_processing:
Fastq.gz files were generated from raw Illumina BCL files using bcl2fastq
Reads were aligned and corrected from each fastq.gz files using 10X Genomics Cellranger version 2.1.1 with default paramaters (cellranger count), resulting in the "molecule_info.h5" HDF5 files
Reads from multiple channels (gemgroups) of the 10X run were combined using 10X Genomics Cellranger version 2.1.1 (cellranger aggr)
Gene-barcode matrices were determined using 10X Genomics Cellranger version 2.1.1 with default parameters, producing the matrix market exchange files (the UMI matrices) and the TSV files (which are the row and column names of the UMI matrix)
Guide barcode identities were determined as described in the paper from targeted amplicon sequencing, resulting in the "cell_identities.csv" files. Identities were called for all cell barcodes called by cellranger in the previous step.
Genome_build: hg38
Supplementary_files_format_and_content: The experiment consists of one large pooled experiment of ~100,000 single cells that was processed as 8 independent replicate samples (corresponding to lanes on the 10X Chromium machine, and encoded here by gemgroup.) All sequencing data ultimately derive from the same experiment, so they are merged during the creation of the processed data files. Gene-barcode matrices are the UMI-collapsed counts of these reads, representing counts of molecules per cell as determined and filtered by cellranger. These are provided in the format outputted by cellranger: the matrix itself is in matrix market exchange format, with the rows (cell barcodes) and columns (gene identities) labels given in TSV format as described in the cellranger documentation. We have uploaded both the "filtered" and "raw" versions of these files. Guide barcodes were specifically amplified from the RNA-seq libraries and sequenced to higher coverage, and then identities were called as discussed in the paper. These are simply formatted as tables that identify a guide barcode for each of the sets of files from the previous step.

source_name: K562 cells

growth_protocol: K562 cells expressing dCas9-KRAB were transduced with lentivirus carrying the sgRNA expression cassettes and a BFP marker. Transduced cells were isolated by FACS 3 days after transduction and grown for 2 additional days. Growth was performed in RPMI media supplemented with FBS and Pen/Strep/Gln.

extract_protocol:
Single cells were lysed in droplets using the 10X Chromium instrument
Reverse transcription was performed in droplet and library construction was performed according to the 10X Chromium Single Cell 3' Reagent Kit User Guide (v2 chemistry)

value: K562 chronic myelogenous leukemia cell line


title: Rescue_c_8h2h [PDK1]

description: Gene expression data from Esrrb rescued ESCs, treated 8hrs

source_name: Esrrb rescued ESCs, treated 8hrs


title: B0358 CHB YTC

description: Expression data of peripheral blood leukocytes in patients with CHB YTC


title: Rescue_c_8h [PDK1]

description: Gene expression data from Esrrb rescued ESCs, treated 8hrs and subsequently 2hrs with Mek inhibitor


title: Rescue_c_0h [PDK1]

description: Gene expression data from Esrrb rescued ESCs, untreated

source_name: Esrrb rescued ESCs, untreated


title: KO_b_8h2h [PDK1]


title: Barcodes identifying perturbations (gemgroup 7)


title: B0326 CHB YTC


title: B0364 CHB WTC

description: Expression data of peripheral blood leukocytes in patients with CHB WTC


title: SF295_MTF1_sg1_C


title: KO_b_8h [PDK1]

source_name: Esrrb KO ESCs, treated 8hrs and subsequently 2hrs with Mek inhibitor


title: Barcodes identifying perturbations (gemgroup 6)


title: SF295_MTF1_sg1_B


title: Barcodes identifying perturbations (gemgroup 5)


title: KO_b_0h [PDK1]


title: B0312 CHB WTC


title: Barcodes identifying perturbations (gemgroup 4)


title: SF295_MTF1_sg1_A


title: SF295_GFP_sg1_C


title: B0346 CHB WTC


title: B0335 CHB WTC


title: Barcodes identifying perturbations (gemgroup 3)


title: SF295_GFP_sg1_B


title: SF295_GFP_sg1_A


title: B0308 CHB YTC


title: B0289 CHB YTC


title: B0268 CHB YTC


title: B0246 CHB WTC


title: Rescue_b_8h [PDK1]

source_name: Esrrb rescued ESCs, treated 8hrs and subsequently 2hrs with Mek inhibitor


title: Barcodes identifying perturbations (gemgroup 1)


title: TH6729_38 min_replicate 2

city: Beijing

first: Yanni

last: Liu

address: Qinghuayuan, Haidian district

department: Medicine of School

institute: Tsinghua University

description: Sample 18

data_processing:
Base calliing: Illumina Casava software version 1.8
Quality control: FastQC v0.11.5
Trimming: Trimmomatic v0.32
S. pneumoniae reads were mapped with Tophat 2.1.1 and Bowtie 2.3.1
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated internally by Cufflink version 2.2.1 after aligning reads.
Genome_build: Streptococcus pneumoniae R6 (accession NC_003098.1, assembly GCA_000007045.1) was used directly in the analysis.
Supplementary_files_format_and_content: Tab-delimited text file includes FPKM values for each sample.

organism: Streptococcus pneumoniae

source_name: Streptococcus pneumoniae cells competence at 38 min

growth_protocol: S. pneumoniae cells were grown in acidified THY medium (pH6.8) supplemented with 0.5% glycine to OD620~0.06 in tubes at 37ºC with 5% CO2.

extract_protocol:
Total RNAs were extracted with the TIANGEN RNA extraction kit (TIANGEN, Beijing, China) based on the supplier’s instructions, treated with RNase-free DNase I (New England Biolabs, Beijing, China), and final purified with QIAGEN RNA purification kit (QIAGEN, Beijing, China) according to manufacturer's protocol.
Sample 1-6: The ribosomal RNA was removed from total RNA (~2 µg) using RiboZeroTM Magnetic Kit (EpiCentre, Cleveland, OH).  The processed RNA samples were used to prepare double-stranded complementary DNA (cDNA) libraries with the M-MuLV Reverse Transcriptase and NEBNext® mRNA Second Strand Synthesis Module.  The cDNA molecules were fragmented by sonication, and further processed for end repair, adaptor attachment, and sequence amplification.
Sample 7-18: The ribosomal RNA was removed from total RNA (~1.5 µg) using poly-T oligo-attached magnetic beads. Fragmentation of mRNAs and sequencing libraries were generated using NEBNext® UltraTM RNA  Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations. The cDNA molecules were ligated with the NEBNext Adaptor, and further processed for selected, purifed, and sequence amplification.

treatment_protocol: BSA and CaCl2 were added with to final concentration of 0.2% and 1mM. Pre-competence sample was taken at 0 min before the addition of 250 ng/ml CSP, fastly cooled down and kept at 4 oC. Other competence-ON samples were taken at each pre-set time and treated as that with sample at 0 min.

value: rpsL1 (StreptomycinR)

tag: time

value: 38 min


title: B0253 CHB YTC

value: peripheral blood leukocytes


title: KO_a_8h2h [PDK1]


title: Rescue_b_0h [PDK1]


title: Rescue_b_8h2h [PDK1]


title: KO_a_8h [PDK1]


title: Rescue_a_8h2h [PDK1]


title: B0234 CHB YTC


title: sgRNA perturb-seq experiment (gemgroup 8)

description:
Single-cell RNA-seq data, gemgroup 8
Single-cell RNA-seq data, gemgroups 1-8 aggregated and collapsed to UMI tables:
filtered_cell_identities.csv
filtered_barcodes.tsv
filtered_genes.tsv
filtered_matrix.mtx
raw_cell_identities.csv
raw_barcodes.tsv
raw_genes.tsv
raw_matrix.mtx


title: sgRNA perturb-seq experiment (gemgroup 7)

description:
Single-cell RNA-seq data, gemgroup 7
Single-cell RNA-seq data, gemgroups 1-8 aggregated and collapsed to UMI tables:
filtered_cell_identities.csv
filtered_barcodes.tsv
filtered_genes.tsv
filtered_matrix.mtx
raw_cell_identities.csv
raw_barcodes.tsv
raw_genes.tsv
raw_matrix.mtx


title: TH6729_28 min_replicate 2

description: Sample 17

source_name: Streptococcus pneumoniae cells competence at 28 min

value: 28 min


title: sgRNA perturb-seq experiment (gemgroup 6)

description:
Single-cell RNA-seq data, gemgroup 6
Single-cell RNA-seq data, gemgroups 1-8 aggregated and collapsed to UMI tables:
filtered_cell_identities.csv
filtered_barcodes.tsv
filtered_genes.tsv
filtered_matrix.mtx
raw_cell_identities.csv
raw_barcodes.tsv
raw_genes.tsv
raw_matrix.mtx


title: TH6729_16 min_replicate 2

description: Sample 16

source_name: Streptococcus pneumoniae cells competence at 16 min

value: 16 min


title: Rescue_a_8h [PDK1]


title: sgRNA perturb-seq experiment (gemgroup 5)

description:
Single-cell RNA-seq data, gemgroup 5
Single-cell RNA-seq data, gemgroups 1-8 aggregated and collapsed to UMI tables:
filtered_cell_identities.csv
filtered_barcodes.tsv
filtered_genes.tsv
filtered_matrix.mtx
raw_cell_identities.csv
raw_barcodes.tsv
raw_genes.tsv
raw_matrix.mtx


title: Barcodes identifying perturbations (gemgroup 2)


title: B0227 CHB WTC

source_name: CHB WTC


title: KO_c_8h2h

data_processing: gProcessed signal

growth_protocol: mESCs were grown in serum containing medium, supplemented with 1x LIF (made in house) and 2uM Chir99021. 24hrs prior to treatment, media was changed to serum containing media supplemented with 1x LIF and 250nM PD173074.

treatment_protocol: Cells were left untreated (0h), or treated with 250nM 4OHT (2h, 8h), or treated with 4OHT for 8hrs followed by a subsequent 2h Mek inhibitor treatment (8_2h).

value: Esrrb Knockout Expressing Raf-ErT2

tag: protocol

value: Empty Vector Control


title: B0233 CHB YTC


title: sgRNA perturb-seq experiment (gemgroup 3)

description:
Single-cell RNA-seq data, gemgroup 3
Single-cell RNA-seq data, gemgroups 1-8 aggregated and collapsed to UMI tables:
filtered_cell_identities.csv
filtered_barcodes.tsv
filtered_genes.tsv
filtered_matrix.mtx
raw_cell_identities.csv
raw_barcodes.tsv
raw_genes.tsv
raw_matrix.mtx


title: TH6729_38 min_replicate 1

description: Sample 12


title: TH6729_8 min_replicate 2

description: Sample 14

source_name: Streptococcus pneumoniae cells competence at 8 min

value: 8 min


title: KO_c_8h


title: TH6729_0 min_replicate 2

description: Sample 13

source_name: Streptococcus pneumoniae cells 0 min (pre-competence)

value: 0 min (pre-competence)


title: B0222 CHB YTC

source_name: CHB YTC

value: CHB YTC


title: TH6729_12 min_replicate 2

description: Sample 15

source_name: Streptococcus pneumoniae cells competence at 12 min

value: 12 min


title: B0206 CHB WTC

value: CHB WTC


title: Rescue_c_8h2h

value: Rescued with an Esrrb Transgene


title: KO_c_0h


title: sgRNA perturb-seq experiment (gemgroup 2)

description:
Single-cell RNA-seq data, gemgroup 2
Single-cell RNA-seq data, gemgroups 1-8 aggregated and collapsed to UMI tables:
filtered_cell_identities.csv
filtered_barcodes.tsv
filtered_genes.tsv
filtered_matrix.mtx
raw_cell_identities.csv
raw_barcodes.tsv
raw_genes.tsv
raw_matrix.mtx


title: B0199 CHB WTC


title: sgRNA perturb-seq experiment (gemgroup 1)

description:
Single-cell RNA-seq data, gemgroup 1
Single-cell RNA-seq data, gemgroups 1-8 aggregated and collapsed to UMI tables:
filtered_cell_identities.csv
filtered_barcodes.tsv
filtered_genes.tsv
filtered_matrix.mtx
raw_cell_identities.csv
raw_barcodes.tsv
raw_genes.tsv
raw_matrix.mtx


title: B0139 CHB WTC


title: B0195 CHB YTC


title: N2_gld-1_edit2_elution, replicate 2 [miRNA-seq]

description:
change site specificity_gld1
26_gld1_S1_R1_001

value: miR-84 site conversion (N2 CRISPR)

tag: developmental stage

value: young adult

value: Pulldown elution; small RNA


title: KO_b_8h2h

description: Gene expression data from Esrrb KO ESCs, treated 8hrs

tag: cell type

value: ESCs


title: Rescue_c_8h


title: Rescue_c_0h


title: sgRNA perturb-seq experiment (gemgroup 4)

description:
Single-cell RNA-seq data, gemgroup 4
Single-cell RNA-seq data, gemgroups 1-8 aggregated and collapsed to UMI tables:
filtered_cell_identities.csv
filtered_barcodes.tsv
filtered_genes.tsv
filtered_matrix.mtx
raw_cell_identities.csv
raw_barcodes.tsv
raw_genes.tsv
raw_matrix.mtx

value: K562 chronic myelogenous leukemia cell line


title: TH6729_28 min_replicate 1

description: Sample 11

value: rpsL1 (StreptomycinR)


title: N2_gld-1_edit1_elution, replicate 2 [miRNA-seq]

description:
seed destruction_gld1
C3_gld1_S2_R1_001

value: miR-84 site destruction (N2 CRISPR)


title: N2_gld-1_elution, replicate 2 [miRNA-seq]

description:
PD1_N2_gld1
PD1_N2_gld1_S7_R1_001


title: N2_lin-41_elution, replicate 2 [miRNA-seq]

description:
PD3_N2_lin41
PD3_N2_lin41_S14_R1_001


title: TH6729_38 min

description: Sample 6

value: 38 min


title: TH6729_0 min_replicate 1

description: Sample 7


title: TH6729_12 min_replicate 1

description: Sample 9


title: TH6729_8 min_replicate 1

description: Sample 8


title: TH6729_16 min_replicate 1

description: Sample 10

value: 16 min


title: N2_alg-1_elution, replicate 2 [miRNA-seq]

description:
PD1_N2_alg1
PD1_N2_alg1_S6_R1_001


title: SF295_MTF1_sg2_A

tag: cell line


title: N2_gfp_elution, replicate 3 [miRNA-seq]

description:
PD1_N2_gfp
PD1_N2_gfp_S5_R1_001


title: B0110 CHB WTC

value: peripheral blood leukocytes


title: B0026 CHB YTC


title: B0132 CHB YTC


title: B0034 CHB YTC


title: B0011 CHB YTC


title: Rescue_b_0h

value: Esrrb Knockout Expressing Raf-ErT2


title: Rescue_b_8h2h


title: gld-1::gfp_elution, replicate 2 [miRNA-seq]

description:
PD1_BS1080_gfp
PD1_BS1080_gfp_S8_R1_001


title: KO_b_0h

description: Gene expression data from Esrrb KO ESCs, untreated

value: Empty Vector Control


title: N2_gld-1_edit2_elution, replicate 1 [miRNA-seq]

description:
PD3_change site specificity_gld1
PD3_26_gld1_S15_R1_001


title: KO_b_8h

description: Gene expression data from Esrrb KO ESCs, treated 8hrs and subsequently 2hrs with Mek inhibitor


title: TH6729_16 min

description: Sample 4


title: TH6729_8 min

description: Sample 2

value: 8 min


title: TH6729_28 min

description: Sample 5

value: 28 min


title: N2_gld-1_edit1_elution, replicate 1 [miRNA-seq]

description:
PD3_seed destruction_gld1
PD3_C3_gld1_S16_R1_001


title: B0017 CHB WTC


title: KO_a_8h2h


title: B0012 CHB YTC

description: Expression data of peripheral blood leukocytes in patients with CHB YTC

value: CHB YTC


title: siw14Δ H2O2 versus wt H2O2

city: Tucson

first: Andrew

last: Capaldi

state: AZ

address: 1007 E Lowell St

department: MCB

institute: Univ of Arizona

hyb_protocol: Hybridization was performed using Agilent Hyb buffers and chambers following the manufactures suggested protocols

scan_protocol: Arrays were scanned on a Genepix 300b scanner

data_processing: Arrays were analyzed using GenePix 6.1, and then LOWESS normalized

organism: Saccharomyces cerevisiae

source_name: BY4741 in SD

label_protocol: mRNA was reverse transcribed incooperatigin aa-UTP and then labelled with Cy5 or Cy3

growth_protocol: Cells were grown to log phase in synthetic complete medium

extract_protocol: Cells were lysed in hot phenol and the polyA RNA purified using oligoDT cellulose

treatment_protocol: select cell cultures were treated with 0.4M KCl or 0.4mM H2O2 for 20min

source_name: Siw14D in SD


title: siw14Δ KCl versus wt KCL

value: 0.4 M KCl, 20min


title: N2_gld-1_elution, replicate 1 [miRNA-seq]

description:
PD3_N2_gld1
PD3_N2_gld1_S13_R1_001


title: KO_a_0h

city: Copenhagen


title: Rescue_b_8h

description: Gene expression data from Esrrb rescued ESCs, treated 8hrs and subsequently 2hrs with Mek inhibitor

value: Rescued with an Esrrb Transgene


title: TH6729_12 min

description: Sample 3

value: 12 min


title: T_6_3

city: Changchun

first: Tao

last: Zhang

state: Jilin

address: 2888 Xincheng Street

department: College of Chinese Medicinal Material

institute: Jilin Agriculture University

data_processing:
Cutadapt and perl scripts in house were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases.
Sequence quality was verified using FastQC，including the Q20, Q30 and GC-content of the clean data. All downstream analyses were based on clean data of high quality. De novo assembly of the transcriptome was performed with Trinity 2.4.0. Trinity groups transcripts into clusters based on shared sequence content. Such a transcript cluster is very loosely referred to as a 'gene'. The longest transcript in the cluster was chosen as the 'gene' sequence.
All assembled Unigenes were aligned against the non-redundant (Nr) protein database，Gene ontology (GO), SwissProt, Kyoto Encyclopedia of Genes and Genomes (KEGG) and eggNOG databases using DIAMOND with a threshold of Evalue<0.001.
Salmon was used to perform expression level for Unigenes by calculating TPM. The differentially expressed Unigenes were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with statistical significance (p value < 0.05) by R package edgeR. Next, GO and KEGG enrichment analysis were again performed on the differentially expressed Unigenes by perl scripts in house.
Genome_build: The Trinity transcriptome assembly is available on the series record.
Supplementary_files_format_and_content: tab-delimited text file includes TPM values for each Sample

organism: Panax ginseng

source_name: Panax ginseng_treatment

growth_protocol: we performed transcriptome sequencing to select the Panax ginseng Embryogenic Calli of the number of treatment days—2, 4, and 6 days under 5 °C (Treatment) and 20 °C (Control).

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

value: Embryogenic Calli

tag: days


title: T_6_2


title: Rescue_a_8h2h

description: Gene expression data from Esrrb rescued ESCs, treated 8hrs


title: N2_lin-41_elution, replicate 1 [miRNA-seq]

description:
PD2_N2_lin41
PD2_N2_lin41_S11_R1_001

value: young adult

value: Pulldown elution; small RNA


title: B0005 CHB WTC

description: Expression data of peripheral blood leukocytes in patients with CHB WTC

value: CHB WTC


title: T_4_2


title: N2_alg-1_elution, replicate 1 [miRNA-seq]

description:
PD2_N2_alg1
PD2_N2_alg1_S10_R1_001


title: N2_gfp_elution, replicate 2 [miRNA-seq]

description:
PD2_N2_gfp
PD2_N2_gfp_S9_R1_001


title: T_2_3


title: N2_lin-41_elution_cXL

source_name: Pulldown elution

extract_protocol:
Rnase H-mediated human ribosomal RNA depletion; contains HEK293 RNA
Trizol
TruSeq Stranded Total LT Sample Prep Kit (Illumina)

value: wild type


title: T_4_1


title: KO_a_8h

value: ESCs