title: C98

description:
Single cell from mouse hippocampus
Single_cell_19


title: C96

status: Public on Aug 18 2016

type: SRA

city: Stanford

first: Spyros

last: Darmanis

state: California

address: Clark Center, E300

department: Bioengineering

country: USA

institute: Stanford University

description:
Single cell from mouse hippocampus
Single_cell_17

library_source: transcriptomic

data_processing:
Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65).  We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore  (--stringency 1).
Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ).
Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample

molecule: total RNA

organism: Mus musculus

source_name: CA1 regular-spiking interneuron

extract_protocol:
Clontech SMARTer Kit version: v3
RNA extraction method: NA
Clontech's SMARTer RT and preamplification protocol
Nextera tagmentation protocol

tag: sample type

value: single cell

tag: age

value: post natal week 3-4

tag: cell/tissue type

value: CA1 cholecystokinin cell


title: p14.2

description:
Whole hippocampal tissue lysate
Tissue_sample_8

source_name: hippocampus

extract_protocol:
Clontech SMARTer Kit version: v4
Qiagen AllPrep DNA/RNA Univeral Kit
Clontech's SMARTer RT and preamplification protocol
Nextera tagmentation protocol

value: tissue

value: post natal day 14

value: hippocampus

tag: replicate

value: independent replicate 2


title: p14.1

description:
Whole hippocampal tissue lysate
Tissue_sample_7

value: independent replicate 1


title: p0.3

description:
Whole hippocampal tissue lysate
Tissue_sample_3

value: post natal day 0

value: independent replicate 3


title: C88

description:
Single cell from mouse hippocampus
Single_cell_9

source_name: CA1 fast-spiking interneuron

value: CA1 parvalbumin cell


title: C87

description:
Single cell from mouse hippocampus
Single_cell_8

source_name: CA1 pyramidal cell

value: CA1 pyramidal cell


title: C83

description:
Single cell from mouse hippocampus
Single_cell_4


title: p14.3

description:
Whole hippocampal tissue lysate
Tissue_sample_9


title: p0.1

description:
Whole hippocampal tissue lysate
Tissue_sample_1


title: p0.2

description:
Whole hippocampal tissue lysate
Tissue_sample_2


title: AB585

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

description: Note: Second read contained only cell and molecule barcodes. This information was appended to the fastq entry header

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode and well-barcode-RMT were extracted from the first and second end of the read (respectively) and concatenated to the fastq header, delimited by a underscore i.e. POOL_BARCODE_WELL_BARCODE_RMT while "NNNNNN" was used as a place holders if plate barcode was not used.
Reads were separated by POOL_BARCODE_WELL_BARCODE header data, allowing 1 sequencing error. This process created a single fastq file for each source well.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample

molecule: polyA RNA

source_name: antibiotics ILC

growth_protocol: 8 to 9 weeks-old mice housed at the Weizmann Institute animal facility

extract_protocol:
Cells were extracted using the lamina propria dissociation kit (Miltenyi Biotech).
3' end mRNA libraries were prepared for sequencing using MARS-seq (Jaitin et al, Science 2014)
single cell RNA-seq for gene expression quantitation

treatment_protocol: mice were given a combination of vancomycin (0.5 g/l), ampicillin (1 g/l), kanamycin (1 g/l), and metronidazole (1 g/l) in their drinking water.

tag: strain

tag: organ

value: Small intestine lamina propria

tag: selection marker

tag: treatment

value: vancomycin (0.5 g/l), ampicillin (1 g/l),kanamycin (1 g/l), and metronidazole (1 g/l)

tag: developmental stage

value: adult


title: C93

description:
Single cell from mouse hippocampus
Single_cell_14


title: p7.3

description:
Whole hippocampal tissue lysate
Tissue_sample_6

value: post natal day 7


title: C89

description:
Single cell from mouse hippocampus
Single_cell_10


title: C84

description:
Single cell from mouse hippocampus
Single_cell_5


title: C244

description:
Single cell from mouse hippocampus
Single_cell_91

source_name: Subiculum burst-spiking pyramidal cell

extract_protocol:
Clontech SMARTer Kit version: v4
RNA extraction method: NA
Clontech's SMARTer RT and preamplification protocol
Nextera tagmentation protocol

value: Subiculum burst firing pyramidal cell


title: C85

description:
Single cell from mouse hippocampus
Single_cell_6

value: single cell


title: C90

description:
Single cell from mouse hippocampus
Single_cell_11

value: post natal week 3-4


title: C246

description:
Single cell from mouse hippocampus
Single_cell_93

source_name: Subiculum regular-spiking pyramidal cell

value: Subiculum regular firing pyramidal cell


title: C82

description:
Single cell from mouse hippocampus
Single_cell_3


title: C243

description:
Single cell from mouse hippocampus
Single_cell_90


title: C86

description:
Single cell from mouse hippocampus
Single_cell_7

value: CA1 cholecystokinin cell


title: C238

description:
Single cell from mouse hippocampus
Single_cell_86


title: C245

description:
Single cell from mouse hippocampus
Single_cell_92


title: C242

description:
Single cell from mouse hippocampus
Single_cell_89


title: C80

description:
Single cell from mouse hippocampus
Single_cell_1


title: C91

description:
Single cell from mouse hippocampus
Single_cell_12


title: C240

description:
Single cell from mouse hippocampus
Single_cell_88


title: C237

description:
Single cell from mouse hippocampus
Single_cell_85


title: C225

description:
Single cell from mouse hippocampus
Single_cell_77


title: C92

description:
Single cell from mouse hippocampus
Single_cell_13


title: C226

description:
Single cell from mouse hippocampus
Single_cell_78


title: C227

description:
Single cell from mouse hippocampus
Single_cell_79


title: C224

description:
Single cell from mouse hippocampus
Single_cell_76


title: C231

description:
Single cell from mouse hippocampus
Single_cell_82


title: C235

description:
Single cell from mouse hippocampus
Single_cell_83


title: C239

description:
Single cell from mouse hippocampus
Single_cell_87


title: C228

description:
Single cell from mouse hippocampus
Single_cell_80


title: C236

description:
Single cell from mouse hippocampus
Single_cell_84


title: C216

description:
Single cell from mouse hippocampus
Single_cell_73


title: C211

description:
Single cell from mouse hippocampus
Single_cell_68


title: C217

description:
Single cell from mouse hippocampus
Single_cell_74


title: C210

description:
Single cell from mouse hippocampus
Single_cell_67


title: C205

description:
Single cell from mouse hippocampus
Single_cell_63


title: C223

description:
Single cell from mouse hippocampus
Single_cell_75


title: C208

description:
Single cell from mouse hippocampus
Single_cell_65


title: C214

description:
Single cell from mouse hippocampus
Single_cell_71


title: C203

description:
Single cell from mouse hippocampus
Single_cell_61


title: C137

description:
Single cell from mouse hippocampus
Single_cell_58


title: C207

description:
Single cell from mouse hippocampus
Single_cell_64


title: C213

description:
Single cell from mouse hippocampus
Single_cell_70


title: C204

description:
Single cell from mouse hippocampus
Single_cell_62


title: C134

description:
Single cell from mouse hippocampus
Single_cell_55


title: C136

description:
Single cell from mouse hippocampus
Single_cell_57


title: C133

description:
Single cell from mouse hippocampus
Single_cell_54


title: C212

description:
Single cell from mouse hippocampus
Single_cell_69


title: C202

description:
Single cell from mouse hippocampus
Single_cell_60


title: C229

description:
Single cell from mouse hippocampus
Single_cell_81


title: C201

description:
Single cell from mouse hippocampus
Single_cell_59


title: C215

description:
Single cell from mouse hippocampus
Single_cell_72


title: C135

description:
Single cell from mouse hippocampus
Single_cell_56


title: C129

description:
Single cell from mouse hippocampus
Single_cell_50


title: C131

description:
Single cell from mouse hippocampus
Single_cell_52


title: C132

description:
Single cell from mouse hippocampus
Single_cell_53


title: C209

description:
Single cell from mouse hippocampus
Single_cell_66


title: C128

description:
Single cell from mouse hippocampus
Single_cell_49


title: C130

description:
Single cell from mouse hippocampus
Single_cell_51


title: C122

description:
Single cell from mouse hippocampus
Single_cell_43


title: C125

description:
Single cell from mouse hippocampus
Single_cell_46


title: C127

description:
Single cell from mouse hippocampus
Single_cell_48


title: C119

description:
Single cell from mouse hippocampus
Single_cell_40


title: C124

description:
Single cell from mouse hippocampus
Single_cell_45


title: C120

description:
Single cell from mouse hippocampus
Single_cell_41


title: C121

description:
Single cell from mouse hippocampus
Single_cell_42


title: C117

description:
Single cell from mouse hippocampus
Single_cell_38


title: C115

description:
Single cell from mouse hippocampus
Single_cell_36


title: C116

description:
Single cell from mouse hippocampus
Single_cell_37


title: C113

description:
Single cell from mouse hippocampus
Single_cell_34


title: C111

description:
Single cell from mouse hippocampus
Single_cell_32


title: C112

description:
Single cell from mouse hippocampus
Single_cell_33


title: C110

description:
Single cell from mouse hippocampus
Single_cell_31


title: C109

description:
Single cell from mouse hippocampus
Single_cell_30


title: C106

description:
Single cell from mouse hippocampus
Single_cell_27


title: C107

description:
Single cell from mouse hippocampus
Single_cell_28


title: C126

description:
Single cell from mouse hippocampus
Single_cell_47


title: C108

description:
Single cell from mouse hippocampus
Single_cell_29


title: C114

description:
Single cell from mouse hippocampus
Single_cell_35


title: C105

description:
Single cell from mouse hippocampus
Single_cell_26


title: C81

description:
Single cell from mouse hippocampus
Single_cell_2


title: C123

description:
Single cell from mouse hippocampus
Single_cell_44


title: WT control 48hr2

city: La Jolla

first: Vivek

last: Chandra

state: CA

address: 9500 Gilman Drive MC0377

department: Department of Molecular Biology

institute: University of California, San Diego

data_processing:
RNAseq data were analyzed with the pipeline tool Omics Pipe using the RNA-seq count-based differential expression analysis pipeline
Quality control of the raw fastq files was performed using the software tool FastQC
Sequencing reads were aligned to the mouse genome (mm10) using the STAR aligner
Read quantification was performed at the exon level using htseq-count with UCSC RefSeq annotation
The R BioConductor package DESeq2 was used to calculate size factors to normalize library sizes across replicates and calculate means and variances based on a negative binomial distribution model to detect differentially expressed genes based on an adjusted p-value of < 0.05
Genome_build: mm10
Supplementary_files_format_and_content: csv file include normalized counts for each sample

source_name: B cells from Spleen

growth_protocol: B cells were cultured in RPMI-1640 medium plus 5% FBS, antibiotics, 2mM L-glutamine and β-mercaptoethanol (50μM) at 370C and 5% CO2. They were activated in complete medium at 1*106 cells/ml in the presence of LPS (25mg/ml) and IL4 (5ng/ml).

extract_protocol:
Cells were harvested at the times indicated, washed and RNA was isolated using Rneasy mini kit using standard protocol.
mRNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: B cells were activated in complete medium at 1*106 cells/ml in the presence of LPS (25mg/ml) and IL4 (5ng/ml).

tag: cell type

value: 48hr activated B cell

tag: activation time


title: CD19-Cre;Id3loxP/loxP 48hr rep2


title: C118

description:
Single cell from mouse hippocampus
Single_cell_39


title: CD19-Cre;Id3loxP/loxP 24hr rep1

value: 24hr activated B cell


title: C101

description:
Single cell from mouse hippocampus
Single_cell_22


title: C102

description:
Single cell from mouse hippocampus
Single_cell_23


title: C103

description:
Single cell from mouse hippocampus
Single_cell_24


title: C104

description:
Single cell from mouse hippocampus
Single_cell_25


title: CD19-Cre;Id3loxP/loxP 48hr rep1


title: WT 24hr rep1


title: WT control 48hr1


title: CD19-Cre;Id3loxP/loxP 24hr rep2


title: WT 24hr rep2


title: WT control rep2

value: naive B cell


title: CD19-Cre;Id3loxP/loxP Control rep1


title: CD19-Cre;Id3loxP/loxP Control rep2


title: 53BP1Δ-2 Nutlin-3 replicate 3

city: Oxford

first: Jonathan

middle: Ross

last: Chapman

address: Roosevelt Drive

department: Nuffield Department of Medicine (University of Oxford)

country: United Kingdom

institute: Wellcome Trust Centre for Human Genetics

data_processing:
Reads were aligned  to the human reference genome (GRCh37) using TopHat2 with default parameters except for setting mate-inner-dist=100 and mate-std-dev=50
Duplicate reads were removed using Picard Tools MarkDuplicates
Counts for Ensembl-annotated genes were summarised from the mapped reads using ht-seq, and filtered to exclude genes with fewer than 10 reads on average per sample
Analysis for differential expression was performed using the edgeR package
Genome_build: GRCh37
Supplementary_files_format_and_content: Text files containing raw read counts

organism: Homo sapiens

source_name: MCF-7 breast cancer cells

growth_protocol: Cells were cultured in Dulbecco’s Modified Eagle’s Medium supplemented with 10% fetal bovine serum (Firstlink), Pen-Strep and 2 mM L-Glutamine (Sigma-Aldrich) at 37 oC in 5% CO2

extract_protocol:
Trizol/chloroform-extracted total RNA was further purified with the RNeasy Mini Kit (Qiagen) incorporating a DNaseI step (Qiagen) to remove DNA contamination.
Libraries were prepared from rRNA-depleted total RNA isolates and according to standard Illumina guidelines using in-house adapters (Lamble et al., 2013)

treatment_protocol: Cells were either incubated with 4 uM Nutlin-3 for 8 h, irradiated at 5 Gy and subsequently incubated for 4 h or left untreated.

tag: cell line

tag: genotype


title: C100

description:
Single cell from mouse hippocampus
Single_cell_21


title: WT control rep1


title: 53BP1Δ-2 IR replicate 3

value: IR


title: p53 IR replicate 3


title: p53 Nutlin-3 replicate 3


title: 53BP1Δ-2 untreated replicate 3

value: untreated


title: 53BP1Δ-1 IR replicate 3


title: 53BP1Δ-1 untreated replicate 3


title: 53BP1Δ-1 Nutlin-3 replicate 3


title: Wild-type untreated replicate 3

value: wildtype


title: Wild-type IR replicate 3


title: p53 untreated replicate 3


title: 53BP1Δ-2 IR replicate 2


title: 53BP1Δ-2 untreated replicate 2


title: p53 Nutlin-3 replicate 2


title: 53BP1Δ-1 untreated replicate 2


title: 53BP1Δ-2 Nutlin-3 replicate 2


title: 53BP1Δ-1 IR replicate 2


title: 53BP1Δ-1 Nutlin-3 replicate 2


title: p53 IR replicate 2


title: Wild-type untreated replicate 2


title: Wild-type IR replicate 2


title: Unc22_X1_30_4

city: Kansas City

first: Chris

middle: W

last: Seidel

state: MO

department: Genomics

institute: Stowers Institute

data_processing:
Base calls were performed using CASAVA-1.8.2
Reads were aligned using bowtie with the following parameters: --best --strata -v 2 -m 5 against transcriptome smed_20140614 defined in GEO submission: GSE72389
Read counts to genes were tallied from the SAM files with a custom script. RPKM values were generated after removal of ribosomal RNAs (SMED30027845,SMED30032663,SMED30032887) using the rpkm function from the edgeR library from Bioconductor in R.
Genome_build: Schmidtea_mediterranea_3.1
Supplementary_files_format_and_content: rpkm.txt contains tab-delimited RPKM vales for each sample.

organism: Schmidtea mediterranea

source_name: asexual CIW4 adult

growth_protocol: Asexual Schmidtea mediterranea strain (CIW4) animals were maintained in 1 x Montjuic water supplemented with 100 µg/mL gentamicin sulfate (Gemini Bioproducts, #400-100P) at 20ºC as previously described (Newmark and Sánchez Alvarado, 2000).

extract_protocol:
Worms and isolated cells were homogenized in Trizol reagent. Total RNA extraction was performed following the manufacturer-supplied protocol.
PolyA-selected, single stranded RNA-Sequencing libraries were prepared for four biological replicates per stage using the Illumina TruSeq RNA Sample V2 kit starting with 500 ng total RNA per sample.

treatment_protocol: All genes were cloned into a pPR-T4P vector as described previously (Gurley et al., 2008). RNAi food was prepared by adding 125 µL of liver paste (9 parts of liver to 1 part of water) into a bacterial pellet obtained from a 50 mL overnight culture. Animals used in experiments were starved for 7-14 days. Animals in all RNAi experiments were fed 6 times with 3 days between feedings. 1,250 rads of irradiation was carried out 7 days after the last feeding using a GammaCell 40 Exactor irradiator. Day 0 represents the day of irradiation. X1 stem cells were isolated using a well-established method by Hoechst 33342 staining and flow cytometry.

tag: tissue

tag: RNAi

value: NT

tag: gamma radiation (rads)

tag: feedings

tag: days


title: Wild-type Nutlin-3 replicate 2


title: p53 untreated replicate 2


title: 53BP1Δ-2 Nutlin-3 replicate 1


title: Wild-type Nutlin-3 replicate 3


title: Unc22_X1_30_1


title: 53BP1Δ-2 IR replicate 1


title: Unc22_SR_32_10_4

value: Whole Worm

value: SR


title: 53BP1Δ-2 untreated replicate 1


title: Unc22_X1_30_2


title: Unc22_SR_32_10_2


title: Unc22_SR_30_8_4


title: Unc22_SR_32_10_1


title: Unc22_SR_30_8_3


title: Unc22_SR_32_10_3


title: Unc22_SR_30_8_2


title: Unc22_SR_28_6_4


title: 53BP1Δ-1 IR replicate 1


title: 53BP1Δ-1 untreated replicate 1


title: Unc22_SR_30_8_1


title: Unc22_X1_30_3


title: p53 IR replicate 1


title: Unc22_SR_26_4_2


title: Unc22_SR_28_6_2


title: Unc22_SR_28_6_3


title: p53 untreated replicate 1


title: Unc22_SR_26_4_4


title: Unc22_SR_28_6_1


title: Unc22_SR_23_1_4


title: Unc22_SR_23_1_3


title: Unc22_SR_26_4_1


title: 53BP1Δ-1 Nutlin-3 replicate 1


title: Wild-type IR replicate 1


title: Unc22_SR_22_0_4


title: Unc22_SR_22_0_2


title: Unc22_SR_22_0_3


title: Unc22_SR_23_1_1


title: Unc22_NT_30_4


title: Unc22_SR_23_1_2


title: Unc22_NT_30_2


title: Unc22_NT_30_3


title: Unc22_NT_9_4


title: Unc22_NT_9_2


title: p53 Nutlin-3 replicate 1


title: Unc22_NT_9_3


title: Unc22_SR_26_4_3


title: Y3-CLIP

city: Chicago

first: zhike

last: lu

state: IL

address: 5801 South Ellis Avenue

department: department of chemistry

institute: University of Chicago

data_processing:
library strategy: m6A-CLIP-seq
After removing adapters, the reads was mapped to the HIV(NL4-3) and human genome(hg38). Reads were aligned to the reference genome using Tophat (v2.0.14, ref) with parameter -g 1 --library-type=fr-firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser.The longest isoform was used if the gene has multiple isoforms. Aligned reads were extended to 100bp (average fragments size) and converted from genome-based coordinates to isoform-based coordinates, in order to eliminate the interference from intron in peak calling.
The peak calling method was modified from D. Dominissini et al. To call m6A peaks, the longest isoform of each human gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform, windows with reads counts less than 1/20 of the top window in both m6A-IP and input sample were excluded. For each gene, the reads count in each window was normalized by the median count of all windows of that gene. A fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the fdr<0.01  and log2(Enrichment Score) >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak (or window): reads count of the IP sample in the current peak/window (a), median reads count of the IP sample in all 100bp windows on the current mRNA (b), reads count of the input sample in the current peak/window (c) and median reads count of the input sample in all 100bp windows on the current mRNA (d). The enrichment score of each window was calculated as (a×d)/(b×c).
For CLIPSeq, MACS2 was used for peak calling.
Genome_build: hg38, HIV NL4-3
Supplementary_files_format_and_content: bed,peaks

extract_protocol: m6ASeq libraries were constructed using TruSeq Stranded mRNA Library Prep Kit (Illumina). The CLIP-Seq libraries are made by NEB small RNA kit.

value: HeLa

tag: infected with

tag: molecule subtype

value: protein-bound RNA


title: Unc22_NT_30_1

tag: replicate


title: Unc22_NT_9_1


title: Y2-CLIP


title: nrg7_X1_30_2


title: Wild-type Nutlin-3 replicate 1


title: nrg7_X1_30_4


title: nrg7_X1_30_1


title: Wild-type untreated replicate 1


title: Unc22_SR_22_0_1


title: HIV Tcell infect IP

data_processing:
library strategy: m6A-seq
After removing adapters, the reads was mapped to the HIV(NL4-3) and human genome(hg38). Reads were aligned to the reference genome using Tophat (v2.0.14, ref) with parameter -g 1 --library-type=fr-firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser.The longest isoform was used if the gene has multiple isoforms. Aligned reads were extended to 100bp (average fragments size) and converted from genome-based coordinates to isoform-based coordinates, in order to eliminate the interference from intron in peak calling.
The peak calling method was modified from D. Dominissini et al. To call m6A peaks, the longest isoform of each human gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform, windows with reads counts less than 1/20 of the top window in both m6A-IP and input sample were excluded. For each gene, the reads count in each window was normalized by the median count of all windows of that gene. A fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the fdr<0.01  and log2(Enrichment Score) >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak (or window): reads count of the IP sample in the current peak/window (a), median reads count of the IP sample in all 100bp windows on the current mRNA (b), reads count of the input sample in the current peak/window (c) and median reads count of the input sample in all 100bp windows on the current mRNA (d). The enrichment score of each window was calculated as (a×d)/(b×c).
For CLIPSeq, MACS2 was used for peak calling.
Genome_build: hg38, HIV NL4-3
Supplementary_files_format_and_content: bed,peaks

source_name: Primary CD4+ T_HIV Tcell infect IP

value: Primary CD4+ T

value: mRNA


title: Y1-CLIP


title: nrg7_SR_32_10_4


title: nrg7_SR_32_10_1


title: nrg7_SR_32_10_2


title: nrg7_SR_30_8_2


title: nrg7_SR_30_8_4


title: HIV infect 2 IP

description: processed data file: HIV.Infect.bed

source_name: Jurkat_HIV infect_IP

value: Jurkat


title: nrg7_SR_28_6_4


title: nrg7_SR_30_8_1


title: nrg7_SR_28_6_2


title: nrg7_SR_30_8_3


title: nrg7_SR_28_6_3


title: HIV infect 1 IP

description: processed data file: HIV.Infect.bed


title: HIV Cont 1 IP

description: processed data file: HIV.Cont.bed

source_name: Jurkat_HIV Cont_IP

value: none (control)


title: HIV Cont 2 IP

description: processed data file: HIV.Cont.bed


title: nrg7_SR_32_10_3


title: HIV Tcell cont IP

source_name: Primary CD4+ T_HIV Tcell cont IP


title: nrg7_SR_23_1_4


title: nrg7_SR_28_6_1


title: nrg7_SR_23_1_3


title: nrg7_SR_22_0_4


title: nrg7_X1_30_3


title: nrg7_SR_26_4_4


title: nrg7_SR_26_4_2


title: HIV Tcell infect input

source_name: Primary CD4+ T_HIV Tcell infect input


title: HIV infect 2 input

source_name: Jurkat_HIV infect_input


title: nrg7_SR_22_0_1


title: HIV Tcell cont input

source_name: Primary CD4+ T_HIV Tcell cont input


title: nrg7_NT_30_2


title: nrg7_SR_26_4_3


title: nrg7_SR_26_4_1


title: HIV infect 1 input


title: nrg7_NT_30_1


title: nrg7_SR_23_1_1


title: nrg7_NT_9_4


title: nrg7_SR_23_1_2


title: nrg7_SR_22_0_3


title: HIV Cont 1 input

source_name: Jurkat_HIV Cont_input


title: HIV Cont 2 input


title: RNA_Seq_CT40_6AN

city: Geneva

first: Guillaume

last: Rey

address: Campus Biotech, Chemin des Mines 9

country: Switzerland

institute: University of Geneva

description:
rRNA-depleted RNA
6AN_genes.fpkm_table
6AN_genes.attr_table

data_processing:
RNASeq: rRNA filtering with Bowtie
RNASeq: Tag mapping with TopHat
RNASeq: quantification with Cufflinks
ChIPSeq: Tag mapping with Bowtie2
CHIPSeqHOMER software suite for downstream analyses
Genome_build: RNASeq: hg38
Genome_build: ChIPSeq: hg38
Supplementary_files_format_and_content: RNASeq - cufflinks output files
Supplementary_files_format_and_content: ChIPSeq - HOMER output files

source_name: U2OS cells stably expressing Bmal1:Luc

growth_protocol: Bmal1:luc U2OS cells were grown in DMEM using standard cell culture methods.

extract_protocol:
RNA-Seq: Standard RNA extraction with Zymo Direct-zol™ RNA kits.  ChIP-Seq: Crosslinked nuclei from U2OS cells were sonicated and protein-DNA complexes were isolated with the following antibodies: anti-CLOCK (NB100-126; Novus Biologicals), anti-BMAL1 (ab3350; Abcam), anti-H3K9ac (ab4441; Abcam) and anti-H3K4me3 (#39159; Active Motif).
Illumina TrueSeq platform compatible dual-indexed multiplex library protocol was followed.

treatment_protocol: RNA-Seq: Cells were treated with 5mM 6AN or control (DMSO) and RNA was extracted at the indicated time points.  ChIP-Seq: Cells were treated with 5mM 6AN or control (DMSO) and RNA was extracted after 24h.

value: osteosarcoma cell line U2OS stably expressing Bmal1:Luc

tag: time

tag: agent


title: RNA_Seq_CT44_6AN


title: nrg7_SR_22_0_2


title: nrg7_NT_30_3


title: nrg6_X1_30_4


title: nrg7_NT_30_4


title: nrg6_X1_30_3


title: EGF20

city: Warszawa

first: Krzysztof

last: Goryca

address: Banacha 2c

department: CeNT

country: Poland

institute: Uniwersytet Warszawski

library_source: genomic

data_processing:
Basecalls performed using Real-Time Analysis (RTA) software
BCL2FASTQ Conversion Software was used to generate fastq files
ChIP-seq reads were aligned to the hg19 genome assembly using bowtie2 version 2.1.0 with parameter -N 1
sam files were converted to bam and technical replicates were merged with samtools
differential binding locations were called with Macs version 1.4.2, default parameters
Genome_build: hg19
Supplementary_files_format_and_content: bed files were generated with Macs 1.4.2

molecule: genomic DNA

source_name: cervix

growth_protocol: Hela S3 cell were  grown in DMEM F-12 Ham media (Sigma; D8437) supplemented with 10% heat-inactivated fetal bovine serum (FBS) and penicillin-streptomycin at 50 IU/ml in a humidified 5% CO2 atmosphere at 37oC.

extract_protocol:
1E+07 cells were crosslinked with 1% formaldehyde for 10 minutes at then formaldehyde quenched with 125mM glycine for 5 minutes room temperature. After harvest cells were spun down at 1600 x g then washed with 5 ml PBS, spun down again and stored at -80oC as pellets. The pellet was suspended in a 2 mL of hypotonic buffer A [10 mM HEPES, pH 7.9, 2 mM MgCl2, 2 mM KCl and NP-40 0.5% vol/vol] supplemented with protease and phosphatase inhibitors (Thermo; 78441) and suspension was kept for 5min on ice then spun down at 10 000 x g / 4 oC for 3 min. Pellets of nuclei were resuspended in lysis buffer [12.5 mM Tris-HCl, pH 8.0, 2.5 mM EDTA, and 0.1% SDS vol/vol] containing protease and phosphatase inhibitors (Thermo, 78441). Chromatin was sheared in a Bioruptor Plus (Diagenode) using a 30 sec on-off cycle for 15 min at high intensity then centrifuged 12 000 x g for 15 min at 4 °C, aliquoted and stored at -80oC. A modified Fast-ChIP protocol was used for the ChIP-Seq libraries . Briefly, a volume of chromatin (20-30 µl) with equivalent of 5E+06 cells was adjusted to 200 µl with IP buffer [150 mM NaCl, 50 mM Tris-HCl (pH 7.5), 5 mM EDTA, NP-40 (0.5% vol/vol), Triton X-100 (1.0% vol/vol), (pH 7.6)] containing protease and phosphatase inhibitors (Thermo) and incubated with 5µg of a given antibody for 30 minutes in ultrasonic bath (Branson, B3510) at 4 oC. Next, the chromatin was cleared by centrifugation at 12 000 x g for 10 min at 4 °C and transferred to a new tube containing 20µl of Dynabeads® Protein A (Life Technologies). Tubes were then rotated at 4 °C for 60 min on a rotating platform (15 rotations per min). Beads were separated on a magnetic stand and washed five times with 800 µl of ice cold IP buffer. DNA was recovered by beads incubation with 50 µl elution buffer [0.5% SDS, 0.1M NaHCO3, 20mg/ml Proteinase K] at 56oC for 30 min with mixing (1000rpm) in a ThermoMixer (Eppendorf). Sample was separated on a magnetic stand, transferred to a PCR tube and then NaCl was added to final concentration of 0.2M followed by overnight reverse crosslinking at 65oC in a thermocycler. DNA was cleaned up with ChIP DNA Purification Kit (Active motif; 58002) according to manufacturer's protocol and DNA concentration was determined with Qubit dsDNA HS Assay Kit (Life Technologies) while the respective size distribution with High Sensitivity DNA Analysis Kit on Bioanalyzer 2100 (Agilent). The antibodies used in ChIP studies were as follow: non-specific rabbit IgG (I-1000, Vector Labs), Pol 2 (4H8) (Santa cruz; sc-47701), pEGFR (Tyr845) (Cell signaling; 6963), pMek1/2 (Ser217/221) (Cell signaling; 9121S), pErk1/2 (Thr202/Tyr204) (Cell signaling; 4370P).
DNA libraries were prepared from up to 20 ng of DNA using TruSeqTM ChIP Sample Prep Kit (Illumina Inc.), according to standard protocol with modifications. Briefly, DNA fragments were end repaired into blunt ends and single ‘A’ nucleotide was added to the 3’ ends. Adenylated fragments were ligated with Illumina indexed adapters and then amplified during 18-cycles PCR for selective enrichment. Finally, library fragments with insert length of about 120-200 bp were automatically selected using LabChip XT DNA 750 Assay Kit and LabChip XT DNA sizing system. The quality and quantity of all libraries were assessed on 2100 Bioanalyzer using High Sensitivity DNA Kit (Agilent Technologies) and by qPCR with Kapa Library Quantification Kit (KapaBiosystems), respectively.
ChIP-Seq samples were sequenced during single 50 bp read run on Illumina HiSeq 2500 system in High Output mode (using TruSeq SR Cluster Kit v3-cBot-HS and TruSeq SBS Kit v3-HS) or Rapid mode (using TruSeq Rapid Duo Sample Loading Kit, TruSeq Rapid SR Cluster Kit and TruSeq Rapid SBS Kit). Base calling, demultiplexing and generation of fastq files was carried on using Illumina RTA (v1.18.42.0) and bcl2fastq (v1.8.4) software.

treatment_protocol: Cells were starved for 48 hours in serum-free medium and then stimulated for 20 minutes with EGF (100 ng/ml) (Sigma; E9644).

tag: cell line/vendor

value: HeLa S3 (ATCC CCL2.2)

tag: stimulated with

value: EGF (100 ng/ml) for 20min

tag: chip antibody


title: nrg7_NT_9_1

tag: treatment


title: nrg7_NT_9_2


title: nrg7_NT_9_3


title: RNA_Seq_CT36_6AN


title: nrg6_SR_32_10_4


title: CTRL


title: nrg6_X1_30_2


title: nrg6_SR_32_10_2


title: RNA_Seq_CT28_6AN


title: nrg6_X1_30_1


title: nrg6_SR_32_10_1


title: RNA_Seq_CT20_6AN


title: nrg6_SR_30_8_4


title: RNA_Seq_CT16_6AN


title: nrg6_SR_32_10_3


title: nrg6_SR_30_8_3


title: nrg6_SR_30_8_1


title: nrg6_SR_28_6_4


title: nrg6_SR_28_6_2


title: RNA_Seq_CT08_6AN


title: RNA_Seq_CT32_6AN


title: RNA_Seq_CT12_6AN


title: nrg6_SR_30_8_2


title: nrg6_SR_26_4_4


title: RNA_Seq_CT04_6AN


title: RNA_Seq_CT24_6AN


title: nrg6_SR_28_6_1


title: nrg6_SR_26_4_3


title: nrg6_SR_26_4_2


title: RNA_Seq_CT00_6AN


title: nrg6_SR_26_4_1


title: RNA_Seq_CT44_DMSO

description:
rRNA-depleted RNA
DMSO_genes.fpkm_table
DMSO_genes.attr_table

value: DMSO


title: RNA_Seq_CT40_DMSO


title: Vegetative Meristem & Surrounding Tissue 1

first: Joseph

middle: R

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

data_processing:
Data were mapped to the ZmB73_RefGen_v2 reference genome and the ZmB73_5a.59_WGS_exons.tfp was used for annotations of gene models
RNA-Seq RPKM data were generated using Bowtie version 2.1.0 and Tophat version 2.0.8b (flags = –F 0 -i 30 -M). Gene expression values were calculated using Cufflinks version 2.1.1 (flags = -u --library-type fr-firststrand -b)
Genome_build: ZmB73_RefGen_v2
Supplementary_files_format_and_content: The processed data for the FPKM.tsv file contains a row of headers indicating the sample name. this first colum is the unique gene identifier and the all of columns represent the expression value represented in Fragments per Kilobase of exons per gene per million reads. This is a tab delimited file.

organism: Zea mays

extract_protocol: RNA-seq libraries were prepared as follows. Approximately four micrograms of total RNA was used as input. Each sequencing library was constructed using the TruSeq RNA Sample Prep Kit V2 (Illumina, San Diego, CA) according to manufacturer’s instructions with the following modifications to confer strand-specificity. The polyA-selected RNA was used for first strand synthesis and the resulting cDNA:RNA hybrid was purified using RNAClean XP beads (Beckman, Brea, CA). The second strand synthesis was performed using a dNTP mix containing dUTPs (10mM dATPs, 10mM dGTPs, 10mM dCTPs, and 20mM dUTPs) and DNA Polymerase I (New England Biolabs, Ipswich, MA). The purified ligation products were incubated with Uracil DNA Glycosylase (Fermentas) before PCR amplification.


title: Internode 7-8 3

source_name: Internode 7-8

value: Internode 7-8


title: Vegetative Meristem & Surrounding Tissue 2


title: Internode 7-8 2


title: Internode 7-8 1


title: nrg6_SR_23_1_4


title: nrg6_SR_28_6_3


title: RNA_Seq_CT32_DMSO


title: nrg6_SR_23_1_3


title: nrg6_SR_23_1_2


title: Internode 6-7 2

source_name: Internode 6-7

value: Internode 6-7


title: nrg6_SR_22_0_4


title: Internode 6-7 1


title: nrg6_SR_23_1_1


title: RNA_Seq_CT20_DMSO


title: RNA_Seq_CT16_DMSO


title: nrg6_SR_22_0_3


title: mature female spikelets 3

source_name: mature female spikelets

value: mature female spikelets


title: RNA_Seq_CT24_DMSO


title: RNA_Seq_CT28_DMSO


title: mature female spikelets 2


title: nrg6_SR_22_0_2


title: RNA_Seq_CT12_DMSO


title: nrg6_SR_22_0_1


title: mature female spikelets 1


title: RNA_Seq_CT36_DMSO


title: silks 3

source_name: silks

value: silks


title: RNA_Seq_CT04_DMSO


title: Internode 6-7 3


title: RNA_Seq_CT00_DMSO


title: Mature pollen 3

source_name: Mature pollen

value: Mature pollen


title: silks 1


title: nrg6_NT_30_1

value: Whole Worm

value: NT


title: Mature pollen 2


title: nrg6_NT_9_4


title: Mature pollen 1


title: RNA_Seq_CT08_DMSO


title: nrg6_NT_9_3


title: 30_pMEK_control_repl_2

description: processed data file: macs.pMEK_Egf.vs.pMEK.merged.peaks.bed

source_name: HeLa S3_pMEK_control

extract_protocol:
1E+07 cells were crosslinked with 1% formaldehyde for 10 minutes at then formaldehyde quenched with 125mM glycine for 5 minutes room temperature. After harvest cells were spun down at 1600 x g then washed with 5 ml PBS, spun down again and stored at -80oC as pellets. The pellet was suspended in a 2 mL of hypotonic buffer A [10 mM HEPES, pH 7.9, 2 mM MgCl2, 2 mM KCl and NP-40 0.5% vol/vol] supplemented with protease and phosphatase inhibitors (Thermo; 78441) and suspension was kept for 5min on ice then spun down at 10 000 x g / 4 oC for 3 min. Pellets of nuclei were resuspended in lysis buffer [12.5 mM Tris-HCl, pH 8.0, 2.5 mM EDTA, and 0.1% SDS vol/vol] containing protease and phosphatase inhibitors (Thermo, 78441). Chromatin was sheared in a Bioruptor Plus (Diagenode) using a 30 sec on-off cycle for 15 min at high intensity then centrifuged 12 000 x g for 15 min at 4 °C, aliquoted and stored at -80oC. A modified Fast-ChIP protocol was used for the ChIP-Seq libraries . Briefly, a volume of chromatin (20-30 µl) with equivalent of 5E+06 cells was adjusted to 200 µl with IP buffer [150 mM NaCl, 50 mM Tris-HCl (pH 7.5), 5 mM EDTA, NP-40 (0.5% vol/vol), Triton X-100 (1.0% vol/vol), (pH 7.6)] containing protease and phosphatase inhibitors (Thermo) and incubated with 5µg of a given antibody for 30 minutes in ultrasonic bath (Branson, B3510) at 4 oC. Next, the chromatin was cleared by centrifugation at 12 000 x g for 10 min at 4 °C and transferred to a new tube containing 20µl of Dynabeads® Protein A (Life Technologies). Tubes were then rotated at 4 °C for 60 min on a rotating platform (15 rotations per min). Beads were separated on a magnetic stand and washed five times with 800 µl of ice cold IP buffer. DNA was recovered by beads incubation with 50 µl elution buffer [0.5% SDS, 0.1M NaHCO3, 20mg/ml Proteinase K] at 56oC for 30 min with mixing (1000rpm) in a ThermoMixer (Eppendorf). Sample was separated on a magnetic stand, transferred to a PCR tube and then NaCl was added to final concentration of 0.2M followed by overnight reverse crosslinking at 65oC in a thermocycler. DNA was cleaned up with ChIP DNA Purification Kit (Active motif; 58002) according to manufacturer's protocol and DNA concentration was determined with Qubit dsDNA HS Assay Kit (Life Technologies) while the respective size distribution with High Sensitivity DNA Analysis Kit on Bioanalyzer 2100 (Agilent). The antibodies used in ChIP studies were as follow: non-specific rabbit IgG (I-1000, Vector Labs), Pol 2 (4H8) (Santa cruz; sc-47701), pEGFR (Tyr845) (Cell signaling; D63B4), pBRAF (Thr 598/Ser 601) (Santa cruz; sc28006-R), pMek1/2 (Ser217/221) (Cell signaling; 9121S), pErk1/2 (Thr202/Tyr204) (Cell signaling; 4370P).
DNA libraries were prepared from up to 20 ng of DNA using TruSeqTM ChIP Sample Prep Kit (Illumina Inc.), according to standard protocol with modifications. Briefly, DNA fragments were end repaired into blunt ends and single ‘A’ nucleotide was added to the 3’ ends. Adenylated fragments were ligated with Illumina indexed adapters and then amplified during 18-cycles PCR for selective enrichment. Finally, library fragments with insert length of about 120-200 bp were automatically selected using LabChip XT DNA 750 Assay Kit and LabChip XT DNA sizing system. The quality and quantity of all libraries were assessed on 2100 Bioanalyzer using High Sensitivity DNA Kit (Agilent Technologies) and by qPCR with Kapa Library Quantification Kit (KapaBiosystems), respectively.
ChIP- Seq samples were sequenced during single 50 bp read run on Illumina HiSeq 2500 system in High Output mode (using TruSeq SR Cluster Kit v3-cBot-HS and TruSeq SBS Kit v3-HS) or Rapid mode (using TruSeq Rapid Duo Sample Loading Kit, TruSeq Rapid SR Cluster Kit and TruSeq Rapid SBS Kit). Base calling, demultiplexing and generation of fastq files was carried on using Illumina RTA (v1.18.42.0) and bcl2fastq (v1.8.4) software.

tag: chip antibody vendor

value: Cell Signaling

tag: chip antibody cat. #


title: SR 2

source_name: Secondary root

value: Secondary root

tag: genotype


title: 25_IgG_control

source_name: HeLa S3_IgG_control

value: rabbit IgG

value: Vector Labs


title: Egfr3_X1_30_4

source_name: asexual CIW4 adult

tag: tissue


title: 32_pMEK_EGF20_repl_2

source_name: HeLa S3_pMEK_EGF20'


title: SR 1


title: 26_IgG_EGF20'

source_name: HeLa S3_IgG_EGF20'


title: silks 2


title: 24_pERK_EGF20_repl_2

description: processed data file: macs.pERK_Egf.vs.pERK.merged.peaks.bed

source_name: HeLa S3_pERK_EGF20'


title: nrg6_NT_9_1

tag: RNAi


title: nrg6_NT_9_2

tag: gamma radiation (rads)


title: 31_pMEK_EGF20_repl_1


title: PR 3

source_name: Primary root

value: Primary root


title: Egfr3_X1_30_3

tag: feedings


title: nrg6_NT_30_4

tag: days


title: nrg6_NT_30_2


title: PR 2


title: Egfr3_X1_30_2


title: Egfr3_X1_30_1


title: 22_pERK_control_repl_2

source_name: HeLa S3_pERK_control

value: none (control)


title: 23_pERK_EGF20_repl_1


title: 29_pMEK_control_repl_1


title: PR 1


title: Cortex_rep3

source_name: Root cortex

value: Root cortex


title: 20_pEGFR_EGF20_repl_2

description: processed data file: macs.pEGFR-Egf.vs.pEGFR.merged.peaks.bed

source_name: HeLa S3_pEGFR_EGF20'

value: HeLa S3 (ATCC CCL2.2)

value: pEGFR (Tyr845)


title: Egfr3_SR_32_10_4

value: SR


title: Egfr3_SR_32_10_3


title: 19_pEGFR_EGF20_repl_1

value: EGF (100 ng/ml) for 20min


title: Egfr3_SR_32_10_2


title: 18_pEGFR_control_repl_2

source_name: HeLa S3_pEGFR_control


title: MZ_rep3

source_name: Root maturation zone

value: Root maturation zone


title: Egfr3_SR_32_10_1


title: Egfr3_SR_30_8_4


title: 17_pEGFR_control_repl_1


title: MZ_rep2


title: 16_Pol2_EGF20_repl_2

description: processed data file: macs.Pol2-Egf.vs.Pol2.peaks.bed

source_name: HeLa S3_Pol2_EGF20'

value: Santa cruz


title: Egfr3_SR_30_8_3


title: Egfr3_SR_30_8_2


title: 15_Pol2_EGF20_repl_1


title: Cortex_rep1


title: Egfr3_SR_30_8_1


title: EZ_rep1

source_name: Root elongation zone

value: Root elongation zone


title: Egfr3_SR_28_6_4


title: 21_pERK_control_repl_1


title: MZ_rep1


title: 13_Pol2_control_repl_1

source_name: HeLa S3_Pol2_control


title: Egfr3_SR_28_6_3


title: EZ_rep3


title: 2-4 mm from tip of ear primordium 3

source_name: 2-4 mm from tip of ear primordium

value: 2-4 mm from tip of ear primordium


title: nrg6_NT_30_3

value: Whole Worm


title: Egfr3_SR_28_6_1


title: Cortex_rep2


title: Egfr3_SR_28_6_2


title: EZ_rep2


title: 6-8 mm from tip of ear primordium 3

source_name: 6-8 mm from tip of ear primordium

value: 6-8 mm from tip of ear primordium


title: Egfr3_SR_26_4_4


title: Egfr3_SR_26_4_3


title: Egfr3_SR_26_4_2


title: 2-4 mm from tip of ear primordium 1


title: 6-8 mm from tip of ear primordium 1


title: 6-8 mm from tip of ear primordium 2


title: Egfr3_SR_26_4_1


title: 14_Pol2_control_repl_2


title: Egfr3_SR_23_1_4


title: Egfr3_SR_23_1_3


title: MATURE LEAF TISSUE (leaf 8) 1

source_name: mature leaf tissue (leaf 8)

value: mature leaf tissue (leaf 8)


title: MATURE LEAF TISSUE (leaf 8) 3


title: MATURE LEAF TISSUE (leaf 8) 2


title: Germinating Kernels 2

source_name: germinating kernels

value: germinating kernels


title: Egfr3_SR_23_1_1

source_name: asexual CIW4 adult


title: Egfr3_SR_23_1_2


title: Germinating Kernels 3


title: Germinating Kernels 1


title: Egfr3_SR_22_0_4


title: Egfr3_SR_22_0_3


title: Egfr3_SR_22_0_2


title: EMBRYOS 2

source_name: embryos

value: embryos


title: Egfr3_SR_22_0_1


title: EMBRYOS 3


title: 2-4 mm from tip of ear primordium 2


title: EMBRYOS 1


title: embryos_20DAP_r3

source_name: embryos 20 days after pollination

value: embryos 20 days after pollination


title: Egfr3_NT_30_3

value: NT


title: Egfr3_NT_30_2


title: embryos_20DAP_r2


title: embryos_20DAP_r1


title: Egfr3_NT_30_1


title: GROWTH ZONE 3

source_name: growth zone

value: growth zone


title: Egfr3_NT_9_4


title: GROWTH ZONE 2


title: Egfr3_NT_9_3


title: GROWTH ZONE 1


title: STOMATAL_DIVISION_ZONE_r3

source_name: stomatal division zone

value: stomatal division zone


title: STOMATAL_DIVISION_ZONE_r2


title: Egfr3_NT_9_2


title: STOMATAL_DIVISION_ZONE_r1


title: SYMMETRICAL_DIVISION_ZONE_r3

source_name: symmetrical division zone

value: symmetrical division zone


title: SYMMETRICAL_DIVISION_ZONE_r2


title: endosperm_crown_r3

source_name: endosperm crown

value: endosperm crown


title: endosperm_crown_r2


title: Egfr3_NT_30_4


title: endosperm_crown_r1


title: pericarp_aleurone_r1

source_name: pericarp and aleurone

value: pericarp and aleurone


title: endosperm_12DAP_r3

source_name: endosperm 12 days after pollination

value: endosperm 12 days after pollination


title: endosperm_12DAP_r2


title: pericarp_aleurone_r2


title: endosperm_12DAP_r1


title: MLN Memory Cells immunized mouse 3

city: Gothenburg

first: Mats

last: Bemark

address: PO Box 435

department: Departement of microbiology and immunity

country: Sweden

institute: University of Gothenburg

description: Flow sorted CD19+CD80+GL7-CD138- cells

data_processing:
Remove sequences shorter than 250 bp using CLC genomic workbench and export as fasta files
Submission to IMGTHighV-Quest for alignment to V, D and J regions and mutational analysis
Identification of  NP binding sequences by filtering for sequences that used the Vh1-72 gene, had 11-14 aa long CDR3 region, had a tyrosine at position four in the CDR3 region, and at least two more tyrosines in the following three amino acids in excell
Upstream and downstream sequences from the same sample were pooled, and filtering for sequences that was found in at least two identical copies to avoid mutations due to misreads or PCR errors fin excell
Compare clonotypes between organs in each mouse to identifiy clones that were shared between organs
Supplementary_files_format_and_content: Summary .txt files with V region alignments returned from IMGT

source_name: MLN Memory Cells

extract_protocol:
Total RNA was prepared from bone marrow cells, lamina propria or memory B cells sorted based on expression of CD80 from spleen, MLN or spleen. cDNA was prepared using a IgA specific primer and a first PCR was conducted with primers binding to leader sequene of the Vh1-72  and related genes and IgA for 25 cycles.
A second round of PCR for 25 cycles was conducted with primers in FRW1 (AAGCTGTCCTGCAAGGCTTC) and IgA (CTTGACAGAGCTCGTGGGAG) with barcodes, A and trP1 sequnces attached as described in ThermoFisher publication 4468326. Eight barcodes were used for multiplexing, and attaching the A or trP1 sequence to either primers allowed for sequencing in either direction (although not paired). After PCR the libraries were purified using Qiagen minElute PCR purification columns

tag: strain

tag: cell type

value: MLN memory B cells

tag: organ

value: Lamina Propria


title: PP Memory Cells immunized mouse 3

description: Flow sorted CD19+CD80+GL7-CD138- cells

source_name: PP Memory Cells

value: PP memory B cells


title: Egfr3_NT_9_1

tag: replicate


title: pericarp_aleurone_r3


title: E18 retina replicate 1

city: Charlottesville

first: Stephen

last: Turner

state: VA

address: 1670 Discovery Drive

institute: Signature Science, LLC

data_processing:
Basecalls performed using CASAVA
Data were aligned to the Galgal4 genome using STAR with the following parameters: --outSAMstrandField intronMotif --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000
Aligned reads were counted against genes from the Ensembl Galgal4 annotation using the featureCounts program in the subread package.
Data were normalized for library size using the DESeq2 median ratio normalization procedure described in Ander and Huber (2010).
Differential gene expression was assessed using the DESeq2 package in R.
Genome_build: Galgal4
Supplementary_files_format_and_content: DESeq-normalized count matrix text file

organism: Gallus gallus

source_name: Retina cells

growth_protocol: tissue was harvested from chicken embryos grown under normal incubation conditions

extract_protocol:
Qiagen all prep min kit was used to extract nucleic acids
cDNA libraries were prepared from poly A+ RNAs according to Illumina's instructions accompanying the Illumina TruSeq kit.

treatment_protocol: no treatments were used

tag: age

value: Retina


title: E8 retina replicate 2


title: E18 cornea replicate 1

source_name: Cornea cells

value: Cornea


title: E18 retina replicate 2


title: E16 retina replicate 2


title: Bone Marrow immunized mouse 3

source_name: Bone Marrow

value: Isolated Bone Marrow cells


title: Spleen Memory Cells immunized mouse 3

description: Flow sorted CD19+CD80+GL7-CD138- cells

source_name: Spleen Memory Cells

value: Spleen memory B cells


title: Lamin Propria immunized mouse 3

source_name: Lamin Propria

value: Whole


title: SYMMETRICAL_DIVISION_ZONE_r1


title: E8 retina replicate 1


title: PP Memory Cells immunized mouse 2

description: Flow sorted CD19+CD80+GL7-CD138- cells


title: E16 retina replicate 1


title: MLN Memory Cells immunized mouse 2

description: Flow sorted CD19+CD80+GL7-CD138- cells


title: Lamin Propria immunized mouse 2


title: Bone Marrow immunized mouse 2


title: E18 cornea replicate 2


title: Spleen Memory Cells immunized mouse 2

description: Flow sorted CD19+CD80+GL7-CD138- cells


title: MLN Memory Cells immunized mouse 1

description: Flow sorted CD19+CD80+GL7-CD138- cells


title: PP Memory Cells immunized mouse 1

description: Flow sorted CD19+CD80+GL7-CD138- cells


title: Bone Marrow immunized mouse 1


title: Bos indicus sire semen

status: Public on Aug 17 2016

city: Columbia

first: Rocío

middle: Melissa

last: Rivera

address: 920 East Campus Drive, ASRC 164

department: Animal Sciences

institute: University of Missouri, Columbia

data_processing:
Library strategy: DNA-Seq
Base calling was perfomed using version 1.8 of the CASAVA package from Illumina
Adator sequences of the reads were removed with the use of FastqMcf program (version 1.04.636). Low quality reads were filtered out using DynamicTrim (version 3.3.1)
DNAseq read pairs were aligned to the bovine reference genome assembly UMD3.1 using Bowtie2 (version 2.2.3)
Genome Analysis Tool Kit (version 3.3-0) and SAMtools mpileup (version 0.1.19) were used for SNP calling from the uniquely aligned DNAseq reads
A pseudo Bos indicus genome was generated by editing the reference allele (UMD3.1; i.e. Bos taurus) with the SNPs identified in the Bos indicus sire. A diploid genome was generated by combining the Bos taurus and the pseudo Bos indicus FASTA files.
RNAseq reads of the Bos indicus X Bos taurus F1 conceptuses were aligned to the diploid genome using HISAT2 (version: 2.0.0) and BWA mem (version:0.7.7)
Cufflinks (version: 2.2.1) and Cuffmerge (version: 2.2.1) were used to assemble transcripts from the uniquely aligned RNAseq reads
RNAseq read counts for each gene model were generated using Htseq-count (version: 0.5.4) and read counts were normalized using edgeR (version: 3.8.6)
SNPiR pipeline (Piskol et al., 2013) was adapted to identify SNPs in RNAseq data.  The parental-allele-origin of the RNA variants were assigned accoding to the Bos indicus sire DNAseq reads
Allele-specific read counts for SNPs in the same gene were aggregated for allele-specific expression analyes.
Genome_build: UMD3.1
Supplementary_files_format_and_content: The SNPs of the Bos indicus sire used to assgin allele-origin of the RNAseq reads from the Bos indicus X Bos taurus F1 hybrids, allele-sepcific read counts of the monoallelically expressed genes identified in this study

organism: Bos indicus

source_name: Nelore semen (ABS CSS MR N OB 425/1 677344 29NE0001 97155)

extract_protocol:
Total RNA was isolated using Trizol Reagent (Invitrogen) according to the manufacturer's instructions. Semen DNA was isolated using phenol chloroform method.
RNAseq libraries were prepared using Illumina TruSeq RNA sample preparation kit. Briefly, poly-A containing RNA was purified using magnetic beads with oligo-dT attached. The purified RNA was fragmented and used as a template for cDNA synthesis using random primers. In the following end-repair procedure, an "A" was added to the 3' end of the cDNA. The cDNA fragments with A-tailing were then ligated with T-tailing adaptors. PCR amplifications of cDNA fragments were followed to generate the final RNAseq library.  Two DNAseq libraries (one with 350bp target insert size, the other with 550bp target insert size) were prepared using Illumina TruSeq DNA PCR-Free Sample Preparation Kit according to the manufacturer’s instructions (Illumina)

value: semen


title: Lamin Propria immunized mouse 1


title: Zr1292_1

first: Katie

middle: J

last: Trella

address: 1611 W. Harrison St, Suite 401A

department: Orthopedics

institute: Rush University Medical Center

data_processing:
Sequence reads from bisulfite-treated EpiQuest libraries were identified using standard Illumina base-calling software and then analyzed using a Zymo Research proprietary analysis pipeline, which is written in Python and used Bismark (http://www.bioinformatics.babraham.ac.uk/projects/bismark/) to perform the alignment
Index files were constructed using the bismark_genome_preparation command and the entire reference genome. The --non_directional parameter was applied while running Bismark. All other parameters were set to default.
Filled-in nucleotides were trimmed off when doing methylation calling. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T.
Fisher’s exact test or t-test was performed for each CpG site which has at least five reads coverage, and promoter, gene body and CpG island annotations were added for each CpG included in the comparison.
For post-processing, CpG sites with methylation differentials greater than 80% (0.8) for any experimental group relative to UI were used.

source_name: Achilles tendons

extract_protocol:
Libraries were prepared from 200-500 ng of genomic DNA (from 5-6 tendons) digested with 60 units of TaqαI and 30 units of MspI (NEB) sequentially and then extracted with Zymo Research (ZR) DNA Clean & Concentrator™-5 kit (Cat#: D4003)
Fragments were ligated to pre-annealed adapters containing 5’-methyl-cytosine instead of cytosine according to Illumina’s specified guidelines (www.illumina.com). Adaptor-ligated fragments of 150–250 bp and 250–350 bp in size were recovered from a 2.5% NuSieve 1:1 agarose gel (Zymoclean™ Gel DNA Recovery Kit, ZR Cat#: D4001). The fragments were then bisulfite-treated using the EZ DNA Methylation-Lightning™ Kit (ZR, Cat#: D5020).
Preparative-scale PCR was performed and the resulting products were purified (DNA Clean & Concentrator™ - ZR, Cat#D4005) for sequencing on an Illumina HiSeq.

treatment_protocol: Chronic Achilles tendinopathy was induced via two injections of TGF-β1 directly into the body of the tendon. Mice were then sacrificed on day 3 or underwent normal cage activity or treadmill running for 14 or 28 days

tag: group

value: 28 days


title: Zr1292_2

value: 28 days with TM


title: SR 3

source_name: Secondary root

value: Secondary root


title: Zr1087_3

value: 14 days


title: Zr1087_4

value: 14 days with TM


title: Zr1087_2

value: Acute (3 days)


title: Zr1087_1

value: Un-Injured


title: Sample_WT-TKO_rep8

city: Gottingen

first: Ramon

last: Oliveira Vidal

address: Grisebachstraße 5

department: Bioinformatics

country: Germany

institute: DZNE

data_processing:
Basecalls performed using CASAVA version 1.8.2
RNA-seq reads were aligned to the mm10 genome assembly using STAR aligner version 2.3.0e_r291 with default options
Genome_build: mm10
Supplementary_files_format_and_content: Read counts for all genes and all exons (Ensembl annotation v72) were obtained using FeaturesCount. DEGs were calculated using DESEQ2

source_name: hippocampus

growth_protocol: newborn mice (p0)

extract_protocol:
Total RNA was extracted using RNeasy Mini kit (Qiagen) or NucleoSpin RNA (Macherey-Nagel) according to manufacturer instructions
Libraries were prepared using the TruSeq RNA Sample Preparation v2 kit (Illumina).

treatment_protocol: no treatment was performed

tag: genotype/variation

value: wild type controls


title: Sample_WT-TKO_rep7


title: Sample_WT-TKO_rep6


title: Sample_WT-TKO_rep4


title: Sample_WT-TKO_rep3


title: Sample_WT-TKO_rep2


title: ddb2-3

city: Strasbourg

first: Jean

last: Molinier

address: 12 rue du General Zimmer

country: France

institute: IBMP-CNRS

data_processing:
Quality control using FastQC and adapter removal using Cutadapt. Short reads (<20 bp) were removed Trim Galore
Mapping : BISMARK (1 MM) Bowtie 2.0 unique mapping,Giving unmapped reads / ambiguous reads. Deduplication script provided by BISMARK to delete PCR biais
Methylation information : Methylation extraction script provided by BISMARK
Filtering : Coverage filter (<100). Windows : 100 bp consecutive windows. Methaltion levels expressed as percent of methylted readfs over totla reads. Difference between identical windows (same start same stop). Apply a Fisher test with a filtering value p<0.01 and difference >40% for CG and >10% for CHG and CHH
DMRs were called in joined windows as same direction (hyper DMR and hypo DMR allowing 1 window gap). Filtering for less that 4 C
Genome_build: TAIR10
Supplementary_files_format_and_content: gff files

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: Ten day old in vitro grown seedlings. MS liquid medium (1.5% sucrose). 16H/8H light/dark photoperiod (21°C/18°C). Roudier et al. EMBO J. (2011)

extract_protocol:
Genomic DNA was prepared using the Macherey Nagel plant DNA extraction kit
Library construction protocol: According to BGI company

tag: developemental stage

value: 10 old days in vitro grown seedling

value: ddb2-3 (DsLoxHs195_05H)

value: seedling


title: Sample_WT-TKO_rep1


title: nrpd1a_smallRNA

data_processing:
basecalling performed by FASTERIS company (HiSeq Control Software 2.0.5 - RTA 1.17.20.0 - CASAVA 1.8.2)
3' adapter removal performed by FASTERIS company
mapping performed on Arabidopsis genome (TAIR10) with bowtie (parameters -t -q -y -e 50 -n 0 -a --best --strata)
filter reads of 24 and 25 nt
overlap with DMR calculated with BEDTools-IntersectBed (parameter -f 0.5) and normalised by read per million
Genome_build: TAIR10
Supplementary_files_format_and_content: gff files contains the DMR of interest and the number of reads (in read per million) of 24-25 nt overlapping this region (score column). The annotation column contain the name of the arabidopsis gene which include this region.

extract_protocol:
Total RNA were prepared using Trizol (Sigma)
Library construction protocol: According to FASTERIS company


title: Sample_KOWTKO_rep7

value: KOWTKO littermate controls


title: Sample_WT-TKO_rep5


title: Sample_KOWTKO_rep8


title: Spleen Memory Cells immunized mouse 1

description: Flow sorted CD19+CD80+GL7-CD138- cells

value: Lamina Propria


title: Sample_KOWTKO_rep6


title: st567_tossed_16-cell_r9

city: New York

first: Sophia

middle: C

last: Tintori

state: NY

address: 29 Washington Pl - rm 951

institute: New York University

data_processing:
Identical reads were collapsed to one copy using fastx_collapser (FASTX Toolkit 0.0.13.2), using the option -Q33
Reads were aligned to the ce10 genome using Tophat2 (v2.0.11), allowing for 1 splice mismatch, no coverage search and a mate inner distance of 200
Alignments were sorted and indexed using samtools v1.3
Bedgraphs were generated using bedtools genomecov -bg -split -ibam
Read counts were generated using htseq-count (with WBcel235.78.gtf as reference file). These counts were used to generate RPKMs by our own calculations, based on gene length and total number of reads in experiment.
Genome_build: ce10
Supplementary_files_format_and_content: RPKM tables have four colums; gene name, number of reads that mapped to gene locus, gene length, RPKM normalized to gene length and number of reads in transcriptome
Supplementary_files_format_and_content: .bed files have four columns; chromosome number, start position on chromosome, end position, and score (which corresponds to number of reads that aligned to this region of the genome)

organism: Caenorhabditis elegans

source_name: embryonic cell

growth_protocol: N2 worms were grown at 20°C

extract_protocol:
Single cells were simultaneously lysed and flash frozen in liquid nitrogen and stored at -80°C
mRNA libraries were generated using the Clontech SMARTer Ultra Low Input - HV kit and the Nextera XT library preparation kit, according to manufacturers recommendations.

treatment_protocol: Gravid adults were dissected, embryos were treated with bleach, chitinase and chymotripsin to weaken eggshells, cells were dissociated from each other manually by aspiration.

value: tossed

tag: embryo stage


title: st566_tossed_16-cell_r9


title: st568_tossed_16-cell_r9


title: Sample_KOWTKO_rep4


title: st565_tossed_16-cell_r9


title: st563_tossed_16-cell_r9


title: st561_tossed_16-cell_r9


title: st558_tossed_16-cell_r9


title: st562_tossed_16-cell_r9


title: Col

value: WT


title: st564_tossed_16-cell_r9


title: st554_tossed_16-cell_r9


title: st556_tossed_16-cell_r9


title: Sample_KOWTKO_rep1


title: st520_D_16-cell_r8

value: D


title: st519_P4_16-cell_r8


title: st518_Cx2_16-cell_r8


title: Sample_TKO_rep8

value: endoA1A2A3 triple KO (TKO)


title: Sample_TKO_rep9


title: Sample_KOWTKO_rep5


title: st517_MSx2_16-cell_r8


title: st514_Ea_16-cell_r8

value: Ea


title: st515_Cx1_16-cell_r8


title: Sample_KOWTKO_rep3


title: Sample_TKO_rep6


title: st510_ABplx_16-cell_r8

value: ABplx


title: st509_ABprx_16-cell_r8

value: ABprx


title: Sample_TKO_rep5


title: st508_ABarx_16-cell_r8

value: ABarx


title: Sample_TKO_rep4


title: Sample_KOWTKO_rep2


title: st513_MSx1_16-cell_r8


title: st506_ABarx_16-cell_r8


title: st555_tossed_16-cell_r9


title: st557_tossed_16-cell_r9


title: st505_ABprx_16-cell_r8


title: st507_ABplx_16-cell_r8


title: Sample_TKO_rep3


title: st479_D_16-cell_r7


title: st475_Ea_16-cell_r7


title: Sample_TKO_rep1


title: st474_MSx2_16-cell_r7


title: st516_Ep_16-cell_r8

value: Ep


title: Sample_TKO_rep2


title: Sample_WT-DKO_rep9


title: st477_Cx2_16-cell_r7


title: st472_ABprx_16-cell_r7


title: st473_Ep_16-cell_r7


title: Sample_WT-DKO_rep10


title: st471_ABplx_16-cell_r7


title: Sample_WT-DKO_rep8


title: Sample_WT-DKO_rep7


title: st468_ABplx_16-cell_r7


title: st469_ABalx_16-cell_r7

value: ABalx


title: st478_P4_16-cell_r7


title: Sample_WT-DKO_rep5


title: st467_ABalx_16-cell_r7


title: st476_MSx1_16-cell_r7


title: st466_ABarx_16-cell_r7


title: st541_ABplx_16-cell_r6


title: st542_ABplx_16-cell_r6


title: st540_ABprx_16-cell_r6


title: st539_ABalx_16-cell_r6


title: st538_ABarx_16-cell_r6


title: Sample_WT-DKO_rep2


title: Sample_WT-DKO_rep4


title: st536_ABalx_16-cell_r6


title: st537_ABprx_16-cell_r6


title: st535_ABarx_16-cell_r6


title: Sample_WT-DKO_rep1


title: st470_ABarx_16-cell_r7


title: Sample_KOWT_rep7

value: KOWT littermate controls


title: st532_P4_16-cell_r6


title: st530_Cx2_16-cell_r6


title: st531_Cx1_16-cell_r6


title: st465_ABprx_16-cell_r7


title: st533_D_16-cell_r6


title: st529_MSx1_16-cell_r6


title: st528_MSx2_16-cell_r6


title: Sample_KOWT_rep6


title: Sample_KOWT_rep5


title: st527_Ep_16-cell_r6


title: st440_tossed_16-cell_r5


title: Sample_KOWT_rep4


title: st438_tossed_16-cell_r5


title: st439_tossed_16-cell_r5


title: Sample_KOWT_rep3


title: Sample_WT-DKO_rep3

value: wild type controls


title: st436_tossed_16-cell_r5


title: st437_tossed_16-cell_r5


title: Sample_KOWT_rep1


title: Sample_KOWT_rep2


title: st432_tossed_16-cell_r5


title: st435_tossed_16-cell_r5


title: Sample_WT-DKO_rep6


title: st433_tossed_16-cell_r5


title: Sample_DKO_rep7

value: endoA1A2 double KO (DKO)


title: st431_tossed_16-cell_r5


title: st429_tossed_16-cell_r5


title: st434_tossed_16-cell_r5


title: Sample_DKO_rep6


title: st426_tossed_16-cell_r5


title: Sample_DKO_rep5


title: st428_tossed_16-cell_r5


title: Sample_DKO_rep4


title: st430_tossed_16-cell_r5


title: st392_tossed_16-cell_r4


title: st389_tossed_16-cell_r4


title: st425_tossed_16-cell_r5


title: st387_tossed_16-cell_r4


title: Sample_DKO_rep3


title: Sample_DKO_rep2


title: st427_tossed_16-cell_r5


title: st391_tossed_16-cell_r4


title: Sample_DKO_rep1

tag: age:


title: st388_tossed_16-cell_r4


title: st390_tossed_16-cell_r4


title: st382_tossed_16-cell_r4


title: st383_tossed_16-cell_r4


title: Sample_5_RNASeq

city: Lübeck

first: Hauke

last: Busch

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Lübeck Institute of Experimental Dermatology

institute: University of Lübeck

description: primary TICs

data_processing:
Raw sequence reads were first subjected to trimming using Trimmomatic (version 0.32), where adapter sequences and low quality bases were removed (parameters: HEADCROP 3, TRAILING 20, MINLEN 35).
Afterwards reads were aligned to the GRCm38 mouse genome using the STAR alignment algorithm (version 2.4.0) (parameters: --runThreadN 4).
Alignment post-processing included the creation of bam-files, sorting of reads and the removal on non-uniquely mapped reads from further analysis and was carried out using samtools (version 1.1).
Read-counts per gene were calculated with HTSeq.
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited text files include read count values for each Sample.

source_name: Mammary tumor

extract_protocol:
Primary sorted breast cancer cells were collected via FACS sorting and RNA was isolated using the RNA Nanoprep kit (Agilent Technologies). RNA quality was assessed using the Agilent Bioanalyzer 2100. 120ng of total RNA per sample was used for the construction of the sequencing libraries
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Breast

value: breast cancer cell


title: st385_tossed_16-cell_r4


title: st386_tossed_16-cell_r4


title: st380_tossed_16-cell_r4


title: st378_tossed_16-cell_r4


title: Sample_4_RNASeq

description: primary TICs


title: Sample_3_RNASeq

description: primary cells


title: st360_P4_16-cell_r3


title: st377_tossed_16-cell_r4


title: Sample_2_RNASeq

description: primary cells


title: st359_D_16-cell_r3


title: st358_Cx2_16-cell_r3


title: st357_Cx1_16-cell_r3


title: st356_Ea_16-cell_r3


title: st352_ABprx_16-cell_r3


title: st354_MSx2_16-cell_r3


title: st353_MSx2_16-cell_r3


title: st351_ABalx_16-cell_r3


title: st379_tossed_16-cell_r4


title: st381_tossed_16-cell_r4


title: st350_ABprx_16-cell_r3


title: st349_ABplx_16-cell_r3


title: st348_ABarx_16-cell_r3


title: Sample_6_RNASeq

description: primary TICs


title: st346_ABarx_16-cell_r3


title: st347_ABplx_16-cell_r3


title: st328_P4_16-cell_r2


title: st327_D_16-cell_r2


title: 11Oct25_FMC

city: St Louis

first: Winnie

last: Pong

address: 660 S. Euclid Avenue

department: Department of Neurology

institute: Washington University School of Medicine

description: FMC biological replicate 1

data_processing:
Basecalls performed using Illumina Real-Time Analysis (RTA) version 1.13.48.0 (1.13.56.0 for MiSeq) followed by demultiplexing of the index sequence using CASAVA 1.8.2.
SPIA adapter sequence aligned and trimmed from raw sequence reads using FAR 2.17 with command line parameters : --adapter CTTTGTGTTTGA --trim-end left --adaptive-overlap yes --format fastq --write-lengthdist yes --nr-threads 4 --min-overlap 7 --max-uncalled 150 --min-readlength 25
Aligned with TopHat 2.0.4, Bowtie 2.0.0-beta7 and Ensembl 67 annotation (-G param)
FPKM calculated per sample with Cufflinks 2.0.2  and Ensembl 67 annotation with -G param
Genome_build: mm9
Supplementary_files_format_and_content: FMC-FM_gene_fpkm.tsv a tab delimited file with columns for gene ID and the normalized expression values per sample name

source_name: microglia

growth_protocol: not applicable

extract_protocol:
Total RNA was isolated from snap-frozen flow sorted cell pellets using TRIzol-chloroform extraction. RNA was resuspended in 10µl Ambion Nuclease-free water (Life Technologies) and DNAse treated (Ambion TURBO DNA-free Kit)
For cDNA synthesis, we added 5µl of isolated RNA into the Ovation® RNA-Seq method.  500ng cDNA was fragmented using covaris shearing and processed for Illumina library construction with the Illumina paired-end LT indexing protocol as previously published (Mardis et al., 2009; Govindan et al., 2012). Each library was sequenced on the Illumina HiSeq, generating between 15-22Mbp per lane.
RNA-Seq (300-500bp size fractionation): cDNA samples were constructed into Illumina libraries according to the manufacturer’s protocol (Illumina Inc, San Diego, CA) with the following modifications:  1) DNA was fragmented using Covaris S2 DNA Sonicitor using the following condtions: Duty Cycle: 5, Intensity: 4, Cycles/Burst: 200, Time: 90sec (Covaris, Inc. Woburn, MA).  Fragment sizes ranged between 100 and 500bp.  2) Illumina adapter-ligated DNA was amplified in a single 50ml PCR for five cycles.  3) Solid Phase Reversible Immobilization (SPRI) bead cleanup was used to purify the PCR and select for 300-500bp fragments.   We added 0.8 volumes of the AmpureXP solution (preformulated with polyethylene glycol and sodium chloride) to size select DNA molecules greater than 300 bp.  The size-fractioned cDNA was washed three times with 750 µl of 70% ethanol, the beads were dried, and the cDNA library was eluted off the beads by adding 20µl 10 mM Tris-HCl (pH 8.0).  The size-fractioned libraries were assayed using the Agilent BioAnalyzer High Sensitivity DNA chips.

treatment_protocol: Tissue was dissociated, enriched by Percoll gradient, and cells were flow sorted.

value: optic nerve

value: 3 months

tag: gender

value: F

value: Nf1 flox/mut; GFAP-Cre


title: 11Nov10_FM

description: FM biological replicate 1

value: M

value: Nf1 flox/mut


title: 11Nov30_FMC

description: FMC biological replicate 3


title: 11Dec01_FM

description: FM biological replicate 2


title: st355_Ep_16-cell_r3

tag: genotype


title: st324_MSx2_16-cell_r2


title: Sample_1_RNASeq

description: primary cells

tag: tissue


title: 11Nov11_FMC

description: FMC biological replicate 2


title: st321_Cx2_16-cell_r2


title: st322_Cx1_16-cell_r2


title: st320_ABarx_16-cell_r2


title: st317_ABplx_16-cell_r2


title: st319_ABalx_16-cell_r2


title: st315_tossed_16-cell_r2

value: tossed


title: st318_ABprx_16-cell_r2


title: st345_ABalx_16-cell_r3


title: st314_ABalx_16-cell_r2


title: st261_Ep_16-cell_r1


title: st316_ABarx_16-cell_r2


title: st262_Cx1_16-cell_r1


title: st260_Ea_16-cell_r1

value: Ea


title: st313_ABprx_16-cell_r2

value: ABprx


title: st263_P4_16-cell_r1


title: st323_MSx1_16-cell_r2


title: st325_Ep_16-cell_r2


title: st259_Cx2_16-cell_r1


title: st258_MSx2_16-cell_r1


title: st254_ABarx_16-cell_r1

value: ABarx


title: st257_MSx1_16-cell_r1


title: st250_ABprx_16-cell_r1


title: st256_ABalx_16-cell_r1


title: st255_ABalx_16-cell_r1


title: st253_ABarx_16-cell_r1


title: st252_ABplx_16-cell_r1

value: ABplx


title: st251_ABprx_16-cell_r1


title: st487_C_8-cell_r6

value: C


title: st264_D_16-cell_r1

value: D


title: st486_E_8-cell_r6

value: E


title: st485_MS_8-cell_r6

value: MS


title: st483_ABpl_8-cell_r6

value: ABpl


title: 11Dec09_FMC

description: FMC biological replicate 4


title: st424_tossed_8-cell_r5


title: st481_ABpr_8-cell_r6

value: ABpr


title: st423_tossed_8-cell_r5


title: st482_ABar_8-cell_r6

value: ABar


title: st422_tossed_8-cell_r5


title: st484_ABal_8-cell_r6

value: ABal


title: st420_tossed_8-cell_r5


title: st419_tossed_8-cell_r5


title: Sample_TKO_rep7

value: endoA1A2A3 triple KO (TKO)


title: st417_tossed_8-cell_r5


title: st488_P3_8-cell_r6


title: st249_ABplx_16-cell_r1


title: st400_P3_8-cell_r4


title: st418_tossed_8-cell_r5


title: st399_MS_8-cell_r4


title: st398_E_8-cell_r4


title: st396_ABal_8-cell_r4


title: st397_C_8-cell_r4


title: st394_ABpl_8-cell_r4


title: st375_E_8-cell_r3


title: st376_P3_8-cell_r3


title: st393_ABar_8-cell_r4


title: st374_MS_8-cell_r3


title: st373_C_8-cell_r3


title: st372_ABar_8-cell_r3


title: st421_tossed_8-cell_r5


title: st371_ABpl_8-cell_r3


title: st369_ABpr_8-cell_r3


title: st342_MS_8-cell_r2


title: st339_ABpr_8-cell_r2


title: st343_E_8-cell_r2


title: st340_ABpl_8-cell_r2


title: Control #4 Placenta

description: Bos indicus X Bos taurus F1 hybrid

data_processing:
Base calling was perfomed using version 1.8 of the CASAVA package from Illumina
Adator sequences of the reads were removed with the use of FastqMcf program (version 1.04.636). Low quality reads were filtered out using DynamicTrim (version 3.3.1)
DNAseq read pairs were aligned to the bovine reference genome assembly UMD3.1 using Bowtie2 (version 2.2.3)
Genome Analysis Tool Kit (version 3.3-0) and SAMtools mpileup (version 0.1.19) were used for SNP calling from the uniquely aligned DNAseq reads
A pseudo Bos indicus genome was generated by editing the reference allele (UMD3.1; i.e. Bos taurus) with the SNPs identified in the Bos indicus sire. A diploid genome was generated by combining the Bos taurus and the pseudo Bos indicus FASTA files.
RNAseq reads of the Bos indicus X Bos taurus F1 conceptuses were aligned to the diploid genome using HISAT2 (version: 2.0.0) and BWA mem (version:0.7.7)
Cufflinks (version: 2.2.1) and Cuffmerge (version: 2.2.1) were used to assemble transcripts from the uniquely aligned RNAseq reads
RNAseq read counts for each gene model were generated using Htseq-count (version: 0.5.4) and read counts were normalized using edgeR (version: 3.8.6)
SNPiR pipeline (Piskol et al., 2013) was adapted to identify SNPs in RNAseq data.  The parental-allele-origin of the RNA variants were assigned accoding to the Bos indicus sire DNAseq reads
Allele-specific read counts for SNPs in the same gene were aggregated for allele-specific expression analyes.
Genome_build: UMD3.1
Supplementary_files_format_and_content: The SNPs of the Bos indicus sire used to assgin allele-origin of the RNAseq reads from the Bos indicus X Bos taurus F1 hybrids, allele-sepcific read counts of the monoallelically expressed genes identified in this study

organism: Bos indicus x Bos taurus

source_name: Placenta of day ~105 conceptus

value: placenta

tag: developmental stage

value: four day ~105 conceptus


title: st341_C_8-cell_r2


title: st338_ABar_8-cell_r2


title: Control #2 Placenta

description: Bos indicus X Bos taurus F1 hybrid


title: st395_ABpr_8-cell_r4


title: Control #3 Placenta

description: Bos indicus X Bos taurus F1 hybrid


title: Control #1 Placenta

description: Bos indicus X Bos taurus F1 hybrid


title: st337_ABal_8-cell_r2


title: ddb2-3_smallRNA

value: 10 old days in vitro grown seedling

value: ddb2-3 (DsLoxHs195_05H)

value: seedling


title: st230_C_8-cell_r1


title: st231_E_8-cell_r1


title: st232_P3_8-cell_r1


title: Col_smallRNA

description: Col

value: WT


title: st229_MS_8-cell_r1


title: RNA-sequencing of murine HSC, Huwe1 KO (Vav-Cre), replicate 1

first: Bryan

last: King

department: Cancer Biology and Genetics

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Fastq files were aligned to mm9 using TopHat allowing 2 mismatches
Aligned features were sorted with samtools
Gene features were counted with htseq-count
Differential expression was determined using the ‘edgeR’ package in Bioconductor
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited .txt file of raw and normalized counts

source_name: murine bone marrow-derived hematopoietic stem cells

growth_protocol: cells were collected from bone marrow without culturing them in vitro

extract_protocol:
Cells were extracted from the bone marrow of the mice, sorted for Lin-Sca+Kit+CD48-CD150+ and directly collected into Trizol reagent (Life Technologies) for RNA extraction.
RNA libraries were prepared for sequencing using SMARTer Ultra Low Input RNA kit from Clonetech. End repair, A-tailing and Illumina adaptor ligation reactions were carried out using a NEBNext Library Prep Kit by New England BioLabs. Unstranded protocol

treatment_protocol: no treatment

value: murine bone marrow hematopoietic stem cells

value: Huwe1 KO (Vav-Cre)


title: st227_ABar_8-cell_r1


title: RNA-sequencing of murine HSC, Huwe1 KO (Mx1-Cre), replicate 2

value: Huwe1 KO (Mx1-Cre)


title: st344_P3_8-cell_r2


title: Brachypodium distachyon methylC-seq

city: Athens

first: Adam

middle: James

last: Bewick

state: GA

address: 120 East Green Street

department: Genetics

institute: University of Georgia

data_processing:
MethylC-seq analysis were performed as described in Schultz et al. (2015). Human body epigenome maps reveal noncanonical DNA methylation variation. Nature 523:212–216.
Genome_build: JGI v2.0 (B. distachyon); Brassica database v1.0 (B. oleracea); JGI v2.0 (M. guttatus); JGI v3.0 (P. trichocarpa); JGI v2.0 (S. bicolor)
Supplementary_files_format_and_content: Tab delimited text file, column headers
Supplementary_files_format_and_content: Column1: chromosome
Supplementary_files_format_and_content: Column2: cytosine position
Supplementary_files_format_and_content: Column3: strand
Supplementary_files_format_and_content: Column4: CNN (N = A, T, C, G)
Supplementary_files_format_and_content: Column5: methylated cytosines at this site
Supplementary_files_format_and_content: Column6: total detected cytosines at this site

organism: Brachypodium distachyon

source_name: Brachypodium distachyon methylC-seq

extract_protocol: Genomic DNA (gDNA) was purified from 0.5 g of leaves by using DNeasy Plant MiniKit (Qiagen, Valencia, CA), according to the manufacturer’s instructions. MethylC-Seq libraries were constructed according to Urich MA, Nery JR, Lister R, Schmitz RJ, Ecker JR. (2015) MethylC-seq: Base resolution whole genome bisulfite sequencing library preparation. Nature Protocols Feb(10):475–483

value: leaf

value: wild-type


title: st225_ABpl_8-cell_r1


title: st408_P2_4-cell_r5


title: RNA-sequencing of murine HSC, Huwe1 WT, replicate 3

value: wild type


title: RNA-sequencing of murine HSC, Huwe1 WT, replicate 2


title: RNA-sequencing of murine HSC, Huwe1 KO (Vav-Cre), replicate 2


title: st405_ABp_4-cell_r5

value: ABp


title: st407_ABa_4-cell_r5

value: ABa


title: st370_ABal_8-cell_r3


title: st406_EMS_4-cell_r5

value: EMS


title: st366_P2_4-cell_r4


title: RNA-sequencing of murine HSC, Huwe1 WT, replicate 1


title: st364_EMS_4-cell_r4


title: st363_ABa_4-cell_r4


title: EO6_MC3545

city: Cambridge

first: Silvia

last: Buonamici

state: MA

address: 300 Technology Square #5

institute: H3 Biomedicine

data_processing:
Raw data were aligned to hg19 using the STAR alignment package
Unique junction counts as determined by STAR are output to a tabular file
Genome_build: hg19 for human samples, mm10 for mouse
Supplementary_files_format_and_content: Raw junction counts for each sample as output by STAR

extract_protocol:
RNA was extracted using the PrepEase RNA Spin Kit
Human RNA libraries were prepared for sequencing using TrueSeq, while mouse RNA libraries were prepared using the NEBNext Ultra Library Preparation Kit

value: Bone Marrow

tag: mutation

tag: cell population

value: Myeloid progenitors

tag: library prep

value: NEBNext Ultra Library Prep Kit


title: EO1_MC3493


title: EO4_MC3552


title: EO3_MC3551


title: EO5_MC3553


title: st365_ABp_4-cell_r4


title: st336_P2_4-cell_r3


title: EO2_MC3496


title: st334_ABa_4-cell_r3


title: st333_ABp_4-cell_r3


title: st308_P2_4-cell_r2


title: st307_ABp_4-cell_r2


title: MDS_341

value: Total blood

value: TrueSeq


title: RNA-sequencing of murine HSC, Huwe1 KO (Mx1-Cre), replicate 1


title: st305_EMS_4-cell_r2


title: MDS_334


title: st306_ABa_4-cell_r2


title: MDS_260


title: MDS_292


title: st196_P2_4-cell_r1


title: MDS_228


title: st194_ABa_4-cell_r1


title: st193_EMS_4-cell_r1


title: st410_P1_2-cell_r5


title: st409_AB_2-cell_r5

value: AB


title: st335_EMS_4-cell_r3


title: MDS_361


title: MDS_314


title: st362_P1_2-cell_r4


title: MDS_328


title: Control_diet_germ_cell_smallRNA_rep4

first: Michael

last: Morgan

state: Oxfordshire

address: South Parks Road

department: Department of Physiology, Anatomy and Genetics

institute: University of Oxford

data_processing:
RNAseq reads were aligned to rn5 using Star v2.3.0, with a custom splice junction database constructed from Ensembl v73 protein-coding gene models (--outFilterMismatchNoverLmax 0.05)
smallRNAseq reads were trimmed with trimmomatic to remove adaptor contamination to a minimum length of 22 nucleotides(MINLEN:22)
Trimmed smallRNAseq reads were iteratively aligned to rn5 using Butter (perl wrapper for bowtie designed to iteratively map small RNA seq reads to maximize read assignment to the genome).
Reads were counted over ensembl v73 protein-coding gene models (collapsed models where multiple transcripts exist) and repBase repeats for aligned RNAseq data using featureCounts. Aligned smallRNA seq data were counted over miRBase, piRNAQuest annotations using featureCounts
Genome_build: rn5
Supplementary_files_format_and_content: .tsv.gz files contain integer read counts over genome annotations from featureCounts; tab delimited.
Each file contains 7 columns, with rows representing a single aggregated feature. For instance, an aggregate feature may be all of the exons of a gene, or transcribed repeat elements of the same class/type that are indistinguishable at multiple locations.
The columns (in order) are:
* Geneid - annotation ID for the aggregated features
* Chr - ";" separated list of genome contigs for all component features
* Start - ";" separated list of contig start positions for all component features
* End - ";" separated list of contig end positions for all component features
* Strand - ";" separated list of strand annotation for all component features
* Length - total genomic length of aggregated features
* <samplefilename> - number of read counts over aggregated features
For more details on the featureCounts software see the user guide:
http://bioinf.wehi.edu.au/subread-package/SubreadUsersGuide.pdf

organism: Rattus norvegicus

source_name: Control diet, germ cell

extract_protocol:
smallRNA libraries were assembled using the Truseq small RNA kit (Illumima) according to the maunfacturers instructions. smallRNAs of 22-10nt in length were selected for sequencing.
6x10e6 sorted cells were then centrifuged and RNA immediately extracted using the Qiagen miRNAeasy mini kit (Qiagen, UK) according to the manufacturer’s instructions. Quality and purity of the extracted total RNA was verified using spectrophotometry and the Agilent RNA 6000 nano kit according to manufacturer’s instructions

treatment_protocol: Rats were fed from weaning on control diet (10% calories from fat) (D06072701, Research diets) or high fat diet (40% calories from fat) (D06071701, Research Diets) until 19 weeks of age. Testes were decapsulated and minced with scalpels in 5 ml ice cold Hanks Buffered Saline Solution with calcium and magnesium and supplemented with 0.1% Collagenase IV (Sigma, UK). The suspension was mechanically dissociated by pipetting before incubation at 37°C with gentle rotation for 10 minutes. The suspension was then passed through a 40µm cell strainer (Becton Dickinson and Company, UK) which was further washed with 10 ml of phosphate buffered saline (PBS) supplemented with 2% FCS (Invitrogen, UK). The cells were washed by centrifugation at 500xg for 5 mins and resuspended in 10ml 2% FCS three times. Samples were kept on ice until FACS on a BD Aria II, gating for expression of eGFP.

value: germ cell

tag: strain

value: Sprague-Dawley

value: male

tag: diet

value: control diet


title: Control_diet_germ_cell_smallRNA_rep3

tag: cell type


title: MDS_253


title: st228_ABpr_8-cell_r1

value: ABpr

tag: replicate


title: High_fat_diet_germ_cell_smallRNA_rep4

source_name: High fat diet, germ cell

value: High fat diet


title: Control_diet_germ_cell_smallRNA_rep2


title: st195_ABp_4-cell_r1


title: High_fat_diet_germ_cell_smallRNA_rep3


title: st361_AB_2-cell_r4


title: st226_ABal_8-cell_r1

value: ABal


title: st302_P1_2-cell_r2


title: High_fat_diet_germ_cell_smallRNA_rep2


title: High_fat_diet_germ_cell_smallRNA_rep1


title: Control_diet_germ_cell_mRNA_rep4

extract_protocol:
assembled using the Truseq RNA sample prep kit v2 (Illumina) according to the manufactureres instructions.
6x10e6 sorted cells were then centrifuged and RNA immediately extracted using the Qiagen miRNAeasy mini kit (Qiagen, UK) according to the manufacturer’s instructions. Quality and purity of the extracted total RNA was verified using spectrophotometry and the Agilent RNA 6000 nano kit according to manufacturer’s instructions


title: st451_P0_1-cell_r6


title: st311_AB_2-cell_r3


title: st312_P1_2-cell_r3


title: Populus trichocarpa methylC-seq

organism: Populus trichocarpa

source_name: Populus trichocarpa methylC-seq

value: leaf

value: wild-type


title: st301_AB_2-cell_r2


title: Control_diet_germ_cell_smallRNA_rep1


title: Control_diet_germ_cell_mRNA_rep2


title: High_fat_diet_germ_cell_mRNA_rep1


title: High_fat_diet_germ_cell_mRNA_rep2


title: Ric_SG_hv_2

status: Public on Aug 16 2016

city: St. Louis

first: Blake

middle: C.

last: Meyers

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

data_processing:
For data processing, the adapter sequences were trimmed from raw sequence reads. The small RNA sequences were further trimmed to the lengths between 18 and 34 nucleotides.
For read alignment to the reference genome, we typically use Bowtie and only consider perfect matches. No matching data were included with these files.
The abundance measurements are raw counts; to normalize, we typically divide the raw count for a given read by the sum of abundances for all reads, and multiple this by an arbitrary round number (million, five million, ten million, etc)
Genome_build: Reads were mapped to the reference Vitis vinifera L. genomic sequence V1 (PN40024 clone)
Supplementary_files_format_and_content: tag count (sequence plus abundance).

organism: Vitis vinifera

source_name: Sangiovese berries at harvest grown in Riccione vineyard, replicate 2

growth_protocol: Grapevine plants (age between 10 and 12 years old) were grown side by side in open fields. The clone type (Sangiovese clone R5 and Cabernet Sauvignon clone VCR23), the rootstock (Vitis  berlandieri x Vitis riparia) and the cultivation techniques (training system: low cordon; planting space: 2,40 x 0,8 m) are identical for each environment.

extract_protocol:
Total RNA was isolated from 200 mg of berries (pulp and skin, without seeds) using Plant RNA Isolation Reagent ( Life Technologies) following manufacturer’s recommendations. The small RNA fraction was isolated from the total RNA using the mirPremier® microRNA Isolation kit (Sigma-Aldrich)
Small RNA libraries were prepared according to Illumina's instructions accompanying the TruSeq Small RNA Sample Prep Kit

value: harvest grapevine berries

value: Sangiovese

tag: environment

value: Riccione vineyard

tag: library

value: small RNA


title: Sorghum bicolor methylC-seq

organism: Sorghum bicolor

source_name: Sorghum bicolor methylC-seq


title: st266_P1_2-cell_r1


title: Control_diet_germ_cell_mRNA_rep3


title: st411_P0_1-cell_r1


title: Mimulus guttatus methylC-seq

organism: Erythranthe guttata

source_name: Mimulus guttatus methylC-seq


title: st265_AB_2-cell_r1


title: Ric_SG_19_2

source_name: Sangiovese 19° Brix berries grown in Riccione vineyard, replicate 2

value: 19° Brix grapevine berries


title: Ric_SG_19_1

source_name: Sangiovese 19° Brix berries grown in Riccione vineyard, replicate 1


title: Control_diet_germ_cell_mRNA_rep1


title: High_fat_diet_germ_cell_mRNA_rep3


title: st449_P0_1-cell_r5


title: st441_P0_1-cell_r4


title: High_fat_diet_germ_cell_mRNA_rep4


title: Ric_SG_ps_2

source_name: Sangiovese pea-size berries grown in Riccione vineyard, replicate 2

value: pea-size grapevine berries


title: st413_P0_1-cell_r2


title: Ric_CS_hv_2

source_name: Cabernet Sauvignon berries at harvest grown in Riccione vineyard, replicate 2

value: Cabernet Sauvignon


title: Ric_SG_hv_1

source_name: Sangiovese berries at harvest grown in Riccione vineyard, replicate 1


title: Brassica oleracea methylC-seq

organism: Brassica oleracea

source_name: Brassica oleracea methylC-seq


title: Ric_CS_19_1

source_name: Cabernet Sauvignon 19° Brix berries grown in Riccione vineyard, replicate 1


title: Ric_CS_19_2

source_name: Cabernet Sauvignon 19° Brix berries grown in Riccione vineyard, replicate 2


title: Ric_SG_bc_1

source_name: Sangiovese bunch-closure berries grown in Riccione vineyard, replicate 1

value: bunch-closure grapevine berries


title: Ric_CS_bc_2

source_name: Cabernet Sauvignon bunch-closure berries grown in Riccione vineyard, replicate 2


title: Ric_SG_bc_2

source_name: Sangiovese bunch-closure berries grown in Riccione vineyard, replicate 2


title: st415_tossed_1-cell_r3

source_name: embryonic cell

value: tossed


title: Ric_CS_ps_2

source_name: Cabernet Sauvignon pea-size berries grown in Riccione vineyard, replicate 2


title: Bolg_SG_hv_1

source_name: Sangiovese berries at harvest grown in Bolgheri vineyard, replicate 1

value: Bolgheri vineyard


title: Bolg_SG_19_1

source_name: Sangiovese 19° Brix berries grown in Bolgheri vineyard, replicate 1


title: Ric_CS_hv_1

source_name: Cabernet Sauvignon berries at harvest grown in Riccione vineyard, replicate 1


title: Ric_CS_ps_1

source_name: Cabernet Sauvignon pea-size berries grown in Riccione vineyard, replicate 1


title: Ric_CS_bc_1

source_name: Cabernet Sauvignon bunch-closure berries grown in Riccione vineyard, replicate 1


title: Bolg_CS_19_2

source_name: Cabernet Sauvignon 19° Brix berries grown in Bolgheri vineyard, replicate 2


title: Bolg_CS_bc_2

source_name: Cabernet Sauvignon bunch-closure berries grown in Bolgheri vineyard, replicate 2


title: Ric_SG_ps_1

source_name: Sangiovese pea-size berries grown in Riccione vineyard, replicate 1


title: Bolg_SG_19_2

source_name: Sangiovese 19° Brix berries grown in Bolgheri vineyard, replicate 2


title: Bolg_CS_bc_1

source_name: Cabernet Sauvignon bunch-closure berries grown in Bolgheri vineyard, replicate 1


title: Mont_SG_hv_2

source_name: Sangiovese berries at harvest grown in Montalcino vineyard, replicate 2

value: Montalcino vineyard


title: Bolg_CS_ps_1

source_name: Cabernet Sauvignon pea-size berries grown in Bolgheri vineyard, replicate 1


title: Mont_SG_hv_1

source_name: Sangiovese berries at harvest grown in Montalcino vineyard, replicate 1


title: Bolg_SG_bc_2

source_name: Sangiovese bunch-closure berries grown in Bolgheri vineyard, replicate 2


title: Bolg_SG_ps_2

source_name: Sangiovese pea-size berries grown in Bolgheri vineyard, replicate 2


title: Bolg_SG_ps_1

source_name: Sangiovese pea-size berries grown in Bolgheri vineyard, replicate 1


title: Bolg_CS_19_1

source_name: Cabernet Sauvignon 19° Brix berries grown in Bolgheri vineyard, replicate 1


title: Mont_SG_ps_2

source_name: Sangiovese pea-size berries grown in Montalcino vineyard, replicate 2


title: Mont_SG_bc_2

source_name: Sangiovese bunch-closure berries grown in Montalcino vineyard, replicate 2


title: Mont_SG_19_2

source_name: Sangiovese 19° Brix berries grown in Montalcino vineyard, replicate 2


title: Bolg_CS_hv_2

source_name: Cabernet Sauvignon berries at harvest grown in Bolgheri vineyard, replicate 2


title: Bolg_CS_ps_2

source_name: Cabernet Sauvignon pea-size berries grown in Bolgheri vineyard, replicate 2


title: Bolg_CS_hv_1

source_name: Cabernet Sauvignon berries at harvest grown in Bolgheri vineyard, replicate 1


title: Bolg_SG_hv_2

source_name: Sangiovese berries at harvest grown in Bolgheri vineyard, replicate 2


title: Mont_CS_hv_2

source_name: Cabernet Sauvignon berries at harvest grown in Montalcino vineyard, replicate 2


title: Mont_SG_19_1

source_name: Sangiovese 19° Brix berries grown in Montalcino vineyard, replicate 1


title: Mont_CS_19_1

source_name: Cabernet Sauvignon 19° Brix berries grown in Montalcino vineyard, replicate 1


title: Mont_CS_bc_2

source_name: Cabernet Sauvignon bunch-closure berries grown in Montalcino vineyard, replicate 2


title: Bolg_SG_bc_1

source_name: Sangiovese bunch-closure berries grown in Bolgheri vineyard, replicate 1


title: Mont_CS_bc_1

source_name: Cabernet Sauvignon bunch-closure berries grown in Montalcino vineyard, replicate 1


title: Mont_SG_bc_1

source_name: Sangiovese bunch-closure berries grown in Montalcino vineyard, replicate 1


title: Mont_SG_ps_1

source_name: Sangiovese pea-size berries grown in Montalcino vineyard, replicate 1


title: Mont_CS_hv_1

source_name: Cabernet Sauvignon berries at harvest grown in Montalcino vineyard, replicate 1


title: Mont_CS_19_2

source_name: Cabernet Sauvignon 19° Brix berries grown in Montalcino vineyard, replicate 2


title: Nucleus from Hippocampus brain region VGAT-A2-P2-DG_S186_L001_R1

first: Naomi

last: Habib

address: 75 Ames st

department: Zhang

institute: Broad Institute

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
VGAT-A2-P2-DG_S186_L001_R1_001

data_processing:
sNUc-Seq libraries were aligned using Bowtie2 to the mouse transcriptome (RefSeq mm10 and Ensemble GRCm38 merged using Cufflink). RSEM v1.27 was used to estimate gene expression, in transcript per million (TPM) values, and TPM estimates were transformed to log-space by taking log(TPM+1).  A library was filtered out if it had less than 2,000 detected genes or more than 8,000 detected genes. All libraries were normalized using a normalization procedure based on Bland-Altman (MA) plot and density estimation. For a pair of cells, we normalize one cell with respect to another so that genes are not differentially expressed on average, but using only a small set of highly expressed and lowly variable genes, which provides robustness against typical noise in single cells RNA-seq data.
Genome_build: RefSeq mm10 and Ensembl GRCm38
Supplementary_files_format_and_content: tab delimited matrix with RSEM computed log(TPM+1) values after normalization

molecule: nuclear RNA

source_name: Mouse Hippocampus region

extract_protocol:
nuclei isolation by gradient centrifugation and FACS sorting
SMART-Seq2 protocol, with MAXIMA -h RT enzyme, applied on single nuclei sorted by FACS

tag: age

value: 12 weeks

value: vGAT-Cre, Slc32a1tm2(cre)Lowl


title: Nucleus from Hippocampus brain region VGAT-A2-P2-DG_S174_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
VGAT-A2-P2-DG_S174_L001_R1_001


title: Mont_CS_ps_2

source_name: Cabernet Sauvignon pea-size berries grown in Montalcino vineyard, replicate 2


title: Nucleus from Hippocampus brain region VGAT-A2-P2-DG_S173_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
VGAT-A2-P2-DG_S173_L001_R1_001


title: Nucleus from Hippocampus brain region VGAT-A2-P2-DG_S179_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
VGAT-A2-P2-DG_S179_L001_R1_001


title: Nucleus from Hippocampus brain region VGAT-A2-P2-DG_S185_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
VGAT-A2-P2-DG_S185_L001_R1_001


title: Mont_CS_ps_1

source_name: Cabernet Sauvignon pea-size berries grown in Montalcino vineyard, replicate 1


title: Nucleus from Hippocampus brain region VGAT-A2-P2-DG_S178_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
VGAT-A2-P2-DG_S178_L001_R1_001


title: Nucleus from Hippocampus brain region VGAT-A2-P2-DG_S172_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
VGAT-A2-P2-DG_S172_L001_R1_001


title: Nucleus from Hippocampus brain region VGAT-A2-P2-DG_S171_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
VGAT-A2-P2-DG_S171_L001_R1_001


title: Nucleus from Hippocampus brain region VGAT-A2-P2-DG_S177_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
VGAT-A2-P2-DG_S177_L001_R1_001


title: Nucleus from Hippocampus brain region VGAT-A2-P2-DG_S175_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
VGAT-A2-P2-DG_S175_L001_R1_001


title: Nucleus from Hippocampus brain region VGAT-A2-P2-DG_S164_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
VGAT-A2-P2-DG_S164_L001_R1_001


title: Nucleus from Hippocampus brain region VGAT-A2-P2-DG_S163_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
VGAT-A2-P2-DG_S163_L001_R1_001


title: Nucleus from Hippocampus brain region VGAT-A2-P2-DG_S165_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
VGAT-A2-P2-DG_S165_L001_R1_001


title: Nucleus from Hippocampus brain region VGAT-A2-P2-DG_S160_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
VGAT-A2-P2-DG_S160_L001_R1_001


title: Nucleus from Hippocampus brain region VGAT-A2-P2-DG_S170_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
VGAT-A2-P2-DG_S170_L001_R1_001


title: Nucleus from Hippocampus brain region VGAT-A2-P2-DG_S169_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
VGAT-A2-P2-DG_S169_L001_R1_001


title: Nucleus from Hippocampus brain region VGAT-A2-P2-DG_S161_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
VGAT-A2-P2-DG_S161_L001_R1_001


title: Nucleus from Hippocampus brain region VGAT-A2-P2-DG_S162_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
VGAT-A2-P2-DG_S162_L001_R1_001


title: Nucleus from Hippocampus brain region VGAT-A2-P2-DG_S154_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
VGAT-A2-P2-DG_S154_L001_R1_001


title: Nucleus from Hippocampus brain region VGAT-A2-P2-DG_S155_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
VGAT-A2-P2-DG_S155_L001_R1_001


title: Nucleus from Hippocampus brain region VGAT-A2-P2-DG_S157_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
VGAT-A2-P2-DG_S157_L001_R1_001


title: Nucleus from Hippocampus brain region VGAT-A2-P2-DG_S153_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
VGAT-A2-P2-DG_S153_L001_R1_001