title: MEL6

city: Prague 4

first: Martin

last: Sládek

address: Videnska 1083

country: Czech Republic

institute: Institute of Physiology of the Czech Academy of Sciences

data_processing:
Basecalling by Illumina 1.5
Reads were filtered and mapped to rn6 by BWA v.0.7.10-r789 (genome alignment success rate average 85.7 %, parameters: -o 1 -e 50 -i 50 -L -k 2 -l 31 -t 4 -q 10) and Bowtie2 (gene alignment success rate average 52.1 %, parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200); all samples passed quality control.
Fragments per kb of transcript per million mapped reads (FPKM) were calculated by RSEM (Li and Dewey. BMC bioinformatics 2011). Differentially expressed genes (DEGs) were screened by NOISeq (Tarazona, et al. Genome Research, 2011) and those with log2 fold change ≥ 2 and diverge probability ≥ 0.8 were reported as significantly different between VEH and MEL groups.
Genome_build: rn6
Supplementary_files_format_and_content: tab-delimited text file with FPKM values for each sample, mean FPKM values, mean log2ratios of MEL/VEH, probability of differential expression between MEL and VEH, KEGG and GO for each identified transcript

source_name: MEL, inner epithelial layer, colon

extract_protocol:
Total RNA was isolated using a GenElute Mammalian Total RNA Miniprep kit (Sigma) according to the manufacturer’s instructions. DNAse I digestion (On-Column DNAse I digestion set, Sigma) was performed using a modified manufacturer’s protocol (15 minutes at 37°C on column). RNA concentrations were determined by spectrophotometry at 260 nm using Nanodrop (ThermoFisher). Moreover, the RNA quality was tested by Agilent 2100 Bioanalyzer (Agilent Technologies). RNA integrity number (RIN) range was 9.0-9.7.
Library construction by BGI International; mRNA was enriched by oligo (dT) magnetic beads and fragmented. Then the first strand of cDNA was synthesized by using random hexamer-primer. Buffer, dNTPs, RNase H and DNA polymerase I were added to synthesize the second strand. The double-stranded cDNA was purified with magnetic beads. End reparation, 3’-end single nucleotide A (adenine) addition and sequencing adaptor ligation was then performed. The fragments were enriched by PCR amplification

treatment_protocol: Animals injected i.p. with either melatonin (MEL, 1mg/kg of body weight, n = 3) or vehicle (VEH, 2.5% ethanol in PBS, n = 3) 4 h before sacrifice.

value: Wistar

tag: gender

value: male

tag: tissue

value: colonic epithelium

tag: surgery

value: pineal gland ablation

value: melatonin


title: MEL5

status: Public on Dec 04 2016

type: SRA

library_source: transcriptomic

molecule: total RNA

organism: Rattus norvegicus

tag: strain

tag: treatment


title: EF27

city: Oxford

first: Helio

last: Pais

address: Jonh Radcliffe Hospital

department: Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

data_processing:
Sequences were mapped to the genome using Tophat2 with default parameters
Mapped sequences were assigned to genes with in-house script using GenomicFeatures package in Bioconductor
Gene lengths were obtained from Ensembl (version 73)
RPKM values were calculated with in-house R script
Genome_build: hg19
Supplementary_files_format_and_content: comma separated value file contains gene RPKMs

organism: Homo sapiens

source_name: A673_EWS-FLI1 shRNA

extract_protocol:
RNA was extracted from cells using the mirVana Paris kit (Life Technologies) according to the manufacturer's protocol.
mRNA fraction was selected from total RNA and converted to cDNA. The cDNA was end-repaired, A-tailed and adapter-ligated. Prior to amplification, samples underwent uridine digestion. The prepared libraries were size-selected, multiplexed and subsequently paired end sequenced over two lanes of a flow cell.

tag: cell line

tag: cell type

value: Ewing Sarcoma cells

tag: genotype/variation

value: stably expressing shRNA targeting EWS-FLI1


title: Matched control for LF only rep  2

city: Sydney

first: Chi Nam Ignatius

last: Pang

state: NSW

address: School of Biotechnology and Biomolecular Sciences, UNSW Australia

department: The NSW Systems Biology Initiative

country: Australia

institute: The University of New South Wales

description:
10g
Illumina lane: 3

data_processing:
Counting: The number of reads mapped to each gene is counted using HTSeq (0.5.3p9) using the options “-s no -m union -t CDS -i gene_id”. Reads are mapped to the coding sequence (CDS) irrespective of the strand and reads found in ambiguous overlapping CDS were not counted. The GFF gene co-ordinates file was obtained from the Saccharomyces Genome Database and converted to GTF format using custom Perl scripts.
Genome_build: Saccharomyces cerevisiae S288C genome reference (R64-1-1 build)

organism: Saccharomyces cerevisiae S288C

source_name: Saccharomyces cerevisiae S288C

growth_protocol: The S. cerevisiae S288C strain was used for all RNA-seq analyses. Cells were grown in RPMI-1640 at 30 °C in a shaking incubator at 180 rpm. Amphotericin B (Sigma-Aldrich, Australia) was made to 1,600 µg/mL and bovine lactoferrin (MP Biomedical, Australia) was made to 5,120 µg/mL in sterile MilliQ water.   The cells at an ID20 were used for RNA-Seq analysis. At this point, cells are stressed but the confounding effects of cell death are avoided, allowing a direct comparison of the AMB and the AMB + LF treatment. The ID20 for AMB only treatment was 60 minutes. For the  AMB + LF treatment, the ID20 was close to 50 minutes and the cell counts at 60 minutes has dropped beyond the ID20 point, therefore 50 minutes was chosen as the time point for RNA-seq analyses. The same incubation time of 50 minutes and 60 minutes were applied for the matched control samples for AMB only and AMB + LF treatments, respectively. The LF only experiments were grown for 50 min at the ID20 of AMB + LF experiments to enable a comparable analysis between the treatments.

extract_protocol:
Equal volumes of RNAse zap treated 0.4 μm beads and lyophilised cells were bead beaten in a Minilys tissue homogenizer at 5,000 rpm for 2 min. Cells were cooled on ice at 1 min intervals. Total RNA was then isolated with the Qiagen total RNA mini isolation kit. RNA quality was analysed with a Nanodrop (Thermo Scientific) to ensure an OD260/230 and OD260/280 ratio between 1.8 – 2, and a RNA Quality Indicator (RQI) of at least 8 with a Bioanalyser (Bio-Rad). The concentration was checked using the Qubit BR RNA assay (InVitrogen).
For the AMB only treatment, the AMB+LF treatment and their corresponding matching controls, the TruSeq RNA Library prep kit v2 (Illumina) with a poly-A pulldown was used according to the manufacturer’s instructions, with 2 μg of total RNA for each of the three biological triplicate samples as input. The libraries were enriched using 15 cycles of PCR and the insert size ranged from 80 to 330 base pair (bp). The libraries were randomized and sequenced in two separate lanes using HiSeq 2000 with the TruSeq v3 SBS reagents to generate 100 bp paired-end reads. The data was demultiplexed using Casava 1.8.2.     For the LF only treatment and the corresponding matching controls, the TruSeq Stranded mRNA-seq prep kit was used to prepare the RNA samples as per protocol using 1ug of total RNA for each of the three biological triplicate samples as input. The libraries were enriched using 12 cycles of PCR to minimize the number of PCR duplicates. The libraries were multiplexed and sequenced on the same flow cell using NextSeq500 v2 reagents to generate 75 bp single reads. The data was demultiplexed using Casava 1.8.2.

treatment_protocol: The concentration of AMB used for the AMB only experiment was 0.03 µg/mL, the concentration of LF used for the LF only experiment was 2 µg/mL and the concentration of AMB + LF for the synergy experiment was 0.03 µg/mL and 2 µg/mL, for AMB and LF respectively. No drugs were added for the matched control samples.

value: control

tag: growth time

value: 50 minutes


title: EF11


title: EF26


title: LF only rep 2

description:
10d
Illumina lane: 3

value: lactoferrin (2 µg/mL)


title: VEH3

source_name: VEH, inner epithelial layer, colon

value: vehicle


title: MEL4


title: VEH2


title: ChIP_SRC1_E2

city: Houston

first: kaifu

last: chen

address: 1 Baylor plaza, suite 450A

country: USA

institute: Baylor College of Medicine

library_source: genomic

data_processing: Reads are mapped to genome using ELAND. Reads that are uniquely mapped and have no more than 2 mismatches are selected for future analysis. MACS is used to call peaks with p value 1e-10.

molecule: genomic DNA

source_name: Cell line

extract_protocol: Purified DNA given A overhang by Klenow exo, adapters ligated, gel size selected (300±25bp), PCR amplified and sequenced

value: U2OS-ERalpha (stable)

tag: antibody

value: anti-SRC1 M341

tag: antibody vendor, catalog#

value: Santa Cruz, sc-8995


title: EF08


title: PMG-Cont-1

city: Ansan

first: Young Gyu

last: Chai

state: Gyeonggi-do

address: 55 Hanyangdaehak-ro

department: Molecualr & Life Science

country: South Korea

institute: Hanyang Univ.

data_processing:
Illumina CASAVA v1.8.2 software was used for basecalling.
To avoid low-quality data, we clipped and trimmed the reads using Trimmomatic (v0.33)
For the analysis of differentially expressed genes, the data of quality-checked reads for each condition were processed with the TopHat (version 2.0.10) software based on reference genome sequence (Mus musculus UCSC mm10) and the differential gene expressed values of each sample were calculated by Cufflinks(v2.2.1)
the number of reads mapped to gene ID features were counted using HTSeq v0.6.1.
Genome_build: Mus musculus UCSC mm10
Supplementary_files_format_and_content: tab-delimited text files including normalized read counts for each sample

organism: Mus musculus

source_name: primary microglia cells

growth_protocol: PM were seeded in poly-L-lysine-coated T-75 flask in DMEM/nutrient mixture F-12 (DMEM/F12, 1:1) containing 20% FBS (catalog # 26140), 100 IU/ml penicillin and 10 µg/ml streptomycin (catalog # 15140) from Invitrogen (CA, USA). The cells were maintained in a humidified incubator with a 95% air/5% CO2 atmosphere at 37°C. The medium was changed every 2-3 days. After two weeks in culture, mixed glial cell cultures are shaken at 150 rpm at 37°C for 45 min, and the glial cell suspension was collected from each flask and seeded on poly-L-lysine coated cell culture plate. PM were sub-plated and used for further experiments.

extract_protocol:
RNA was extracted using RNAiso Plus (Takara, Shiga, Japan) and QIAGEN RNeasy® Mini kit (QIAGEN, Hilden, Germany) according to the manufacturer’s protocol. For RNA-Seq, RNA libraries were created from each group using the NEBNext® Ultra™ Directional RNA Library preparation kit from Illumina® (Illumina, San Diego, CA, USA). The first step in the workflow involved the removal of ribosomal RNA using the RNAMius™ Transcriptome Isolation kit (Life Technologies, Carlsbad, CA, USA).  Following purification, total RNA was fragmented into small pieces using divalent cations at elevated temperature. The cleaved RNA fragments were copied into first-strand cDNA using reverse transcriptase and random primers, followed by second-strand cDNA synthesis using DNA polymerase I and RNase H. The cDNA fragments were then processed through an end-repair reaction by the addition of a single ‘A’ base, followed by ligation of the adapters. The products of these reactions were then purified and enriched by PCR to create the final cDNA library. The cDNA fragments were sequenced using the Illumina HiSeq2000 (101 cycles PE lane)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Murine microglial PM, were treated with LPS (10ng/ml) for 4 hrs.

value: primary microglia cells


title: IL17

source_name: A673_control shRNA

value: stably expressing shRNA targeting Luciferase gene


title: LF only rep 1

description:
10b
Illumina lane: 3


title: j11-infected (human rotavirus strain Ito), ME41541

status: Public on Dec 03 2016

first: Lukas

last: Simon

address: 1 Baylor Plaza

department: THINC

description:
rRNA-reduced total RNA
ME41541

data_processing:
Reads were aligned to the human hg19 reference genome using STAR (version 2.3.1) with default parameters.
Read summarization was performed using the featureCounts function of the Subread package and the ENSEMBL gene annotation gtf file with genome-build-accession identifier NCBI:GCA_000001405.14.
Genes with less than 1 read per 10 million sequenced reads in 2 or more samples were excluded from subsequent analysis.
Samples were normalized for sequencing depth using the function estimateSizeFactors from the DESeq2 R package.
Genome_build: hg19
Supplementary_files_format_and_content: Gene expression count matrix was generated using the featureCounts function of the Subread package and the ENSEMBL gene annotation gtf file with genome-build-accession identifier NCBI:GCA_000001405.14.

source_name: small intestinal epithelial cells from individual j11

growth_protocol: Human intestinal enteroids were proliferated for 4 days in CMGF(+) medium and then differentiated for 4 days in differentiation medium.

extract_protocol:
At 6 hours post infection, total RNA was extracted from human intestinal enteroids using the Qiagen Qiashredder kit and RNeasy Mink Kit extraction protocol and buffer sets
The library wa prepared using the Illumina TruSeq Standard RNA Sample preparation protocol

treatment_protocol: Differentiated human intestinal enteroids were either mock-treated (1X TNC buffer) or human rotavirus-treated (strain Ito)

value: female

tag: secretor-status

value: positive

tag: culture

value: 3-dimensional human intestinal enteroid

tag: agent

value: human rotavirus (strain Ito)


title: VEH1

value: Wistar

value: male

value: colonic epithelium

value: pineal gland ablation


title: j11-unifected (mock), ME41535

description:
rRNA-reduced total RNA
ME41535

value: mock-infected


title: NA1000_rep2

city: Geneva

first: Antonio

last: Frandi

address: rue michel servet 1

department: Microbiology and Molecular Medicine

country: Switzerland

institute: University of Geneva

data_processing:
The TSS-EMOTE protocol and  analyses were performed according to the  protocol described in Prados J. LP, Redder P., BMC genomics. 2016;17:849. doi: 10.1186/s12864-016-3211-3.
Genome_build: Caulobacter crescentus : NC_011916.1
Supplementary_files_format_and_content: Position of the TSS; P-value for the position to be a TSS, This is the result of the betabinomial model for each assay;    Combined p-value for the repliacted samples using Fishers' method; FDR correction of the combined p-values; FDR below 0.01 (Boolean); Is the TSS inside a Gene (Boolean); 50bp sequence surrounding the TSS. The sequence span positions -45:+5. Uppercase letters shows identified elements -10 TATAAT, -35 TTGACA, +1:+5; Position,  #error and sequence of identified elements arround the TSS; Information regarding TSS clusters: identifiers of he clusters, size of the cluster; Q values: corrected number of read starting at the position in each sample.

organism: Caulobacter vibrioides

source_name: Caulobacter crescentus

growth_protocol: Caulobacter crescentus and derivatives were grown at 30°C in PYE (Peptone yeast extract) or LB

extract_protocol:
total RNA was extracted as described in  Prados J. LP, Redder P., BMC genomics. 2016;17:849. doi: 10.1186/s12864-016-3211-3.
The TSS-EMOTE library preparation was performed according to the  protocol described in Prados J. LP, Redder P., BMC genomics. 2016;17:849. doi: 10.1186/s12864-016-3211-3.
TSS-EMOTE (Transcription Start Specific Exact Mapping Of Transcriptome Ends), a global assay  that reveals the sequence of the 20 first nucleotides of 5’-triphosphorylated RNA in a sample based on  an XRN-1 digest of transcripts lacking the 5’ triphosphate ends.
The TSS-EMOTE protocol and  analyses were performed according to the  protocol described in Prados J. LP, Redder P., BMC genomics. 2016;17:849. doi: 10.1186/s12864-016-3211-3.

value: wild type

tag: replicate


title: j2-uninfected (mock), ME41538

description:
rRNA-reduced total RNA
ME41538

source_name: small intestinal epithelial cells from individual j2


title: ∆R1R2_rep2

value: {delta}mucR1 {delta}mucR2

value: dMucR


title: NA1000_rep1


title: Pomc-hrGFP+ neuron #6

city: Boston

first: John

middle: N

last: Campbell

state: Massachusetts

address: Center for Life Science, room 7-717

department: Medicine

institute: Beth Israel Deaconess Medical Center

description: Arcuate non-MC4R neuron 29

data_processing:
alignment by Tophat with these parameters: -g 1 --b2-very-fast --no-coverage-search --segment-length 25 --no-novel-juncs
quantification by Cufflinks with these parameters: p 2 -G genes.gtf -o cuff --no-length-correction
Gene counts presented in raw Reads Per Kilobase of exon per Megabase of library size (RPKM) as output from Cufflinks ("genes" output file)
Genome_build: Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: CSV file containing a table of RPKM values by sample (columns) and gene (rows)

molecule: polyA RNA

source_name: arcuate hypothalamus

extract_protocol:
fluorescently-labeled and -unlabeled cells were manually isolated from a cell suspension made from triturating freshly-dissected, papain-digested PVH and ARC
Single cells were frozen at -80degC and then processed into RNA-seq libraries using a published protocol (Tang, F. et al. RNA-Seq analysis to capture the transcriptome landscape of a single cell. Nat. Protoc. 5, 516–535 (2010)) and NuGen's Rapid Library DR kit according to manufacturer's instructions

value: mixed background

value: arcuate hypothalamus

tag: Sex

value: M

tag: developmental stage

value: adult

tag: mouse id

value: K


title: ∆R1R2_rep1


title: Pomc-hrGFP+ neuron #3

description: Arcuate non-MC4R neuron 26

tag: tissue


title: Pomc-hrGFP+ neuron #2

description: Arcuate non-MC4R neuron 25


title: Pomc-hrGFP+ neuron #4

description: Arcuate non-MC4R neuron 27


title: Pomc-hrGFP+ neuron #7

description: Arcuate non-MC4R neuron 30


title: Pomc-hrGFP+ neuron #5

description: Arcuate non-MC4R neuron 28


title: Pomc-hrGFP+ neuron #1

description: Arcuate non-MC4R neuron 24


title: vGLUT2-IRES-Cre::AAV-mCherry+ neuron #8

description: Arcuate non-MC4R neuron 22

value: J


title: vGLUT2-IRES-Cre::AAV-mCherry+ neuron #7

description: Arcuate non-MC4R neuron 21


title: vGLUT2-IRES-Cre::AAV-mCherry+ neuron #4

description: Arcuate non-MC4R neuron 18


title: vGLUT2-IRES-Cre::AAV-mCherry+ neuron #3

description: Arcuate non-MC4R neuron 17


title: vGLUT2-IRES-Cre::AAV-mCherry+ neuron #5

description: Arcuate non-MC4R neuron 19


title: vGLUT2-IRES-Cre::AAV-mCherry+ neuron #1

description: Arcuate non-MC4R neuron 15


title: Agrp-IRES-Cre::L10-GFP+ neuron #14

description: Arcuate non-MC4R neuron 14

value: F

value: I


title: vGLUT2-IRES-Cre::AAV-mCherry+ neuron #2

description: Arcuate non-MC4R neuron 16


title: j2-infected (human rotavirus strain Ito), ME41543

description:
rRNA-reduced total RNA
ME41543

tag: gender

value: female

value: positive

value: 3-dimensional human intestinal enteroid

value: human rotavirus (strain Ito)


title: Agrp-IRES-Cre::L10-GFP+ neuron #12

description: Arcuate non-MC4R neuron 12

tag: strain


title: LF only rep 3

description:
10f
Illumina lane: 3

tag: treatment

value: lactoferrin (2 µg/mL)

value: 50 minutes


title: Agrp-IRES-Cre::L10-GFP+ neuron #13

description: Arcuate non-MC4R neuron 13


title: Agrp-IRES-Cre::L10-GFP+ neuron #10

description: Arcuate non-MC4R neuron 10


title: Agrp-IRES-Cre::L10-GFP+ neuron #11

description: Arcuate non-MC4R neuron 11


title: Agrp-IRES-Cre::L10-GFP+ neuron #9

description: Arcuate non-MC4R neuron 9


title: Agrp-IRES-Cre::L10-GFP+ neuron #7

description: Arcuate non-MC4R neuron 7


title: Agrp-IRES-Cre::L10-GFP+ neuron #8

description: Arcuate non-MC4R neuron 8


title: Agrp-IRES-Cre::L10-GFP+ neuron #4

description: Arcuate non-MC4R neuron 4


title: Agrp-IRES-Cre::L10-GFP+ neuron #1

description: Arcuate non-MC4R neuron 1

value: H


title: Mc4r-2a-Cre::AAV-mCherry-negative neuron #4

description: Unlabeled PVH neuron 4

source_name: paraventricular hypothalamus

value: paraventricular hypothalamus

value: G


title: Mc4r-2a-Cre::AAV-mCherry-negative neuron #5

description: Unlabeled PVH neuron 5

value: mixed background


title: vGLUT2-IRES-Cre::AAV-mCherry+ neuron #9

description: Arcuate non-MC4R neuron 23

value: arcuate hypothalamus


title: Mc4r-2a-Cre::AAV-mCherry-negative neuron #2

description: Unlabeled PVH neuron 2

value: M


title: Mc4r-2a-Cre::AAV-mCherry-negative neuron #3

description: Unlabeled PVH neuron 3

value: adult


title: Mc4r-2a-Cre::AAV-mCherry-negative neuron #1

description: Unlabeled PVH neuron 1


title: Mc4r-2a-Cre::AAV-mCherry+ neuron #7

description: Cre-labeled PVH neuron 30

value: D


title: vGLUT2-IRES-Cre::AAV-mCherry+ neuron #6

description: Arcuate non-MC4R neuron 20

value: J


title: Mc4r-2a-Cre::AAV-mCherry+ neuron #6

description: Cre-labeled PVH neuron 29


title: Mc4r-2a-Cre::AAV-mCherry+ neuron #8

description: Cre-labeled PVH neuron 31

value: E


title: Mc4r-2a-Cre::AAV-mCherry+ neuron #5

description: Cre-labeled PVH neuron 28


title: Mc4r-2a-Cre::AAV-mCherry+ neuron #4

description: Cre-labeled PVH neuron 27

value: C


title: Mc4r-2a-Cre::AAV-mCherry+ neuron #2

description: Cre-labeled PVH neuron 25


title: Mc4r-2a-Cre::AAV-mCherry+ neuron #1

description: Cre-labeled PVH neuron 24


title: Mc4r-2a-Cre::AAV-GFP+ neuron #15

description: Cre-labeled PVH neuron 22

value: B


title: Mc4r-2a-Cre::AAV-GFP+ neuron #14

description: Cre-labeled PVH neuron 21


title: Mc4r-2a-Cre::AAV-GFP+ neuron #16

description: Cre-labeled PVH neuron 23


title: Mc4r-2a-Cre::AAV-GFP+ neuron #13

description:
Cre-labeled PVH neuron 20
note technical replicates (duplicate libraries made from same single-cell cDNA sample)


title: Agrp-IRES-Cre::L10-GFP+ neuron #2

description: Arcuate non-MC4R neuron 2

value: F


title: Mc4r-2a-Cre::AAV-GFP+ neuron #11

description: Cre-labeled PVH neuron 18


title: Agrp-IRES-Cre::L10-GFP+ neuron #3

description: Arcuate non-MC4R neuron 3


title: Mc4r-2a-Cre::AAV-GFP+ neuron #12

description: Cre-labeled PVH neuron 19


title: Mc4r-2a-Cre::AAV-GFP+ neuron #7

description: Cre-labeled PVH neuron 14


title: Mc4r-2a-Cre::AAV-GFP+ neuron #8

description: Cre-labeled PVH neuron 15


title: Mc4r-2a-Cre::AAV-GFP+ neuron #10

description:
Cre-labeled PVH neuron 17
note technical replicates (duplicate libraries made from same single-cell cDNA sample)


title: Mc4r-2a-Cre::AAV-GFP+ neuron #6

description:
Cre-labeled PVH neuron 13
note technical replicates (duplicate libraries made from same single-cell cDNA sample)
Raw data file available for only one of the technical reps.  Raw data file for the other technical rep is corrupt.


title: IgG_1_RIP_mouse

city: Shanghai

first: Ningning

last: Niu

address: 160 Pu Jian Road, Shanghai

department: Clinical Stem Cell Research Center

country: China

institute: Shanghai Jiao Tong University School of Medicine Affiliated Renji Hospital

data_processing:
Basecalling using Illumina Casava1.8.2 software.
High-throughput sequencing reads were separated according to 6-nt experimental barcodes.
Reads were aligned against the mm9 mouse reference genome with the UCSC Genes annotation (mm9 knownGene.txt) using TopHat2 (Kim et al., 2013) 2.0.9 (parameters: -g 1 -no-coverage-search -microexon-search -m 2).
Peak-calling using peak enrichment program.
Genome_build: mm9 for mouse samples

source_name: Osteoblast cells, IgG RIP-SEQ

growth_protocol: Primary murine osteoblasts were isolated from calvaria of P5-P7 mice, and maintained in minimum essential medium (MEM) alpha containing 10% FBS. After infection by SV40 and Flag-Samd4 lentivirus, immortalized osteoblasts were used in RIP analysis.

extract_protocol:
Flag-Samd4 expressing Samd4PB/PB osteoblasts were resuspended in IP buffer (50 mM Tris-HCl Ph 7.5, 150 mM NaCl, 1% NP-40, 0.5% sodium deoxycholate and 1mM phenylmethanesulfonyl fluoride (PMSF)), subjected to gentle sonication, and centrifuged to obtain cell extracts.
Libraries were prepared according to Illumina's instructions accompanying the RNA Sample Kit. The purified RNA was captured on an Illumina flow cell for cluster generation.

value: Immortalized osteoblast

value: FVB

tag: rip antibody

value: Flag (Sigma, I5006)


title: IgG_2_RIP_mouse

tag: cell type

value: Flag (Sigma, I5007)


title: Input_RIP_mouse

source_name: Osteoblast cells, input DNA


title: Mc4r-2a-Cre::AAV-GFP+ neuron #3

description:
Cre-labeled PVH neuron 10
note technical replicates (duplicate libraries made from same single-cell cDNA sample)
Raw data file available for only one of the technical reps.  Raw data file for the other technical rep is corrupt.


title: Mc4r-2a-Cre::AAV-mCherry+ neuron #3

description: Cre-labeled PVH neuron 26


title: Mc4r-2a-Cre::AAV-GFP+ neuron #4

description: Cre-labeled PVH neuron 11


title: Mc4r-2a-Cre::L10-GFP+ neuron #4

description: Cre-labeled PVH neuron 4

value: A


title: Mc4r-2a-Cre::L10-GFP+ neuron #5

description: Cre-labeled PVH neuron 5

value: paraventricular hypothalamus


title: IP2_RIP_mouse

source_name: Osteoblast cells, Flag-Samd4 RIP-SEQ

value: Flag (Sigma, F3166)


title: Mc4r-2a-Cre::L10-GFP+ neuron #2

description: Cre-labeled PVH neuron 2

value: mixed background


title: NIH3T3_CTRL

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

country: Japan

institute: Chiba University

data_processing:
Illumina Casava1.7 software used for basecalling.
Read were aligned with TopHat v1.3.2 and Bowtie version 0.12.9. Command,line options for Tophat were '-r 100.'
Fragments per kilobase of exon model per million mapped fragments (FPKM) were calculated using Cufflinks v2.0.2. Command line options for cufflinks were '--max-bundle-flags 4000000.'
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: NIH3T3 fibroblast

growth_protocol: NIH3T3 fibroblasts were grown in IMDM with 10% FBS.

extract_protocol:
Total RNA was extracted by using the MagNA pure compact RNA isolation kit (Roche).
RNA-seq libraries were prepared for sequencing using TruSeqStranded mRNA LT Sample Prep Kit according to standard Illumina protocols

treatment_protocol: NIH3T3 fibroblasts were incubated in serum-free IMDM supplemented with 100 ng/mL of GDF15 or 4 ng/mL of TGF-β for 24 h.

tag: stimulation

value: No stimulation


title: NIH3T3_TGF-β

value: 4 ng/mL of TGFβ protein


title: NIH3T3_GDF15

value: 100 ng/mL of GDF15 protein


title: col_D_rep3

status: Public on Dec 02 2016

city: fuzhou

first: Lianfeng

last: Gu

address: No.15 Shangxiadian Road, Cangshan District, Fuzhou City, Fujian Province, China

institute: Fujian Agriculture and Forestry University

data_processing:
The RNA-seq reads were aligned to the Arabidopsis genome (TAIR10) using tophat-2.0.11 (Trapnell et al., 2009) with anchor length more than 8nt for spliced alignments. Only uniquely mapped reads were retained for subsequent analysis.
Genome_build: TAIR10
Supplementary_files_format_and_content: bigWig files include raw counts.
Supplementary_files_format_and_content: B2h_FPKM.xls file includes FPKMs for each sample, and fold changes, p values, and FDRs.

organism: Arabidopsis thaliana

source_name: Seedling, wild type, dark

growth_protocol: The seedlings were grown in greenhouse.

extract_protocol:
The total RNA was extracted using TRIZOL reagent.
Strand-specific RNA-Seq libraries generated from samples were constructed using dUTP method (Parkhomchuk et al., 2009) and sequenced on Illumina HiSeq 2500.

treatment_protocol: Blue light 2h or dark.

tag: strain/background

value: Col

tag: genotype/variation

value: wild type

value: seedling

tag: age

value: dark


title: IP1_RIP_mouse

value: Flag (Sigma, F3165)


title: Mc4r-2a-Cre::L10-GFP+ neuron #3

description: Cre-labeled PVH neuron 3

value: M

value: adult


title: col_D_rep2


title: SlCycB2 RNAi

city: wuhan

first: Yanna

last: Gao

address: hongshan area, shizishan street

institute: Huazhong agricultural university

data_processing:
Illumina HiSeq™ 2500 used for RNA-Seq
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Solanum lycopersicum whole genome by Tophat.
Reads per kilobase of exon model per million mapped reads (RPKM) were calculated. RPKM=total exon reads/mapped reads(millions)*exon length(KB)
Supplementary_files_format_and_content: The excel file includes the number of RPKM of each gene for each sample

organism: Solanum lycopersicum

source_name: leaf

extract_protocol:
The young primary leaf samples harvested  were frozen in liquid nitrogen and kept at -80°C until use. Total RNA was extracted using TRIzol reagent (Invitrogen).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cultivar

value: Ailsa Craig (AC)

value: young primary leaf

value: mature plant


title: col_B2_rep3

source_name: Seedling, wild type, blue 2h

value: blue light, 2hr


title: SlCycB2-OE


title: Mc4r-2a-Cre::AAV-GFP+ neuron #9

description: Cre-labeled PVH neuron 16

value: paraventricular hypothalamus

value: B


title: c1c2_D_rep2

source_name: Seedling, cry1cry2, dark


title: c1c2_D_rep3


title: col_D_rep1


title: col_B2_rep2


title: col_B2_rep1


title: setx_ChIP_t4

city: New York

first: Ivan

last: Marazzi

address: 1468 Madison Avenue

department: Department of Microbiology

institute: Icahn School of Medicine at Mount Sinai

description: SETX ChIP-Seq profile in A549 cells, 4 hours after infection with Influenza PR8ΔNS1

data_processing:
Following adapter trimming and quality filtering, reads were mapped to the human reference genome (GRCh37, hg19) using bowtie v0.12.9 (see PMID: 19261174). Unique best matches were kept and normalized to a total level of 44M tags per sample.
Genome_build: hg19
Supplementary_files_format_and_content: Processed data files are in wig format and contain normalized mapped ChIP-Seq read coverage

source_name: A549 cells

extract_protocol:
Previously described protocols (see PMID: 17512414 and PMID: 17406303) with minor modifications were used:  (i) Sonication: A refrigerated  Bioruptor (Diagenode) was used . Sonication conditions were optimized to generate DNA fragments of approximately 200-500 bp. (ii) Antibodies (Ab) were coupled with Invitrogen Dynabeads anti-mouse M-280 #112-02, or Dynabeads anti-rabbit M-280 #112-04 for 6hours. Ab-beads and chromatin were then immunoprecipitated overnight. (iii) After the wash steps, reverse crosslinking was carried out at 65°C for 2 hours in a thermomixer programmed for mixing at 700 rpm 2 min on/ min off. ChIP DNA was then isolated, after RNase digestion and proteinase K digestion, using QIAGEN MinElute kit (28004).
For library preparation, 30 ul of ChIP DNA was used to generate blunt-ended DNA using the Epicenter DNA ENDRepair kit (Epicenter Biotechnologies, cat# ER0720), and purified end-repaired DNA using the QIAGEN PCR purification kit (28104). DNA END Repair was done using Klenow Fragment (NEB M0212L), and purified DNA was collected with QIAGEN MinElute kit. Ligation of Illlumina/Solexa adapters (#FC-102-1003) to DNA fragments overnight was achieved using T4 DNA ligase (NEB M0202L). Adaptor-ligated DNA fragments were purified with the QIAGEN MinElute kit. 18 cycles of PCR was performed with the Illumina/Solexa primers 1.0 and 2.0, and an aliquot of material was used to check the fragment size on agarose gel. The remaining DNA was column purified and bio-analyzed before sequencing.

tag: cell line

tag: chip antibody

value: SETX

tag: infection

value: Influenza PR8ΔNS1


title: BIC1ox_D_rep3

source_name: Seedling, BIC1ox, dark


title: c1c2_B2_rep1

source_name: Seedling, cry1cry2, blue 2h


title: Mc4r-2a-Cre::L10-GFP+ neuron #1

description: Cre-labeled PVH neuron 1

value: mixed background

tag: Sex

value: A


title: c1c2_D_rep1

value: Col


title: BIC1ox_D_rep2


title: BIC1ox_D_rep1


title: BIC1ox_B2_rep2

source_name: Seedling, BIC1ox, blue 2h


title: BIC1ox_B2_rep3


title: BIC1ox_B2_rep1


title: Sample_PR10_TFC_N3a

city: Shenyang

first: Wensu

last: Liu

state: Liaoning

address: 77 Puhe Road, Shenyang North New Area

institute: China Medical University

description: sequenced on Illumina

data_processing:
Illumina Casava1.7 software used for basecalling.
Fastqc assessing quality of data, removing low-quality reads
Tophat2 using default parameters
Cufflinks calculating fpkm using default parameters
R performing statistical analysis and data mining
Genome_build: hg19
Supplementary_files_format_and_content: Excel workbook file including FPKM data of all samples

growth_protocol: GW16 complete prenatal human brain was obtained at autopsy with 3h of spontaneous abortion

extract_protocol:
Brain was dissected in ice-cold artificial cerebrospinal fluid (ACSF). The VZ, OSVZ and CP cellular zones were carefully microdissected in HBSS from the brain slices, and single cells was selected by FACS.
The cDNA library following the manual of NEBNext Ultra DNA Library Prep Kit for Illumina (NEB, E7370L).

value: GW 16

tag: tissue source

value: prenatal human brain

value: human embroynic neuron cells (N)

tag: sequence type

value: single-cell sequencing


title: Sample_PR10_TFC_N1a

description: sequenced on Illumina


title: Sample_PR10_TFC_N2b

description: sequenced on Illumina


title: Sample_PR10_TFC_N1b

description: sequenced on Illumina


title: c1c2_B2_rep3

tag: tissue

value: seedling


title: Sample_PR10_TFC_IPC11b

description: sequenced on Illumina

value: human embroynic intermediate progenitor cell (IPC)


title: Sample_PR10_TFC_IPC24b

description: sequenced on Illumina


title: Sample_PR10_TFC_IPC11a

description: sequenced on Illumina


title: Mc4r-2a-Cre::AAV-GFP+ neuron #5

description: Cre-labeled PVH neuron 12

value: M

tag: developmental stage

value: adult

tag: mouse id


title: c1c2_B2_rep2

tag: treatment


title: Sample_PR10_TFC_oRG21b

description: sequenced on Illumina

value: human embroynic outer radial glial cell (oRG)


title: Sample_PR10_TFC_N2a

description: sequenced on Illumina


title: Sample_PR10_TFC_IPC24a

description: sequenced on Illumina


title: Sample_PR10_TFC_oRG18a

description: sequenced on Illumina


title: setx_ChIP_t0

description: SETX ChIP-Seq profile in uninfected A549 cells

value: uninfected


title: Sample_PR10_TFC_oRG18b

description: sequenced on Illumina


title: Mc4r-2a-Cre::L10-GFP+ neuron #6

description: Cre-labeled PVH neuron 6

tag: strain

value: paraventricular hypothalamus


title: Sample_PR10_TFC_RG5a

description: sequenced on Illumina

tag: cell type

value: human embroynic radial glial cell (RG)


title: Sample_PR10_TFC_RG4a

description: sequenced on Illumina


title: Sample_PR10_TFC_RG4b

description: sequenced on Illumina


title: Sample_PR10_TFC_N3b

description: sequenced on Illumina


title: Lu346A.RNA-seq

city: Rochester

first: Zhifu

last: Sun

state: MN

address: 200 1st ST SW

department: HSR-BSI

institute: Mayo Clinic

description: Frozen tissue

data_processing:
Internal MAPRSeq pipeline (http://bioinformaticstools.mayo.edu/research/maprseq/)
RPKM normalized, Log2 transformed
Genome_build: hg19
Supplementary_files_format_and_content: txt, raw and normalized expression

source_name: Human lung

extract_protocol:
Total RNA extraction was performed using Exiqon’s miRCURY RNA Isolation Kit.
The pair end sequencing was carried out using the Illumina HiSeq 2000 sequencer at 100bps.

tag: diagnosis

value: Lung Adenocarcinoma

value: Lung

value: Female

tag: Stage

value: IA

value: AD

tag: differentiation

value: Well

tag: grade

value: II

tag: survstatus

tag: time to last followup


title: Lu346B.RNA-seq

description: Frozen tissue

tag: age

value: NL


title: Lu587B.RNA-seq

description: Frozen tissue

value: IB

value: I


title: Lu2502B.RNA-seq

description: Frozen tissue


title: Lu2502A.RNA-seq

description: Frozen tissue

value: BAC


title: Lu2499A.RNA-seq

description: Frozen tissue


title: Lu2499B.RNA-seq

description: Frozen tissue


title: Sample_PR10_TFC_oRG21a

description: sequenced on Illumina

value: GW 16

value: prenatal human brain

value: single-cell sequencing


title: Lu2040B.RNA-seq

description: Frozen tissue

value: Mod

value: III


title: Lu2368B.RNA-seq

description: Frozen tissue


title: Lu2368A.RNA-seq

description: Frozen tissue


title: Sample_PR10_TFC_RG5b

description: sequenced on Illumina

value: human embroynic radial glial cell (RG)


title: CMT93c

city: Göttingen

first: Darius

last: Wlochowitz

address: Goldschmidtstr. 1

department: Bioinformatics

country: Germany

institute: Institute of Bioinformatics

data_processing:
Illumina Casava 1.8.2 software used for basecalling. Quality check was done via fastqc (v. 0.10.0, Babraham Bioinformatics)
The Alignment was performed with STAR RNA-Seq aligner version 2.4.0a, by mapping the reads against transcriptome, and counting was performed using RSEM v1.2.5.
The transcriptome was generated with RSEM from Ensembl reference genome version GRCm38.p4
Data analysis was performed using R/Bioconductor (3.0.2/2.12) loading the edgeR package.
1638NT1vsCMT93ATCC.xls RNA-seq raw count data from RSEM
1638NT1_signature_genes Results from Trinity platform analysis: Extraction of transcripts that are most differentially expressed (most significant P-values and fold-changes) and clustering the transcripts according to their patterns of differential expression across the samples
CMT93ATCC_vs_nt1_genes Results from Trinity platform analysis: Extraction of transcripts that are most differentially expressed (most significant P-values and fold-changes) and clustering the transcripts according to their patterns of differential expression across the samples
Genome_build: GRCm38.p4
Supplementary_files_format_and_content: tab-delimited text file include expected counts for each Sample

extract_protocol:
RNA was isolated using Trizol reagent and including a DNase I (Roche, Mannheim, Germany) digestion step.
Library preparation for RNA-Seq was performed using the TruSeq Stranded Sample Preparation Kit (Illumina, RS-122-2201) starting from 1000 ng of total RNA. Accurate quantitation of cDNA libraries was performed using the QuantiFluor TM dsDNA System (Promega). The size range of nal cDNA libraries was determined applying the SS-NGS-Fragment 1-6000 bp Kit on the Fragment Analyzer from Advanced Analytical (320 bp). cDNA libraries were amplied and sequenced by using the cBot and the HiSeq2000 from Illumina (SR; 50 bp; 35 million reads per sample).
Non stranded mRNA-Seq

tag: cell line


title: Lu2029B.RNA-seq

description: Frozen tissue

value: Lung Adenocarcinoma

tag: Sex


title: Lu2040A.RNA-seq

description: Frozen tissue

value: Lung


title: Lu2029A.RNA-seq

description: Frozen tissue

value: Female


title: Lu1943B.RNA-seq

description: Frozen tissue


title: Lu1943A.RNA-seq

description: Frozen tissue


title: CMT93b


title: 1638NT13wt5


title: Lu1942B.RNA-seq

description: Frozen tissue

value: Male


title: Lu587A.RNA-seq

description: Frozen tissue


title: Lu1848A.RNA-seq

description: Frozen tissue

value: AD


title: Lu1821A.RNA-seq

description: Frozen tissue


title: Lu1821B.RNA-seq

description: Frozen tissue


title: 1638NT11wt3


title: Lu1790A.RNA-seq

description: Frozen tissue

value: Well


title: Lu1790B.RNA-seq

description: Frozen tissue

value: II


title: Lu1682B.RNA-seq

description: Frozen tissue

value: IA

value: NL


title: Lu1682A.RNA-seq

description: Frozen tissue


title: Lu1606B.RNA-seq

description: Frozen tissue


title: Lu1659A.RNA-seq

description: Frozen tissue


title: Lu1659B.RNA-seq

description: Frozen tissue


title: Lu1606A.RNA-seq

description: Frozen tissue


title: Lu1942A.RNA-seq

description: Frozen tissue

value: IB


title: Lu1518B.RNA-seq

description: Frozen tissue


title: Lu1479B.RNA-seq

description: Frozen tissue


title: XRN1-delta-2

city: Worcester

first: Allan

last: Jacobson

state: MA

address: 368 Plantation Street Albert Sherman Center AS8-1014

department: MaPS

institute: UMASS Medical School

description: total RNA treated with ribo zero

data_processing:
Quality control with FastQC
Alignment to transcriptome and transcript quantitiation with RSEM and bowtie
Differential expression analysis using DESeq using RSEM expected count data with FDR cutoff 0.01
Genome_build: S288C_reference_genome_R64-2-1
Supplementary_files_format_and_content: normalized expression values  as produced by DESeq, tab delimeted text file

organism: Saccharomyces cerevisiae

source_name: culture grown in YEPD

growth_protocol: Cells grown until O.D ~0.8 and harvested.

extract_protocol:
Hot phenol extraction followed by ethanol precipitation.
Illumina Tru-Seq library prep kit according to manufacturers reccomendations

tag: background


title: XRN1-delta-3

description: total RNA treated with ribo zero


title: XRN1-delta-1

description: total RNA treated with ribo zero


title: Lu1479A.RNA-seq

description: Frozen tissue


title: CMT93a


title: DCP2-delta-3

description: total RNA treated with ribo zero


title: DCP2-delta-2

description: total RNA treated with ribo zero


title: DCP1-delta-3

description: total RNA treated with ribo zero


title: DCP2-delta-1

description: total RNA treated with ribo zero


title: Lu1405A.RNA-seq

description: Frozen tissue


title: DCP1-delta-2

description: total RNA treated with ribo zero


title: Lu1450B.RNA-seq

description: Frozen tissue


title: Lu1405B.RNA-seq

description: Frozen tissue


title: 1638NT12wt4


title: Lu1377B.RNA-seq

description: Frozen tissue


title: Lu1377A.RNA-seq

description: Frozen tissue


title: Lu1518A.RNA-seq

description: Frozen tissue


title: Lu1321A.RNA-seq

description: Frozen tissue


title: Lu1321C.RNA-seq

description: Frozen tissue


title: DCP1-delta-1

description: total RNA treated with ribo zero


title: UPF3-delta-3

description: total RNA treated with ribo zero


title: Lu1182B.RNA-seq

description: Frozen tissue


title: Lu113B.RNA-seq

description: Frozen tissue


title: Lu1182A.RNA-seq

description: Frozen tissue

value: BAC


title: UPF3-delta-2

description: total RNA treated with ribo zero


title: Lu1848B.RNA-seq

description: Frozen tissue


title: Lu106B.RNA-seq

description: Frozen tissue


title: UPF3-delta-1

description: total RNA treated with ribo zero


title: Lu1068B.RNA-seq

description: Frozen tissue


title: UPF2-delta-3

description: total RNA treated with ribo zero


title: UPF2-delta-2

description: total RNA treated with ribo zero


title: Lu106A.RNA-seq

description: Frozen tissue


title: Lu1068A.RNA-seq

description: Frozen tissue


title: UPF2-delta-1

description: total RNA treated with ribo zero


title: Lu1050B.RNA-seq

description: Frozen tissue


title: UPF1-delta-3

description: total RNA treated with ribo zero


title: UPF1-delta-2

description: total RNA treated with ribo zero


title: Lu1031B.RNA-seq

description: Frozen tissue


title: UPF1-delta-1

description: total RNA treated with ribo zero


title: Lu1031A.RNA-seq

description: Frozen tissue


title: WT-2

description: total RNA treated with ribo zero


title: WT-1

description: total RNA treated with ribo zero


title: pr9-iPSC.input.ChIP-Seq

status: Public on Dec 01 2016

first: Xiaobai

last: Zhang

address: 1239 Siping Road

institute: Tongji University

data_processing:
RNA-seq reads were aligned to the UCSC human genes (hg19) using Tophat (version 2.0.13). Only the uniquely mapped reads in proper pairs were retained for analysis in this study.
We used Cuffdiff (version 2.1.1) to calculate the expression abundance of each gene as fragments per kilobase per million mapped reads (FPKM).
ChIP-Seq reads were aligned to the human reference genome (hg19) using Bowtie (version 2.1.0). Only the uniquely mapped reads in proper pairs were retained for analysis in this study.
We used the MACS (version 1.4.1) peak finding algorithm to detect regions of ChIP-Seq signal enrichment (p-value < 1e-5) over background.
Genome_build: hg19
Supplementary_files_format_and_content: For ChIP-Seq data, processed data files are tab-delimited text files with enriched peaks predicted by MACS. For RNA-Seq data, processed data files are tab-delimited files showing gene expresssion levels with FPKM.

source_name: primed iPSCs

growth_protocol: Fibroblasts were isolated from β-thalassemia patients carrying the β-41/42 mutation. Episomal vectors carrying a combination of transcription factors encoded by Oct4, Sox2, Klf4 and c-Myc were transfected into fibroblasts through electroporation and were then cultured in conventional hESM containing DMEM/F12 (Invitrogen) supplemented with 20% Knockout Serum Replacement (Invitrogen), 10 ng/ml bFGF (Peprotech), 10-4M non-essential amino acids (Millipore), 10-4M β-mercaptoethanol (Millipore), 2 mM L-Glutamax (Invitrogen) and 50 µg/ml penicillin/streptomycin (Millipore) for 6 days. Then, the medium was replaced with human naïve medium (5i/L/FA medium) and cultured for 14-20 days. Dome-shaped colonies similar to mouse ESCs were selected and expanded by single cell passaging.

extract_protocol:
For RNA-Seq, total RNA was isolated from naïve iPSC lines and primed PSC lines using Trizol reagent (Invitrogen) according to the manufacturer’s instructions. The RNA sequencing libraries were constructed from the extracted RNA using standard Illumina libraries prep protocols. Sequencing was performed on Illumina HiSeq2000 platform in pair end.
For ChIP-Seq, Cells (~1x10^7) for each sample were fixed in 1% formaldehyde for 10 min. The crosslink reaction was stopped by addition of glycine. Next, cells were washed 3 times with PBS. Then, cells were resuspended in lysis buffer and sonicated in Diagenode Bioruptor (Biosence) to fragments with length range of 200-500bp. Antibodies to H3K4me3 and H3K27me3 (Abcam) were added to supernatants to capture nucleosomes with these two histone modifications, respectively. The nucleosomal DNA was recovered by removal of histones at overnight incubation at 65℃ and purified using QIAquick PCR purification kit (QIAGEN, Maryland). The ChIP’ed DNA was used to construct libraries for sequencing using the ChIP-seq Sample Prep Kit (Illumina) according manufacturer’s instructions.
The RNA sequencing libraries were constructed from the extracted RNA using standard Illumina libraries prep protocols. The ChIP’ed DNA was used to construct libraries for sequencing using the ChIP-seq Sample Prep Kit (Illumina) according manufacturer’s instructions.

tag: subject status

value: Fibroblasts

tag: cell subtype

value: conventional iPSCs


title: pr9-iPSC.H3K4me3.ChIP-Seq

value: β-thalassemia patients carrying the β-41/42 mutation

tag: chip antibody

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat. #

tag: chip antibody lot #


title: n5-iPSC.H3K4me3.ChIP-Seq

source_name: naïve iPSCs

tag: cell type

value: induced pluripotent stem cells generated by a modified 5i/L/FA system


title: pr9-iPSC.H3K27me3.ChIP-Seq

value: Millipore


title: n2-iPSC.input.ChIP-Seq


title: n5-iPSC.input.ChIP-Seq


title: n5-iPSC.H3K27me3.ChIP-Seq


title: n2-iPSC.H3K4me3.ChIP-Seq


title: n2-iPSC.H3K27me3.ChIP-Seq


title: Lu1050A.RNA-seq

description: Frozen tissue

tag: diagnosis

value: Lung Adenocarcinoma

tag: tissue


title: G1+HBP-St

city: Wuhan

first: Zheng

last: Beibei

state: Hubei

address: Shizi shan street No. 1

institute: Huazhong Agricutural University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to citrus sinensis whole genome (http://citrus.hzau.edu.cn/orange/) using tophat -p 24 -G /home/lsun/han/ref/csi.gene.models.gff3 -o /home/lsun/zhengbeibei/tophat/$(basename $index)-tophat /home/lsun/han/ref/csi.genome $x($x is the filename,the format is .fq,tophat v2.0.8b)
Assembles the matched reads to estimates their abundances using cufflinks -p 24 -o $dir/cufflinks $var($dir is a direction name,$var is the mapping file whose format is .bam,cufflinks v2.1.1 )
tests for differential expression and regulation in RNA-Seq samples using cuffdiff v2.1.1 cuffdiff -o /home/lsun/zhengbeibei/diff-2/HB-St-vs-HB-G1-St -b /home/lsun/han/ref/csi.chromosome.fa -p 16 -L HB-St,HB-G1-St -u /home/lsun/zhengbeibei/diff-2/merged_asm_St/merged.gtf \  /home/lsun/zhengbeibei/tophat/HB-St-tophat/accepted_hits.bam /home/lsun/zhengbeibei/tophat/HB-G1-St-tophat/accepted_hits.bam
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Citrus maxima

source_name: RNA-seq data of a male sterile pomelo

growth_protocol: Developing floral buds

extract_protocol:
Total RNA was extracted by Trizol method
20 mg total RNA was prepared to enrich mRNA by using the oligo (dT) magnetic beads. After adding fragmentation buffer, the mRNA was interrupted to short fragments (approximately 200 bp). The first strand cDNA was then synthesized with random hexamer-primer using the mRNA fragments as templates. Buffer, dNTPs, RNase H and DNA polymerase I were added to synthesize the second strand. The double-strand cDNA was purified with QiaQuick PCR extraction kit and washed with EB buffer for end repair and single nucleotide A (adenine) addition. Finally, sequencing adaptors were ligated to the fragments.

treatment_protocol: No treatment

tag: line

value: petal primordia and stamen primordia


title: HBP-St

source_name: RNA-seq data of a male fertile pomelo

value: HBP


title: by1-ESC.RNA-Seq

description: processed data file: gene_expression.txt

source_name: ESCs

value: embryonic stem cells


title: n2-iPSC.RNA-Seq


title: pr9-iPSC.RNA-Seq


title: pr2-iPSC.RNA-Seq


title: n5-iPSC.RNA-Seq


title: RNA_499_STAT1KO_21

city: Philadelphia

first: Yu

last: Qiu

state: PA

address: 421 Curie Blvd

department: Radiation Oncology

institute: University of Pennsylvania

data_processing:
Basecalls performed using Illumina CASAVA software.
Raw reads were trimmed for adaptor sequence using cutadapt v1.9 (parameter -q 10 -m 30 -O 4)
Trimmed reads were mapped to consensus rRNA sequences using bowtie2 v2.2.4 to remove rRNA reads (parameter --fr --no-mixed --no-discordant)
Reads were then aligned with STAR v2.4.0k to GRCm38/mm10 reference genome (parameter --outFilterMultimapNmax 100 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.06)
Non primary alignment and QC failed reads were removed with samtools (parameter -F 772)
Aligned and filtered reads were counted against GENCODE annotation vM4 using Subread v1.4.6 (parameter -s 2 -minReadOverlap 10)
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: tab delimited txt file including raw read count for each gene feature.

source_name: sorted 499 STAT1 CRISPR KO cells

growth_protocol: Mice were injected with tumor cells. On day 15, CD45 negative tumor cells were harvested and sorted.

extract_protocol:
Total RNA was isolated and purified from the cells using Isol-RNA Lysis Reagent (Fisher) and treated with DNase I (Fisher).
RNA-seq libraries were prepared using the TrueSeq Stranded Total RNA Library Prep Kit (Illumina)

tag: strain/genotype

value: 499 STAT1 KO

tag: treatment

value: CD45 negative tumor cells


title: RNA_499_STAT1KO_24


title: RNA_499_STAT1KO_23


title: RNA_499_IFNGRKO_3

source_name: sorted 499 IFNGR CRISPR KO cells

value: 499 IFNGR KO


title: RNA_499_IFNGRKO_4


title: RNA_499_IFNARKO_4

source_name: sorted 499 IFNAR CRISPR KO cells

value: 499 IFNAR KO


title: Lu113A.RNA-seq

description: Frozen tissue

value: Lung

value: Female

tag: Stage

value: IA

value: AD

tag: differentiation

value: Well

tag: grade

value: II

tag: survstatus

tag: time to last followup


title: RNA_499_IFNGRKO_2


title: RNA_499_IFNARKO_3


title: RNA_499_IFNARKO_2


title: RNA_499_IFNARKO_1


title: RNA_499_CRISPR_4

source_name: sorted 499 CRISPR control cells

value: 499 CRISPR control


title: RNA_499_AGKO_5

source_name: sorted 499 IFNAR and IFNGR CRISPR KO cells

value: 499 IFNAR/IFNGR KO


title: RNA_499_AGKO_6


title: RNA_499_AGKO_3


title: RNA_499_CRISPR_1


title: WT Vehicle Striatum Female rep5

city: Princeton

first: Jeff

last: Aaronson

state: New Jersey

address: 155 Village Boulevard, Suite 200

department: Discovery & Systems Biology

institute: CHDI

description: C53811_-_9950_Right_striatum_L4.LB19_clipped

data_processing:
Illumina CASAVA 1.8.2 software used for basecalling
Genome mapped via Omicsoft OSA 4.0
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by using fastq-mcf sequence quality filter, clipping and processor with following settings for Omicsoft: Trimming  /Mode=TrimByQuality /ReadTrimQuality=2;  Options  /ParallelJobNumber=4 /PairedEnd=True /FileFormat=FASTQ /AutoPenalty=True /FixedPenalty=2 /Greedy=false /IndelPenalty=2 /DetectIndels=False /MaxMiddleInsertionSize=10 /MaxMiddleDeletionSize=10 /MaxEndInsertionSize=10 /MaxEndDeletionSize=10 /MinDistalEndSize=3 /ExcludeNonUniqueMapping=False /ReportCutoff=10 /WriteReadsInSeparateFiles=True /GenerateSamFiles=False /ThreadNumber=6 /InsertSizeStandardDeviation=40 /ExpectedInsertSize=300 /MatePair=False /InsertOnSameStrand=False /InsertOnDifferentStrand=True /QualityEncoding=Automatic /CompressionMethod=Gzip /Gzip=True /SearchNovelExonJunction=False /ExcludeUnmappedInBam=False /KeepFullRead=False /Replace=False /Platform=ILLUMINA /CompressBam=False;
Genome_build: Genome version Mouse B.38, gene models version Ensembl R.75
Supplementary_files_format_and_content: Excel files include FPKM and Count values for each Sample

source_name: Corpus striatum of right cerebral hemisphere

extract_protocol:
Tissue specimens were removed, flash frozen on dry ice, and total RNA was harvested using the Qiagen miRNeasy kit. RNA quality and integrity were monitored via Agilent Bioanalyzer. A minimum of 3.75 ug of total RNA were used to collect enriched RNA subfractions for library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Dosing of either vehicle or the  PDE10A inhibitor PF-02545920 (0.32, 1 and 3.2 mg/kg po qd) in the Q175 homozygous knock-in mouse model of Huntington’s disease (dosing from 5-weeks to 9 months of age).

tag: strain

tag: genotype

value: Wild Type

value: Striatum

tag: age

value: 9 months

tag: Sex

value: Vehicle

tag: treatment administration route

value: Oral

tag: treatment frequency

value: Once-Daily

tag: treatment duration

value: from 5 weeks to 9 months


title: WT Vehicle Striatum Female rep4

description: C53811_-_9205_Right_striatum_L7.LB20_clipped


title: WT Vehicle Striatum Male rep4

description: C53811_-_9168_Right_striatum_L4.LB25_clipped

value: Male


title: Hom(Q175) Vehicle Striatum Female rep4

value: Q175 Homozygous knock-in


title: WT Vehicle Striatum Male rep1

description: C53811_-_1179_Right_striatum_L7.LB2_clipped


title: WT Vehicle Striatum Female rep3


title: WT Vehicle Striatum Female rep2

description: C53811_-_9006_Right_striatum_L3.LB22_clipped


title: Hom(Q175) Vehicle Striatum Female rep3

description: C53811_-_9170_Right_striatum_L4.LB12_clipped


title: WT Vehicle Striatum Female rep1

description: C53811_-_8528_Right_striatum_L3.LB21_clipped


title: WT Vehicle Striatum Male rep2

description: C53811_-_9028_Right_striatum_L8.LB27_clipped


title: Hom(Q175) Vehicle Striatum Female rep5

description: C53811_-_9501_Right_striatum_L6.LB14_clipped


title: RNA_499_IFNGRKO_1

value: 499 IFNGR KO

tag: cell type

value: CD45 negative tumor cells


title: WT Vehicle Striatum Male rep3

description: C53811_-_9029_Right_striatum_L3.LB1_clipped

tag: tissue


title: Hom(Q175) Vehicle Striatum Male rep2

description: C53811_-_2133_Right_striatum_L2.LB16_clipped


title: Hom(Q175) Vehicle Striatum Female rep2

description: C53811_-_9136_Right_striatum_L8.LB13_clipped

value: Female


title: WT-3

description: total RNA treated with ribo zero

tag: background


title: Hom(Q175) Vehicle Striatum Female rep1

description: C53811_-_1428_Right_striatum_L2.LB15_clipped


title: Hom(Q175) Vehicle Striatum Male rep1

description: C53811_-_1114_Right_striatum_L8.LB18_clipped


title: Hom(Q175) PF-02545920_3.2mpk Striatum Female rep3

description: C53811_-_9516_Right_striatum_L7.LB5_clipped

tag: treatment dose

value: 3.2 mg/kg


title: RNA_499_CRISPR_2

tag: strain/genotype

tag: treatment


title: Hom(Q175) PF-02545920_3.2mpk Striatum Female rep4

description: C53811_-_9657_Right_striatum_L4.LB6_clipped


title: Hom(Q175) PF-02545920_3.2mpk Striatum Female rep5

description: C53811_-_9924_Right_striatum_L5.LB3_clipped


title: Hom(Q175) PF-02545920_3.2mpk Striatum Male rep4

description: C53811_-_9521_Right_striatum_L2.LB10_clipped


title: Hom(Q175) PF-02545920_3.2mpk Striatum Male rep3

description: C53811_-_9211_Right_striatum_L3.LB7_clipped


title: Hom(Q175) PF-02545920_3.2mpk Striatum Female rep1

description: C53811_-_5489_Right_striatum_L2.LB2_clipped


title: Hom(Q175) PF-02545920_3.2mpk Striatum Female rep2

description: C53811_-_9123_Right_striatum_L5.LB4_clipped


title: Hom(Q175) PF-02545920_3.2mpk Striatum Male rep1

description: C53811_-_9026_Right_striatum_L8.LB9_clipped


title: Hom(Q175) PF-02545920_1.0mpk Striatum Female rep5

description: C53811_-_9915_Right_striatum_L1.LB16_clipped

value: 1.0 mg/kg


title: Hom(Q175) PF-02545920_1.0mpk Striatum Female rep4

description: C53811_-_9515_Right_striatum_L3.LB20_clipped


title: Hom(Q175) PF-02545920_3.2mpk Striatum Male rep2

description: C53811_-_9162_Right_striatum_L5.LB8_clipped


title: Lu1450A.RNA-seq

description: Frozen tissue

tag: diagnosis

value: Lung Adenocarcinoma

value: Lung

tag: Stage

value: IB

value: AD

tag: differentiation

value: Well

value: II


title: Hom(Q175) PF-02545920_1.0mpk Striatum Female rep3

description: C53811_-_9270_Right_striatum_L7.LB21_clipped

value: Striatum

value: 9 months


title: Hom(Q175) PF-02545920_1.0mpk Striatum Female rep1

description: C53811_-_1105_Right_striatum_L1.LB19_clipped

value: Oral

value: Once-Daily


title: Hom(Q175) PF-02545920_1.0mpk Striatum Male rep1

value: Male

value: from 5 weeks to 9 months


title: Hom(Q175) PF-02545920_1.0mpk Striatum Male rep2

description: C53811_-_2143_Right_striatum_L7.LB27_clipped

value: Q175 Homozygous knock-in


title: Hom(Q175) PF-02545920_0.32mpk Striatum Female  rep4

description: C53811_-_9511_Right_striatum_L2.LB9_clipped


title: Hom(Q175) PF-02545920_0.32mpk Striatum Female  rep5

description: C53811_-_9940_Right_striatum_L3.LB6_clipped


title: Hom(Q175) PF-02545920_0.32mpk Striatum Male rep5

description: C53811_-_9201_Right_striatum_L6.LB11_clipped


title: Hom(Q175) PF-02545920_0.32mpk Striatum Male rep4

description: C53811_-_9040_Right_striatum_L8.LB13_clipped


title: Hom(Q175) PF-02545920_1.0mpk Striatum Male rep3

description: C53811_-_9039_Right_striatum_L2.LB22_clipped


title: Hom(Q175) PF-02545920_0.32mpk Striatum Male rep2

description: C53811_-_2302_Right_striatum_L4.LB12_clipped


title: Hom(Q175) PF-02545920_0.32mpk Striatum Female  rep3

description: C53811_-_2546_Right_striatum_L8.LB8_clipped


title: Hom(Q175) PF-02545920_0.32mpk Striatum Male rep1

description: C53811_-_1103_Right_striatum_L4.LB15_clipped


title: WT Vehicle Cortex Female rep5

description: C53811_-_9950_Right_cortex_L3.LB22_clipped

source_name: Cortex of right cerebral hemisphere

value: Wild Type

value: Cortex

value: Vehicle


title: Hom(Q175) PF-02545920_0.32mpk Striatum Female  rep2

description: C53811_-_1410_Right_striatum_L6.LB10_clipped

value: Female


title: Hom(Q175) PF-02545920_0.32mpk Striatum Female  rep1

description: C53811_-_540_Right_striatum_L8.LB7_clipped


title: WT Vehicle Cortex Male rep4

description: C53811_-_9168_Right_cortex_L5.LB2_clipped


title: WT Vehicle Cortex Female rep4

description: C53811_-_9205_Right_cortex_L6.LB23_clipped


title: Hom(Q175) PF-02545920_1.0mpk Striatum Male rep5

description: C53811_-_9506_Right_striatum_L5.LB25_clipped

value: 1.0 mg/kg


title: WT Vehicle Cortex Female rep3

description: C53811_-_9007_Right_cortex_L1.LB1_clipped


title: WT Vehicle Cortex Female rep2

description: C53811_-_9006_Right_cortex_L1.LB27_clipped


title: Hom(Q175) Vehicle Cortex Female rep5

description: C53811_-_9501_Right_cortex_L7.LB18_clipped


title: Hom(Q175) PF-02545920_1.0mpk Striatum Male rep4

description: C53811_-_9044_Right_striatum_L1.LB23_clipped


title: WT Vehicle Cortex Female rep1

description: C53811_-_8528_Right_cortex_L3.LB25_clipped


title: Hom(Q175) PF-02545920_0.32mpk Striatum Male rep3

description: C53811_-_8540_Right_striatum_L6.LB14_clipped


title: Hom(Q175) Vehicle Cortex Female rep4

description: C53811_-_9247_Right_cortex_L5.LB14_clipped


title: WT Vehicle Cortex Male rep1

description: C53811_-_1179_Right_cortex_L7.LB5_clipped


title: Hom(Q175) Vehicle Cortex Female rep3

description: C53811_-_9170_Right_cortex_L6.LB15_clipped


title: RNA_499_STAT1KO_22

value: 499 STAT1 KO

value: CD45 negative tumor cells


title: Hom(Q175) Vehicle Cortex Female rep2

description: C53811_-_9136_Right_cortex_L7.LB16_clipped


title: Hom(Q175) PF-02545920_1.0mpk Striatum Female rep2

description: C53811_-_1184_Right_striatum_L1.LB18_clipped


title: Hom(Q175) PF-02545920_3.2mpk Cortex Female rep3

description: C53811_-_9516_Right_cortex_L4.LB8_clipped

value: 3.2 mg/kg


title: Hom(Q175) Vehicle Cortex Male rep2

description: C53811_-_2133_Right_cortex_L7.LB20_clipped


title: Hom(Q175) Vehicle Cortex Male rep1

description: C53811_-_1114_Right_cortex_L8.LB21_clipped


title: Hom(Q175) PF-02545920_3.2mpk Cortex Female rep2

description: C53811_-_9123_Right_cortex_L5.LB7_clipped


title: Hom(Q175) PF-02545920_3.2mpk Cortex Female rep5

description: C53811_-_9924_Right_cortex_L8.LB6_clipped


title: Hom(Q175) PF-02545920_3.2mpk Cortex Female rep1

description: C53811_-_5489_Right_cortex_L1.LB5_clipped


title: Hom(Q175) Vehicle Cortex Female rep1

description: C53811_-_1428_Right_cortex_L6.LB19_clipped


title: Hom(Q175) PF-02545920_3.2mpk Cortex Female rep4

description: C53811_-_9657_Right_cortex_L1.LB9_clipped


title: Hom(Q175) PF-02545920_3.2mpk Cortex Male rep3

description: C53811_-_9211_Right_cortex_L7.LB10_clipped


title: Hom(Q175) PF-02545920_3.2mpk Cortex Male rep2

description: C53811_-_9162_Right_cortex_L6.LB11_clipped


title: WT Vehicle Cortex Male rep2

description: C53811_-_9028_Right_cortex_L2.LB3_clipped


title: WT Vehicle Cortex Male rep3

description: C53811_-_9029_Right_cortex_L4.LB4_clipped


title: Hom(Q175) PF-02545920_1.0mpk Cortex Female rep5

description: C53811_-_9915_Right_cortex_L1.LB20_clipped


title: Hom(Q175) PF-02545920_1.0mpk Cortex Male rep3

description: C53811_-_9039_Right_cortex_L8.LB27_clipped


title: Hom(Q175) PF-02545920_1.0mpk Cortex Female rep4

description: C53811_-_9515_Right_cortex_L3.LB23_clipped


title: Hom(Q175) PF-02545920_1.0mpk Cortex Male rep4

description: C53811_-_9044_Right_cortex_L7.LB1_clipped


title: Hom(Q175) PF-02545920_1.0mpk Cortex Female rep3

description: C53811_-_9270_Right_cortex_L6.LB25_clipped


title: Hom(Q175) PF-02545920_1.0mpk Cortex Female rep2

description: C53811_-_1184_Right_cortex_L5.LB21_clipped


title: Hom(Q175) PF-02545920_1.0mpk Cortex Male rep5

description: C53811_-_9506_Right_cortex_L8.LB2_clipped


title: Hom(Q175) PF-02545920_1.0mpk Cortex Male rep1

description: C53811_-_1405_Right_cortex_L7.LB4_clipped


title: Hom(Q175) PF-02545920_1.0mpk Cortex Male rep2

description: C53811_-_2143_Right_cortex_L5.LB3_clipped


title: Hom(Q175) PF-02545920_1.0mpk Cortex Female rep1

description: C53811_-_1105_Right_cortex_L3.LB22_clipped


title: Hom(Q175) PF-02545920_3.2mpk Cortex Male rep4

description: C53811_-_9521_Right_cortex_L2.LB13_clipped


title: Hom(Q175) PF-02545920_0.32mpk Cortex Male rep3

description: C53811_-_8540_Right_cortex_L3.LB18_clipped


title: Hom(Q175) PF-02545920_0.32mpk Cortex Female rep2

description: C53811_-_1410_Right_cortex_L8.LB13_clipped


title: Hom(Q175) PF-02545920 _0.32mpk Cortex Female rep1

description: C53811_-_540_Right_cortex_L1.LB10_clipped


title: Hom(Q175) PF-02545920_0.32mpk Cortex Male rep5

description: C53811_-_9201_Right_cortex_L6.LB14_clipped


title: Hom(Q175) PF-02545920_0.32mpk Cortex Male rep1

description: C53811_-_1103_Right_cortex_L7.LB19_clipped


title: Hom(Q175) PF-02545920_0.32mpk Cortex Male rep4

description: C53811_-_9040_Right_cortex_L6.LB16_clipped


title: Hom(Q175) PF-02545920_0.32mpk Cortex Female rep4

description: C53811_-_9511_Right_cortex_L3.LB12_clipped


title: H3 ENRI

city: Tampere

first: Mikko

last: Oittinen

address: Arvo Ylpön katu 34

department: Tampere Center for Child Health Research

country: Finland

institute: Tampere University

description: chromatin immunoprecipitation of H3

data_processing:
Quality analysis was performed with FastQC. Reads were mapped with Bowtie2.
genome build: mm9

source_name: Small intestine; duodenum

extract_protocol:
Mini-gut organoids were isolated from Matrigel with Cell Recovery Solution (Corning 354253). Cells were cross-linked with formaldehyde and nuclei were isolated, lysed, and sonicated with a Covaris S220 ultrasonicator. The resulting nuclear extract was incubated overnight at 4  C with Dynal Protein G beads pre-incubated with 5µg of anti-H3 antibody. Beads were washed and bound complexes eluted, and cross-links were reversed by heating to 65  C. IP and input DNA were then purified by a treatment with RNAse A, proteinase K, and phenol:chloroform extraction.
Libraries were constructed from IP and input DNA by NEBnext® Ultra™ DNA-library preparation kit for Illumina and subjected to 50 bp single-end read sequencing with Illumina Hiseq 2000.

value: duodenum

tag: primary cell type

value: enterocyte

tag: chip-antibody


title: RNA_499_cas9_3

source_name: sorted 499 resistant cells with cas9

value: 499 with cas9


title: RNA_499_STAT1_KO_3


title: Hom(Q175) PF-02545920_0.32mpk Cortex Female rep3

description: C53811_-_2546_Right_cortex_L1.LB11_clipped

tag: strain

tag: genotype

value: 9 months


title: Hom(Q175) PF-02545920_3.2mpk Cortex Male rep1

description: C53811_-_9026_Right_cortex_L8.LB12_clipped

tag: age

tag: Sex

value: Oral


title: H3 WENRC

description: chromatin immunoprecipitation of H3

value: intestinal stem cell


title: RNA_499_STAT1_KO_1


title: RNA_499_cas9_2


title: RNA_499_cas9_1


title: RNA_B16_IFNy_2

source_name: sorted B16 melanoma cells after chronic IFNy treatment

value: 2 week chronic IFNy treatment before mouse injection


title: RNA_B16_NT_1

source_name: sorted B16 melanoma cells


title: Hom(Q175) PF-02545920_0.32mpk Cortex Female rep5

description: C53811_-_9940_Right_cortex_L5.LB9_clipped

tag: treatment administration route

tag: treatment frequency

value: Once-Daily

value: from 5 weeks to 9 months


title: Hom(Q175) PF-02545920_0.32mpk Cortex Male rep2

description: C53811_-_2302_Right_cortex_L8.LB15_clipped

value: Q175 Homozygous knock-in

value: Male

tag: treatment duration


title: RNA_B16_IFNy_3

value: 3 week chronic IFNy treatment before mouse injection

tag: cell type


title: ATAC_499_NT_3

data_processing:
Library strategy: ATAC-seq
Basecalls performed using Illumina CASAVA software.
Raw reads were trimmed for adaptor sequence using cutadapt v1.9 (parameter -m 30 -O 4)
Reads were then aligned with bowtie2 v2.2.4 to GRCm38/mm10 reference genome (parameter --fr --no-mixed --no-discordant --X 2000)
Reads mapped the forward and reverse strands were shifted +5 and -4 bp respectively.
Non primary alignment,duplicates and QC failed reads were filtered out.
Peaks were called with MACS2 (parameter -f BAMPE --no-model -q 0.01)
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: bed files generated from MACS2 for each sample

source_name: sorted 499 resistant cells

growth_protocol: Mice were injected with tumor cells. On day 15, tumors were harvested and sorted.

extract_protocol:
Nuclei were prepared from sorted cells and chromatin were fragmented and taged with transposes loaded with adaptor.
Taged DNA fragments were PCR amplified.


title: ATAC_499_NT_2


title: ATAC_B16_NT_3


title: ATAC_B16_IFNy_3


title: ATAC_B16_IFNy_2


title: ATAC_B16_NT_2


title: ATAC_B16_NT_1


title: ATAC_499_NT_1


title: ATAC_B16_IFNy_1


title: RNA-seq_33h_rep2

city: Cambridge

first: Juan

middle: R

last: Alvarez-Dominguez

address: 7 Divinity Ave

department: Stem Cell and Regenerative Biology

institute: Harvard University

data_processing:
Ribo-seq reads were quality-filtered with the fastq_quality_trimmer (“-t 20” parameter) tool of the FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/index.html) and clipped to remove 3’ linkers using the fastx_clipper tool, discarding non-clipped reads or reads <25nt after linker clipping (“-l 25 -c” parameters). Reads were then aligned to reference rRNA, tRNA, and mitochondrial DNA sequences using Bowtie v.1.1.1 with default parameters and “--seedlen=23”to remove these RNAs species. Finally, we used fastx_trimmer to remove the first 5’ nucleotide from each read, as it often reflects an untemplated addition during cDNA generation. Pre-processed RFPs were then aligned to a reference transcriptome composed of Ensembl v.67 annotations supplemented with erythroid lncRNA and TUCP annotations (Alvarez-Dominguez et al., 2014) using TopHat v2.0.13 with default parameters and “--min-anchor 5 --segment-length 20 --read-mismatches 1 --no-novel-juncs”. For RNA-seq, reads aligned by Bowtie to rRNA, tRNA, or mitochondrial DNA were discarded. As with Ribo-seq analysis, the first 5’ nucleotide was trimmed from each read using fastx_trimmer, reads were subsequently aligned to a composite reference transcriptome using TopHat.
Genome_build: mm9
Supplementary_files_format_and_content: mapped reads in bigwig

source_name: Erythroid progenitors_RNA-seq_33h

growth_protocol: Erythroid progenitors were purified from E14.5 mouse fetal livers by magnetic-assisted cell sorting (Flygare et al., 2011) and cultured for 48hrs in erythropoietin-containing media to induce terminal proliferation and differentiation (Zhang et al., 2003). Samples were collected at 0, 24, 33, and 48 hours and split for RNA-seq and Ribo-seq analysis.

extract_protocol:
Ribo-seq was conducted following published protocols (Ingolia et al., 2012). 50 million cells were harvested at each differentiation time point and no cycloheximide was used. For RNA-seq, total RNA was isolated using the miRNeasy kit (QIAGEN) according to the manufacturer’s instructions. Ribosomal RNA was depleted from 4ug total RNA using the Ribo-Zero Gold Kit (Epicentre, Madison, WI).
Strand-specific cDNA libraries were prepared using a dUTP marking protocol (Borodina et al., 2011) and sequenced on an Illumina HiSeq2000 platform.

tag: developemental age

tag: tissue

value: fetal liver

value: Erythroid progenitors

tag: cultured in

value: erythropoietin-containing media for 33hrs

tag: molecule subtype

value: total RNA minus rRNA


title: RNA-seq_24h_rep2

source_name: Erythroid progenitors_RNA-seq_24h

value: erythropoietin-containing media for 24hrs


title: RNA-seq_48h_rep2

source_name: Erythroid progenitors_RNA-seq_48h

value: erythropoietin-containing media for 48hrs


title: RNA-seq_33h_rep1


title: Ribo-seq_48h_rep2

data_processing:
library strategy: Ribo-seq
Ribo-seq reads were quality-filtered with the fastq_quality_trimmer (“-t 20” parameter) tool of the FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/index.html) and clipped to remove 3’ linkers using the fastx_clipper tool, discarding non-clipped reads or reads <25nt after linker clipping (“-l 25 -c” parameters). Reads were then aligned to reference rRNA, tRNA, and mitochondrial DNA sequences using Bowtie v.1.1.1 with default parameters and “--seedlen=23”to remove these RNAs species. Finally, we used fastx_trimmer to remove the first 5’ nucleotide from each read, as it often reflects an untemplated addition during cDNA generation. Pre-processed RFPs were then aligned to a reference transcriptome composed of Ensembl v.67 annotations supplemented with erythroid lncRNA and TUCP annotations (Alvarez-Dominguez et al., 2014) using TopHat v2.0.13 with default parameters and “--min-anchor 5 --segment-length 20 --read-mismatches 1 --no-novel-juncs”. For RNA-seq, reads aligned by Bowtie to rRNA, tRNA, or mitochondrial DNA were discarded. As with Ribo-seq analysis, the first 5’ nucleotide was trimmed from each read using fastx_trimmer, reads were subsequently aligned to a composite reference transcriptome using TopHat.
Genome_build: mm9
Supplementary_files_format_and_content: mapped reads in bigwig

source_name: Erythroid progenitors_Ribo-seq_48h

value: ribosome-protected RNA


title: RNA_B16_NT_2

tag: strain/genotype

tag: treatment

value: CD45 negative tumor cells


title: RNA_B16_IFNy_1


title: Ribo-seq_48h_rep1


title: RNA-seq_0h_rep1

source_name: Erythroid progenitors_RNA-seq_0h

value: erythropoietin-containing media for 0hr


title: RNA_B16_NT_3


title: Ribo-seq_33h_rep1

source_name: Erythroid progenitors_Ribo-seq_33h


title: Ribo-seq_24h_rep2

source_name: Erythroid progenitors_Ribo-seq_24h


title: Ribo-seq_24h_rep1


title: Ribo-seq_0h_rep2

source_name: Erythroid progenitors_Ribo-seq_0h


title: Ribo-seq_33h_rep2


title: Ribo-seq_0h_rep1


title: BK007

first: Paolo

last: Guarnieri

state: NY

address: 1130 St. Nicholas Avenue

department: Systems Biology

institute: Columbia University

description: Prerenal #3 Glomeruli

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Reads were then mapped to the mouse reference genome (mm9) using Tophat72 (version 2.0.4) allowing 4 mismatches (--read-mismatches = 4) and a maximum of 10 multiple hits (--max-multihits = 10). The relative expression was calculated using cufflinks73 (version 2.0.2) with default settings. Gene expression levels were normalized by library size and gene length into FPKMs74 and log2 transformed. Counts tables were generated with HTSeq version 0.6.1. Transcripts with 0 counts across all samples were removed and mathematical artifacts (e.g. negative infinites) were replaced with “NA”
Genome_build: mm9
Supplementary_files_format_and_content: Individual csv files contain fpkm values, while the series matrix file (GSE81741_dataMatrix_counts.txt) provides counts calculated using htseq count.

source_name: Kidney

extract_protocol:
Total RNA was isolated from segment-specific laser captured kidney sections or whole kidney homegenates using Ambion RNAqueous® Micro Kit. RNA concentration and integrity for each sample were assessed on RNA 6000 Chips using an Agilent 2100 Bioanalyzer. Poly-A pull-down was used to enrich mRNAs (200ng-1ug per sample, sample RIN was above 8.0)
RNA libraries were prepared for sequencing using Illumina TruSeq® RNA prep kits

tag: condition

value: pAKI

tag: region

value: Glomerulus LCM


title: BK006

description: IR10 #3 Glomeruli

value: iAKI


title: BK005

description: IR10 #2 Glomeruli


title: BK009

description: Prerenal #5 Glomeruli


title: BK002

description: WT #4 Glomeruli

value: Control


title: BK001

description: WT #1 Glomeruli


title: BN050

description: Prerenal #5 Inner medulla LCM

value: ISOM LCM


title: BN049

description: Prerenal #5 cortex

value: Cortex LCM


title: RNA-seq_0h_rep2


title: BN052

description: Prerenal #5 whole (contalateral)

value: Whole Kidney


title: RNA-seq_48h_rep1


title: BN048

description: Prerenal #4 whole (contalateral)


title: BN045

description: Prerenal #4 cortex


title: RNA-seq_24h_rep1


title: BN047

description: Prerenal #4 outer medulla LCM

value: OSOM LCM


title: BN044

description: WT #5 whole (contalateral)


title: BN042

description: WT #5 Inner medulla LCM


title: BN043

description: WT #5 outer medulla LCM


title: BN046

description: Prerenal #4 Inner medulla LCM


title: BN041

description: WT #5 cortex


title: BN039

description: WT #4 outer medulla LCM


title: BN034

description: IR10 #3 Inner medulla LCM


title: BN037

description: WT #4 cortex


title: BN036

description: IR10 #3 whole (contalateral)


title: BN038

description: WT #4 Inner medulla LCM


title: BN040

description: WT #4 whole (contalateral)


title: BN033

description: IR10 #3 cortex


title: BN035

description: IR10 #3 outer medulla LCM


title: BN032

description: IR10 #2 whole (contalateral)


title: BN026

description: IR10 #1 Inner medulla LCM


title: BN030

description: IR10 #2 Inner medulla LCM


title: BN028

description: IR10 #1 whole (contalateral)


title: BN029

description: IR10 #2 cortex


title: BN031

description: IR10 #2 outer medulla LCM


title: BN024

description: Prerenal #3 whole (contalateral)


title: BN021

description: Prerenal #3 cortex


title: BN023

description: Prerenal #3 outer medulla LCM


title: BN020

description: Prerenal #2 whole (contalateral)


title: BN019

description: Prerenal #2 outer medulla LCM


title: BN017

description: Prerenal #2 cortex


title: BN022

description: Prerenal #3 Inner medulla LCM


title: BN018

description: Prerenal #2 Inner medulla LCM


title: BN016

description: Prerenal #1 whole (contalateral)


title: BN014

description: Prerenal #1 Inner medulla LCM


title: BN012

description: WT #3 whole (contalateral)


title: BN015

description: Prerenal #1 outer medulla LCM


title: BN013

description: Prerenal #1 cortex


title: BN011

description: WT #3 outer medulla LCM


title: MII, H33K27R, Rep2

city: Bethesda

first: Bertram

middle: J

last: Canagarajah

state: Maryland

address: 9000 Rockville Pike

department: NIDDK

institute: NIH

data_processing:
raw reads quality trimmed and adapters and polyA removed with cutadapt v1.9.1 using --quailty-cutoff=20
aligned to mm10 with TopHat v2.1.0 with default parameters
multiply-mapped reads removed with samtools v1.3 using -q 20
Reads counted in exons of UCSC annotation using featureCounts with default settings
Genome_build: mm10
Supplementary_files_format_and_content: counts table from featureCounts as tab-delimited text file

source_name: egg

extract_protocol:
HISRainbow;Figla-iCre female mice were super-ovulated to isolate MII eggs expressing H3.3-eGFP, H3.3R26K-eCFP, or H3.3K27R-mCherry which were identified by confocal microscopy.
The SMARTer Ultra Low RNA Kit (Clontech) was used for cDNA synthesis and Nextera DNA Sample Preparation Kit (Illumina) was used for library preparation according to the manufacturers’ protocols. Two biological replicates were prepared for each group and samples were sequenced on Illumina HiSeq 2000 as single-end, 50-bp reads.

tag: mouse line

value: HISRainbow;Figla-iCre


title: MII, H33R26K, Rep1


title: MII, H33R26K, Rep2


title: BN009

description: WT #3 cortex


title: MII, H33, Rep2


title: BN010

description: WT #3 Inner medulla LCM


title: BN027

description: IR10 #1 outer medulla LCM


title: MII, H33, Rep1


title: BN025

description: IR10 #1 cortex


title: H3K27me3 ENRI

description: chromatin immunoprecipitation of H3K27me3

data_processing:
Quality analysis was performed with FastQC. Reads were mapped with Bowtie2. Further data analysis was performed with HOMER.
Genome_build: mm9
Supplementary_files_format_and_content: Tab delimited text files containing either ChIP-Seq peaks or GRO-Seq nascent RNA RPKM values from WENRC and ENRI samples.

growth_protocol: To model intestinal crypt-villus axis organoids were grown in Matrigel in the presence of Wnt3A, EGF, Noggin, R-spondin and CHIR-99021 (WENRC stem cell media) and differentiation was induced by omitting Wnt3A and CHIR-99021 and media was supplemented with IWP-2 (ENRI enterocyte differentiation media).

extract_protocol: Mini-gut organoids were isolated from Matrigel with Cell Recovery Solution (Corning 354253). Cells were cross-linked with formaldehyde and nuclei were isolated, lysed, and sonicated with a Covaris S220 ultrasonicator. The resulting nuclear extract was incubated overnight at 4  C with Dynal Protein G beads pre-incubated with 5µg of H3K27me3 (ab6002) antibody. Beads were washed and bound complexes eluted, and cross-links were reversed by heating to 65  C. IP and input DNA were then purified by a treatment with RNAse A, proteinase K, and phenol:chloroform extraction. Libraries were constructed from IP and input DNA by NEBnext® Ultra™ DNA-library preparation kit for Illumina and subjected to 50 bp single-end read sequencing with Illumina Hiseq 2000.

value: duodenum

tag: primary cell type

value: enterocyte

tag: chip-antibody


title: GRO-Seq mouse2 ENRI

description:
global run-on-sequencing
GRO-Seq_WENRC_ENRI_RPKM.txt

data_processing:
Read quality was observed with FastQC and poor quality reads were removed using FastX toolkit. Data was mapped with Bowtie. Further data analysis was performed using HOMER 4.3 and edgeR treating the mouse1 and mouse2 samples as biological replicates.
Genome_build: mm9
Supplementary_files_format_and_content: Tab delimited text files containing either ChIP-Seq peaks or GRO-Seq nascent RNA RPKM values from WENRC and ENRI samples.

extract_protocol: Nuclei were extracted from 3 million cells and were suspended to a final volume of 80-200 µl of freezing buffer. The RNA was extracted using Trizol, fragmented 13 mins in 70°C using RNA Fragmentation Reagents (Life Technologies) and purified by running through RNase-free P-30 column (Bio-Rad, Hercules, CA, USA). The RNA was dephosphorylated with PNK for 2 hours (New England Biolabs, Ipswich, MA, USA) followed by heat-inactivation. Dephosphorylation reactions were purified using 65 µl of blocked anti-BrdU bead slurry (SantaCruz Biotech, Santa Cruz, CA, USA). After binding for 1 h in RT, the beads were washed. The RNA was eluted followed by ethanol precipitation overnight. All buffers were supplemented with SuperAse In (2 µl/10ml; Life Technologies). The libraries were amplified for 14 cycles and the final product of 190-350bp was extracted from on 10% Novex TBE gel (Life Technologies) and gel purified and cleaned using ChIP DNA clean & Concentrator Kit (Zymo Research Corporation, Irvine, CA, USA), quantified using the Qubit fluorometer and sequenced using Illumina HiSeq 2000.


title: GRO-Seq mouse2 WENRC

value: intestinal stem cell


title: GRO-Seq mouse1 WENRC


title: GRO-Seq mouse1 ENRI


title: 1772096175_C12

city: Stockholm

first: Sten

last: Linnarsson

address: Scheeles väg 1

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

data_processing:
Read processing was performed as described (Islam et al., Nat Methods. 2014 Feb;11(2):163-6), except that we removed any RNA molecule (i.e. Unique Molecular Identifier) supported only by a single read ("singleton molecules"). This removed a large number of false positive molecules, artefacts that can arise by sequencing error, PCR-induced mutations or translocations and cross-contamination.
The first 6 bases of each read represent the random Unique Molecular Identifier used for molecule counting. After follows three or more Gs, stemming from the template switching at the mRNA 5' end during first strand cDNA sythesis.
Genome_build: UCSC mm10
Supplementary_files_format_and_content: Tab-delimited file of mRNA molecule counts for each gene and cell. Cells with less than 1500 molecules have been removed from this file.

source_name: hypothalamus

growth_protocol: C57BL/6N mice were housed conventionally (12/12-h light cycle, 55% humidity).

extract_protocol:
Mice were deeply anesthetized (5% isoflurane) and transcardially perfused with 40 ml ice-cold pre-oxygenated (95% O2/5% CO2) cutting solution containing (in mM): 90 NaCl, 26 NaHCO3, 2.5 KCl, 1.2 NaH2PO4, 10 HEPES-NaOH, 5 Na-ascorbate, 5 Na-pyruvate, 0.5 CaCl2, 8 MgSO4 and 20 glucose. A central column of the mouse hypothalamus spanning the preoptic area-Arc (rostrocaudal axis), paraventricular nucleus (dorsal) and the ventrolateral hypothalamic area (lateral) was microdissected from serial 300-micrometer-thick coronal slices under microscopy guidance and dissociated using the Papain Dissociation System (Worthington). Isolated single cells were concentrated by centrifugation to a density of 600-1,000 cells/?microlitre. After mixing C1 suspension reagent (4 microlitre; "C1 reagents", Fluidigm Inc.) to the cell suspension (7 microlitre), this mixture was loaded into a C1-AutoPrep IFC microfluidic chip (Fluidigm Inc.)
Lysis mix, RT mix and PCR mix (described in Islam et al., Nat Methods. 2014 Feb;11(2):163-6) were added to the chip. The plate was placed in the Fluidigm C1 instrument and the 'mRNA Seq: RT + Amp (1772x/1773x)' script was executed, and included lysis, reverse transcription and 21 cycles of PCR. The amplified cDNA was harvested in a total of 13 μL C1 Harvesting Reagent. Amplified cDNA was simultaneously fragmented and barcoded by tagmentation using Tn5 DNA transposase to transfer adaptors to the target DNA as described (Ibid.). 100 µl Dynabeads MyOne Streptavidin C1 beads (Invitrogen) were washed in 2× BWT (10 mM Tris-HCl, pH 7.5, 1 mM EDTA, 2 M NaCl, 0.02% Tween-20) and resuspended in 2 ml 2× BWT. Twenty microliters of beads were added to each well and incubated at room temperature for 15 min. All fractions were pooled, the beads were immobilized and the supernatant removed. The beads were resuspended in 100 μL TNT (20 mM Tris, pH 7.5, 50 mM NaCl, 0.02% Tween), washed in 100 μL Qiagen Qiaquick PB, and twice in 100 μL TNT. The beads were resuspended in 100 μL restriction mix (1× NEB CutSmart, 0.4 U/μL PvuI-HF enzyme), designed to cleave 3′ fragments carrying a PvuI recognition site. The mix was incubated for 1 h at 37 °C, then washed three times in TNT. Finally, to elute DNA, beads were resuspend in 30 µL ddH2O and incubated 10 minutes at 70°C. Beads were then immediately bound to magnet and the supernatant was collected. To remove short fragments,  Ampure beads (Beckman Coulter) were used at 1.8× volume and eluted in 30 µL.

treatment_protocol: Formalin stress was induced by injection of 4% PFA into the left paw

tag: strain

tag: age (days postnatal)

value: M

tag: acute stress

value: Y

tag: cell diameter

tag: total molecules

tag: level1 class

value: oligos


title: MII, H33K27R, Rep1

tag: age

tag: genotype


title: 1772096175_E10

tag: Sex

value: astrocytes


title: 1772096175_C05

value: endothelial


title: 1772096175_C04


title: 1772096175_C07


title: 1772096175_F04

value: neurons

tag: level2 class (neurons only)

value: Vglut2;Gad1-low;Crh-low/- (VMH)


title: 1772096175_C01


title: 1772096175_B12


title: 1772096175_A06


title: 1772096175_A09

value: Galanin


title: 1772096173_H05


title: 1772096173_H08


title: 1772096175_B01


title: 1772096173_G05

value: ependymal


title: H3K27me3 WENRC

tag: tissue


title: 1772096173_H11


title: 1772096173_F12


title: input DNA ENRI


title: input DNA WENRC


title: 1772096173_F10


title: 1772096173_F02


title: 1772096173_E12


title: 1772096173_E09

value: Sst-medium;Cartpt


title: 1772096173_F11


title: 1772096175_B11


title: 1772096175_D04


title: 1772096173_E08


title: 1772096173_C12


title: 1772096173_C09


title: 1772096173_D04


title: 1772096173_D10


title: 1772096173_C04


title: 1772096173_E05

value: vsm


title: 1772096173_B12

value: microglia


title: 1772096173_C02


title: 1772096173_B08


title: 1772096173_B10


title: 1772096173_B03


title: 1772096173_B01

value: Avp-medium


title: 1772096173_A09


title: 1772096173_A06

value: uc


title: 1772096172_G11


title: 1772096172_H08


title: 1772096173_A05


title: 1772096173_B06


title: 1772096172_H01


title: 1772096172_H04

value: Trh-medium


title: 1772096172_G01


title: 1772096172_G08


title: 1772096172_F08


title: 1772096172_F11


title: 1772096172_E11


title: 1772096173_D08


title: 1772096172_E10


title: 1772096172_E12

value: Crh+/-;GABA;Pgr15l (PVH-PVH-galo)


title: 1772096172_E03


title: 1772096173_F06


title: 1772096172_D07


title: 1772096172_E06


title: 1772096172_D02


title: 1772096172_E09


title: 1772096172_C09


title: 1772096172_C10


title: 1772096172_D06


title: 1772096172_C06


title: 1772096172_C04


title: 1772096172_C03


title: 1772096172_B06


title: 1772096172_B09


title: 1772096172_B03


title: 1772096172_B02


title: 1772096172_B12


title: 1772096172_B11


title: 1772096172_A10


title: 1772096172_A09


title: 1772096172_A02


title: 1772096172_A04


title: 1772096172_A08


title: 1772096171_H10


title: 1772096171_H12


title: 1772096171_H11


title: 1772096171_H02


title: 1772096171_G10


title: 1772096171_G05


title: 1772096171_G04


title: 1772096171_F12


title: 1772096172_C08


title: 1772096171_F10

value: Pomc+/- (ARH)


title: 1772096171_F09

value: M


title: 1772096171_F07

value: Y


title: 1772096171_F04

value: oligos


title: 1772096171_F05

value: astrocytes


title: 1772096171_E12


title: 1772096171_E09


title: 1772096171_D06


title: 1772096171_E02


title: 1772096171_E01


title: 1772096171_D11


title: 1772096171_D03


title: 1772096171_E08


title: 1772096171_C11


title: 1772096171_C12


title: 1772096171_C07


title: 1772096171_B12


title: 1772096171_G06


title: 1772096171_C02

value: Crh+/-;Lhx6;GABA (BST;MPO)


title: 1772096171_B05


title: 1772096171_B03

value: endothelial


title: 1772096171_B04

value: neurons

value: Trh-low


title: 1772096171_B11

value: ependymal


title: 1772096171_B01


title: 1772096171_A10

value: Hmit+/-


title: 1772096171_A11


title: 1772096171_A06


title: 1772096171_E11


title: 1772096171_A08


title: 1772096171_A04


title: 1772096171_A02


title: 1772096168_H04


title: 1772096168_H10


title: 1772096168_G10


title: 1772096168_H06


title: BN051

description: Prerenal #5 Outer medulla LCM

value: pAKI

value: OSOM LCM


title: 1772096168_G07


title: 1772096168_G08

value: vsm


title: 1772096168_G06


title: 1772096168_F12


title: 1772096168_F09

value: Sst-medium;Cartpt


title: 1772096168_G05


title: 1772096168_F11


title: 1772096168_F06


title: 1772096168_F03

value: uc


title: 1772096168_F02

value: Avp-medium


title: 1772096168_F04


title: 1772096168_E12


title: 1772096168_E11


title: 1772096168_E08

value: Qrfp


title: 1772096168_E06

value: M


title: 1772096168_E04

value: Y


title: 1772096168_E02


title: 1772096168_D10


title: 1772096168_D08

value: oligos


title: 1772096168_E01

value: Pomc+/- (ARH)


title: 1772096168_D07


title: 1772096168_D05

value: Calcr-high;VMAT+/-;Lhx1 (Sch)


title: 1772096168_D04


title: 1772096168_D02

value: astrocytes


title: 1772096168_C12


title: 1772096168_D03

value: endothelial


title: 1772096168_C11


title: 1772096168_G02


title: 1772096168_C07


title: 1772096168_B12


title: 1772096168_C02

value: neurons

value: Crh+/-;Gal-low (PVH)


title: 1772096168_C03


title: 1772096168_B10


title: 1772096168_E10


title: 1772096168_B07

value: Crh+/-;GABA;Pgr15l (PVH-PVH-galo)


title: 1772096168_B08


title: 1772096168_B05


title: 1772096168_A07


title: 1772096168_A12


title: 1772096168_A11


title: 1772096168_A04


title: 1772096168_A06

value: Hmit+/-


title: 1772096168_A03


title: 1772096165_H11


title: 1772096165_H08

value: ependymal


title: 1772096165_H02


title: 1772096165_G09


title: 1772096165_G04


title: 1772096165_F04


title: 1772096165_F01


title: 1772096168_C05


title: 1772096165_F02


title: 1772096165_E09


title: 1772096165_G08


title: 1772096165_E11

value: vsm


title: 1772096165_E07


title: 1772096168_B02


title: 1772096165_E06


title: 1772096165_D06


title: 1772096165_E04


title: 1772096165_C10


title: 1772096165_E08


title: 1772096165_C12


title: 1772096165_D05


title: 1772096165_C03


title: 1772096165_B11


title: 1772096165_C01


title: 1772096165_B05


title: 1772096165_B03


title: 1772096165_G02


title: 1772096165_B01

value: Vglut2;Gad1-low;Crh-low/- (VMH)


title: 1772096165_A09


title: 1772096165_A10


title: 1772096165_B09


title: 1772096165_A07

value: Avp-high;Oxt-low


title: 1772096162_H02


title: 1772096162_H09


title: 1772096165_A03


title: 1772096162_H06

value: Adcyap1;Tac1 (VMH)


title: 1772096165_A01


title: 1772096165_A04


title: 1772096165_D09


title: 1772096165_C11


title: 1772096165_C04


title: 1772096162_G11


title: 1772096162_G09


title: 1772096162_G05


title: 1772096162_G08


title: 1772096162_G03

value: uc


title: 1772096162_H01

value: M


title: 1772096162_G04

value: Y


title: 1772096162_G02

value: Hcrt


title: 1772096162_E12

value: oligos


title: 1772096162_G01


title: 1772096162_F12


title: 1772096162_E11


title: 1772096162_E01


title: 1772096162_H12


title: 1772096162_E06


title: 1772096162_E04


title: 1772096162_E09


title: 1772096162_D10


title: 1772096162_C09

value: Pomc+/- (ARH)


title: 1772096162_C07


title: 1772096162_D11


title: 1772096162_C08


title: 1772096162_D05


title: 1772096165_A05


title: 1772096162_D04

value: Per2;circadian (SCH)


title: 1772096162_D12


title: 1772096162_C02

value: Vglut2;Prmt8;Ugdh (VMH)


title: 1772096162_E07

value: neurons


title: 1772096162_D03


title: 1772096162_C01


title: 1772096162_C10


title: 1772096162_B12


title: 1772096162_E02


title: 1772096162_B06


title: 1772096162_F11

value: astrocytes


title: 1772096162_B04


title: 1772096162_C03


title: 1772096162_C05


title: 1772096162_D06


title: 1772096162_D07

value: Vip;Grp+/-;circadian (SCH)


title: 1772096162_D08


title: 1772096162_B03


title: 1772096162_B01


title: 1772096162_A05


title: 1772096162_A08


title: 1772096162_A02


title: 1772096161_E11

value: N


title: 1772096161_D06


title: 1772096161_D11


title: 1772096161_E02


title: 1772096161_C10

value: ependymal


title: 1772096161_C08


title: 1772096158_H11


title: 1772096161_C06


title: 1772096161_A05


title: 1772096158_G09

value: Trh-low


title: 1772096161_B03


title: 1772096161_B09

value: Crh+/-;GABA;Pgr15l (PVH-PVH-galo)


title: 1772096158_H07


title: 1772096161_B11


title: 1772096161_C02


title: 1772096161_C05


title: 1772096161_B12

value: Hmit+/-


title: 1772096161_A03

value: Crh+/-;Lhx6;GABA (BST;MPO)


title: 1772096161_C03


title: 1772096158_G07


title: 1772096162_B02

value: uc


title: 1772096158_G06

value: M


title: 1772096158_F07


title: 1772096158_E10


title: 1772096161_D09


title: 1772096158_F06

value: Sst low-medium


title: 1772096161_B02

value: GABA 2


title: 1772096158_E08

value: oligos


title: 1772096158_E09


title: 1772096158_D07

value: Gad-low;Gnrh-/+


title: 1772096158_C03


title: 1772096158_C06

value: GABA 1


title: 1772096158_B12


title: 1772096158_B10

value: Sst-medium;Cartpt


title: 1772096158_B05


title: 1772096158_B01

value: neurons


title: 1772096158_B04


title: 1772096158_A11


title: 1772096158_A07


title: 1772096145_G09

value: Y


title: 1772096145_H12

value: vsm


title: 1772096145_H11

value: Vglut2;Gad1-low;Crh-low/- (VMH)


title: 1772096145_F12

value: Calcr-high;VMAT+/-;Lhx1 (Sch)


title: 1772096145_F06

value: endothelial


title: 1772096145_E12


title: 1772096145_F10

value: astrocytes


title: 1772096145_E10


title: 1772096145_F09


title: 1772096145_G05


title: 1772096145_F11

value: Galanin


title: 1772096145_E07


title: 1772096145_E09


title: 1772096145_F04

value: Crh+/-;GABA;Pgr15l (PVH-PVH-galo)


title: 1772096145_E04

value: Hmit+/-


title: 1772096158_C02

value: M

value: N

value: Crh+/-;Lhx6;GABA (BST;MPO)


title: 1772096145_D01

value: oligos


title: 1772096145_C11


title: 1772096145_D03


title: 1772096145_D04


title: 1772096145_C05

value: Avp-medium


title: 1772096145_D09

value: ependymal


title: 1772096145_B05


title: 1772096145_A11


title: 1772096145_A10


title: 1772096145_B02


title: 1772096145_A06

value: Oxt;Avp-medium;Th+/-;PDYN+/


title: 1772096145_A08

value: neurons


title: 1772096144_G03

value: Y


title: 1772096144_H11


title: 1772096145_A02


title: 1772096145_A05

value: vsm


title: 1772096145_A01


title: 1772096145_A04


title: 1772096158_A09

value: uc


title: 1772096145_C10


title: 1772096144_G11

value: microglia


title: 1772096144_F10

value: endothelial


title: 1772096144_E09


title: 1772096144_H07


title: 1772096144_E08


title: 1772096145_C12


title: 1772096144_E12


title: 1772096144_D10


title: 1772096144_D12


title: 1772096144_F09

value: Vip;Grp+/-;circadian (SCH)


title: 1772096144_E02


title: 1772096144_E04


title: 1772096144_E01

value: astrocytes


title: 1772096145_A12


title: 1772096144_D09


title: 1772096145_A07


title: 1772096144_H06


title: 1772096144_D04


title: 1772096144_F04


title: 1772096144_C12


title: 1772096144_C11


title: 1772096144_C08


title: 1772096144_B05

value: Oxt;Avp-low


title: 1772096144_C03


title: 1772096144_C07


title: 1772096144_C05


title: 1772096144_B03


title: 1772096144_B04


title: 1772096144_A07

value: Vglut2;Gpr149 (PVH;VMH)


title: 1772096144_A11

value: M

value: Vglut2;Gad1-low;Crh-low/- (VMH)


title: 1772096144_B01


title: 1772096144_A04


title: 1772096144_A05


title: 1772096141_G10

value: F

value: N


title: 1772096144_A02


title: 1772096144_A03


title: 1772096141_G08


title: 1772096144_A08


title: 1772096144_C02

value: Vglut2 A


title: 1772096141_H12

value: ependymal


title: 1772096141_H04


title: 1772096144_D08


title: 1772096141_G09

value: oligos


title: 1772096141_G05


title: 1772096141_F08


title: 1772096141_F07


title: 1772096141_F05


title: 1772096141_G03


title: 1772096141_F10


title: 1772096141_F09


title: 1772096141_F02

value: neurons

value: Hmit+/-


title: 1772096141_F04

value: Crh+/-;GABA;Pgr15l (PVH-PVH-galo)


title: 1772096141_E08


title: 1772096141_E06


title: 1772096141_E10


title: 1772096141_E03


title: 1772096141_E05


title: 1772096141_E02


title: 1772096141_D12


title: 1772096141_E01


title: 1772096141_E09


title: 1772096141_D07


title: 1772096141_D10


title: 1772096141_D02


title: 1772096141_D03


title: 1772096141_C10


title: 1772096141_D01


title: 1772096141_C06


title: 1772096141_D08


title: 1772096141_C04


title: 1772096141_C01


title: 1772096141_C03


title: 1772096141_B05


title: 1772096141_B12


title: 1772096141_A11


title: 1772096141_B07


title: 1772096141_A04


title: 1772096141_A08

value: Vglut2;Prmt8;Ugdh (VMH)


title: 1772096141_B10


title: 1772096141_A05


title: 1772096141_B04


title: 1772096141_A02


title: 1772096141_B01


title: 1772096140_H05


title: 1772096141_A01


title: 1772096140_G11

value: uc


title: 1772096140_H11

value: endothelial


title: 1772096141_A03


title: 1772096140_G05


title: 1772096140_G04


title: 1772096140_G06


title: 1772096140_H06


title: 1772096141_C09


title: 1772096140_G03


title: 1772096140_F10


title: 1772096140_F08


title: 1772096140_F04


title: 1772096140_F05

value: Per2;circadian (SCH)


title: 1772096140_E11


title: 1772096141_C02


title: 1772096140_F11


title: 1772096140_G12


title: 1772096140_F12

value: astrocytes


title: 1772096141_B06


title: 1772096140_D10


title: 1772096140_D04


title: 1772096140_D11


title: 1772096140_C12


title: 1772096140_D12


title: 1772096140_A08


title: 1772096140_C06


title: 1772096140_F02


title: 1772096140_C11


title: 1772096140_E04