title: frozen_510f

city: Baltimore

first: Yuji

address: 660 W. Redwood Street

institute: University of Maryland

data_processing:
Blood was drawn into sodium heparin tubes (APP Pharmaceuticals, NDC 63323-540-11); CD4+ and B cells were isolated from whole blood using anti-CD4/B microbeads (Miltenyi Biotec) and MS column purification as per the manufacturer’s instructions. A small portion of the cell isolate was set aside for flow cytometry using anti CD3 APC-H7 and anti CD4/B PE-Cy7 (BD PharMingen) to assess purity. Isolated cells were re-suspended at 1 million/ml in RPMI containing 10 % FBS and either immediately lysed in 0.7 ml QIAzol lysis reagent (Qiagen) or incubated for 4 h at 37 °C with 25 μl/ml anti-CD3/antiCD28 Human T-Activator Dynabeads (Invitrogen) prior to lysis. Lysates were stored at −80 °C until processing for RNAseq.
RNA integrity values of  ≥7.0 by Agilent Bioanalyzer (Santa Clara, CA) were processed by the Mayo Clinic Medical Genome Facility Gene Expression Core into TruSeq libraries according to the manufacturer’s instructions (RNA Prep Kit v2, Illumina, San Diego, CA) and published elsewhere [25]. Paired-end DNA adaptors (Illumina) with a single “T” base overhang at the 3’end were immediately ligated to the “A-tailed” cDNA population. Unique indexes, included in the standard TruSeq Kits (12-Set A and 12-Set B), were incorporated at the adaptor ligation step for multiplex sample loading on the flow cells. Libraries (8–10 pM) were loaded onto paired-end flow cells to generate cluster densities of 700,000/mm2 following Illumina’s standard protocol for cBot and cBot paired-end cluster kit version 3. The flow cells were sequenced as 51 X 2 paired-end reads on an Illumina HiSeq 2000 using TruSeq SBS sequencing kit version 3 and HCS v2.0.12 data collection software. Base-calling was performed using RTA version 1.17.21.3.
All biological samples were sequenced using Illumina HiSeq™ 2000 platform (Illumina) with 50-bp pair-end sequencing protocol in the Mayo DNA Sequencing Core Facility. Raw RNA-seq reads from each RNA-seq library were assessed for duplication rate and gene coverage using FastQC.
Raw RNA-seq reads were aligned to the human genome assembly (GRCh38) for per sample using the Ensembl annotation (Homo_sapiens.GRCh38.84.gtf) by the HISAT2 (Version 2.0.4)
The quality control of RNA-seq was conducted and gene counts were computed by the Qualimap (Version 2.2) with the Ensembl annotation (Homo_sapiens.GRCh38.84.gtf). The results of the quality control based on the Qualimap were assembled using the MultiQC
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text files of gene count values for each Sample

source_name: CD4+ PBL

extract_protocol:
Participant recruitment and blood sample collection were conducted using protocols approval by the Mayo Clinic Institutional Review Board (IRB#12-002580 and IRB#13-002293).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: CD4+ T cell

tag: tumor stage

value: healthy


title: zh11_moderate drought_2_input

status: Public on Feb 09 2019

type: SRA

city: Wuhan

first: Ma

last: Siqi

address: No.1,Shizishan Street

country: China

institute: Huazhong Agricultural Uinveristy

library_source: genomic

data_processing:
For ChIP-seq, the reads were filtered by FASTP and mapped to the rice genome (MSU RGAP, release 7) using Bowtie 2 (version 2.3.4). And the peak calling was performed using MACS2 software (version 2.1.1) with the default parameters. Genes (including gene body and the 3-kb upstream and 3-kb downstream regions) overlapping with the peaks were considered to have the H2Bub1 occupancy. The differential modification of H2Bub1 was determined with a standard of Fold change ≥2 and P-value< 0.05. Gene Ontology (GO) analysis was performed on an online platform named BMKClould (http://www.biocloud.net), and the significance threshold was set at a P-value of 0.001.
For RNA-seq, sequence reads were filtered by FASTP and mapped to the rice genome (MSU RGAP, release 7) using HISAT2 (version 2.0.5) with default parameters. Differentially expressed genes, which were defined with an expression change fold ≥ 2 with P < 0.05, were analyzed using DESeq2 (version 1.20.0).
Genome_build: RGAP 7.0

molecule: genomic DNA

organism: Oryza sativa

source_name: zhonghua11（Oryza sativa）

growth_protocol: Seedlings were grown in sand/paddy (1:3) soil under natural conditions (14 h sun light/ 10 h dark) at July in Wuhan area. Seedlings at the four-leaf stages were harvested and frozen in liquid nitrogen for RNA isolation.

extract_protocol: For The ChIP-Seq, 4 ng DNA were used to construct sequencing libraries following the protocol of TruSeq ChIP Library Preparation Kit (Illumina); For each sample, mRNA purified from 10 μg total RNA was used for constructing sequencing libraries with the TruSeq RNA Sample Preparation Kit (Illumina).

treatment_protocol: To define the moderate and severe drought stresses treatment, rice plants at 4-leaf stage growing in the paddy soil from natural rice field were subjected to progressively (slowly developed) drought stress with the soil water content monitored. It was regarded as moderate drought stress when the relative soil water content was about 20% and severe drought stress when the relative soil water content was about 10%. The relative soil water content was calculated as followings: 100% × (the weight of soil after stress – the weight of air-dried soil) / the weight of soil after stress.

tag: development stage

tag: treatment

value: moderate drought treatment

tag: antibody


title: frozen_507

last: Zhang

state: MD

country: USA

library_source: transcriptomic

molecule: polyA RNA

organism: Homo sapiens


title: frozen_507f


title: frozen_506


title: frozen_506f


title: frozen_501


title: zh11_normal_2_input

value: normal


title: frozen_501f


title: time_110FR


title: frozen_510


title: BPA treated Islet,  biological rep2

type: RNA

city: Sevilla

first: Abdelkrim

last: Hmadcha

address: Avda Américo Vespucio 24, Parque Científico y Tecnológico Cartuja

department: Regeneration and Cell Therapy

country: Spain

institute: CABIMER

description:
Gene expression data from islets (OF1 male mice of 10 weeks treated with PBA)
BPA2

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hours at 45ºC on GeneChip® Mouse Genome 420 2.0 Array. GeneChips were washed and stained in the GeneChip® Fluidics Station 450 according to GeneChip® Expression AnalysisTechnical Manual, Affymetrix.

scan_protocol: Microarrays were scanned using GeneChip® Scanner 3000 7G.

data_processing:
The data were realized with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings from GeneChip® Operating System 1.4.0.036 and global scaling as normalization method.
The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Pancreatic Islets from mouse treated with 1nM BPA during 48 hrs

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA One-Cycle Target Labeling Assays (GeneChip® Expression AnalysisTechnical Manual, Affymetrix, 2004).

growth_protocol: Islets were washed twice with PBS 1X and placed on ice and total RNA was extracted with the Rneasy kit protocol (Qiagen).

extract_protocol: Rneasy mini kit (Qiagen) of total RNA was performed according to the manufacturer's instructions

treatment_protocol: 2 days in vivo treatment with or without BPA 100 μg/kg/day.

tag: strain

tag: agent

value: BPA

tag: tissue

value: pancreatic islets


title: Islet control,  biological rep2

description:
Gene expression data from islets (Control OF1 male mice of 10 weeks of age)
Control2

source_name: Pancreatic Islets from control mouse

value: control


title: 3000 ppm epsilon-momfluorothrin for 2 weeks, biological rep2

city: Osaka

first: Ayako

last: Ohara

address: 1-98, Kasugade-naka 3-chome, Konohana-ku

country: Japan

institute: Sumitomo Chemical Co., Ltd.

description: Gene expression data from liver of rats fed diets containing 5000 ppm epsilon-momfluorothrin for 2 weeks

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip Rat Genome 230 2.0 Arrays. GeneChips were washed and stained with GeneChip Hybridization, Wash and Stain Kit (Affymetrix).

scan_protocol: GeneChips were scanned with a GeneChip Scanner 3000 (Affymetrix) and the image files were obtained.

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

organism: Rattus norvegicus

label_protocol: Biotin-labeled cRNA were prepared from 5 ug of total RNA using GeneChip IVT Labeling Kit (Affymetrix) following the manufacturer's protocol.

growth_protocol: BrlHan:WIST@Jcl(GALAS) male rats aged 4 weeks were purchased, quarantined for 1 weeks and maintained at 22 - 26°C and a relative humidity range of 40 - 70% with frequent ventilation. A powdered diet and water were provided ad libitum.

extract_protocol: The livers were stored in RNAlater RNA Stabilization Reagent (Qiagen, Hilden, Germany) at –20°C. Total RNA samples were extracted from liver using RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions.

treatment_protocol: Animals were fed diets containing 0 (control) and 3000 ppm epsilon-momfluorothrin for periods of 2 weeks.

tag: gender

value: male

value: liver

tag: age

value: age of 7 weeks

tag: diet


title: 3000 ppm epsilon-momfluorothrin for 2 weeks, biological rep1

source_name: liver of rats fed diets containing 5000 ppm epsilon-momfluorothrin for 2 weeks


title: Islet control,  biological rep3

description:
Gene expression data from islets (Control OF1 male mice of 10 weeks of age)
Control3


title: 0 (control) for 2 weeks, biological rep2

description: Gene expression data from liver of rats fed diets containing 0 (control) ppm chemical for 2 weeks

value: 0 (control) ppm chemical for 2 weeks


title: time_109FR


title: BPA treated Islet,  biological rep1

description:
Gene expression data from islets (OF1 male mice of 10 weeks treated with PBA)
BPA1


title: muscle from S14_postexercise_ 220 min_female_0

city: Stockholm

first: Hakan

middle: Claes

last: Rundqvist

state: Huddinge

address: Alfred Nobels ale 8

department: Department of Laboratory Medicine

country: Sweden

institute: Karolinska institutet

hyb_protocol: cDNA was fragmented, biotin-labeled and hybridized to the Human Gene 1.0 ST. Arrays were hybridized for 16 hours at 45°C in a Gene Chip Oven 640 (Affymetrix) followed by washing and staining using the Gene Chip Fluidics Station 450 according to the protocol described in WT Sense Target Labeling Assay Manual

scan_protocol: Scanning was carried out using the Affymetrix Gene Chip Scanner 3000 7G

data_processing: Raw intensity data (CEL files) were processed by using Affymetrix Expression Console Software (v.1.0). Background correction (PM-6CBG), global median normalization and summarization of probe intensity (Plier) were performed

source_name: Vastus lateralis muscle, 240 min after exercise, in female subject

label_protocol: 100 ng of total RNA were amplified and labeled using Whole Transcript (WT) Sense Target Labeling protocol

extract_protocol: total RNA

tag: individual

value: female

value: Skeletal muscle

tag: time

value: post-exercise


title: muscle from S11_postexercise_ 220 min_female_0


title: muscle from S13_postexercise_ 220 min_female_0


title: 3000 ppm epsilon-momfluorothrin for 2 weeks, biological rep3

value: 5000 ppm epsilon-momfluorothrin for 2 weeks


title: muscle from S12_postexercise_ 220 min_female_0


title: Islet control,  biological rep1

description:
Gene expression data from islets (Control OF1 male mice of 10 weeks of age)
Control1


title: 0 (control) for 2 weeks, biological rep3

source_name: liver of rats fed diets containing 0 (control) ppm chemical for 2 weeks


title: BPA treated Islet,  biological rep3

description:
Gene expression data from islets (OF1 male mice of 10 weeks treated with PBA)
BPA3


title: time_107SRN


title: time_107FR


title: muscle from S8_postexercise_ 220 min_female_0

source_name: Vastus lateralis muscle, 240 min after exercise, in male subject


title: time_107SR


title: muscle from S9_postexercise_ 220 min_female_0


title: time_109SR


title: Homo shRNA rep 3

city: Shenyang

first: Zi

last: Yu

state: Liaoning

address: Shenyang North New Area, Shenyang, Liaoning Province, P.R. China

institute: China Medical University

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

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: Data analysis and quality control of the expression data were performed with Expression Console according to Affymetrix default analysis settings. Differential analysis was completed with GeneSpring of   Agilent Technologies Inc..

source_name: 786O, shRNA

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

growth_protocol: 786O cells were cultured in RPMI 1640 with 10% fetal bovine serum in a condition with air at 37℃ with 5% CO2.

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

treatment_protocol: 786O cells were transfected with lentivirus with shRNA targeting PLEKHO1.

value: kidney renal cell carcinoma

tag: cell line

tag: genotype/variation

value: shRNA targeting PLEKHO1


title: muscle from S7_postexercise_ 220 min_male_1


title: time_104SR

value: CD4+ T cell


title: muscle from S10_postexercise_ 220 min_female_0


title: time_104FR

value: healthy


title: time_103FR


title: muscle from S6_postexercise_ 220 min_male_1


title: Homo shRNA rep 1


title: muscle from S5_postexercise_ 220 min_male_1


title: time_101FR


title: Homo shRNA rep 2


title: time_101SR


title: concentration_100 rep2

source_name: B cell PBL

value: B cell


title: time_103SR


title: concentration_500 rep2


title: 0 (control) for 2 weeks, biological rep1


title: concentration_100 rep 2


title: concentration_500 rep1


title: concentration_250 rep1


title: muscle from S3_postexercise_ 220 min_male_1


title: Rnase_E_depletion_3

city: Lodz

first: Przemysław

middle: Adam

last: Płociński

state: lodzkie

address: Lodowa 106

department: Mycobacterium Physiology and Genetics

country: Poland

institute: Institute of Medical Biology of the Polish Academy of Sciences

data_processing:
seqencing adapter removal with Cutadapt software with parameters set -a AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT -A TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -q 15
quality trimming was done with Sickle -pe script setting variable parameters as -t sanger -q 20 -l 20
mapping reads to the reference genome with Bowtie2 with default settings
sorting and indexing of the alignemnt files with Samtools
counting reads to features with HTSeq.count -t gene -i Locus -m intersection-nonempty
count matrix was build in excel by merging the HTSeq.count output files
creating 1x normalised bedgraphs with bamCoverage function of Bedtools with parameters --binSize 1 --normalizeUsing RPGC --effectiveGenomeSize 4411532 -e -p 15 -of bedgraph
Genome_build: NC_000962.3
Supplementary_files_format_and_content: bedgraph files are 1x normalised to remove the sequencing depth discrepancies
Supplementary_files_format_and_content: matrix file is a .txt file (tab delimited) with number of reads counted to features (genes) for all individual samples

organism: Mycobacterium tuberculosis H37Rv

source_name: bacteria grown in 7H9 OADC medium

growth_protocol: Mycobacterium tuberculosis H37Rv laboratory strain was cultured in 7H9 media, supplemented with OADC additive (10% v/v) with Tyloxapol to prevent culture clamping (0.1% v/v). RNase J mutant and wild type control were grown until reaching an optical density at 600nm (OD) of 0.6-0.8, when they were harvested. PNP Cas9, RNE Cas9 and no target Cas9 strains were grown in the presence of anhydrotetracycline (100ng/ml) to induce the expression of Cas9 system for targeted gene silencing. All Cas9 expressing cultures were started at an OD of 0.05, induced with tetracycline after 24 hours and incubated at 370C for 7 days, before harvesting and the strains were grown in the presence of Kanamycin (25mg/ml).

extract_protocol:
Bacteria were harvested during the logarythmic phase of growth. RNA was extracted with Trizol LS(Thermo Fisher Scientific, Waltham, USA) following standard laboratory procedures used for mycobacteria (ribolysing the cells with "lysing matrix B" in MP FastPrep homogenizer).
KAPA Stranded RNA-Seq Library Preparation Kit (cat#KK8401 , from KAPA Biosystems), following ribodepletion of samples with Ribo-Zero(Bacteria)(from Illumina, San Diego, USA)

treatment_protocol: mutant versus control comparison

value: Cas9 mutant

tag: growth condition

value: grown for 7 days in the presence of 100ng/ml of anhydrotetracycline and 25 ug/ml of Kanamycin for Cas9 plasmid retention and Cas9 enzyme expression


title: muscle from S4_postexercise_ 220 min_male_1


title: concentration_100 rep1


title: time_110SR


title: concentration_1 rep1


title: Input_ChIPSeq_KG2

city: Marseille

first: Mathilde

last: Poplineau

address: 27 BOULEVARD LEI ROURE CS 30059

country: France

institute: INSERM

data_processing:
basecalling was performed using Illumina CASAVA
Reads with Phred quality score less than 30 were filtered out
Sequences were mapped to a human genome (hg19) using Bowtie2 alignment tool (ref: PMID 22388286) in paired-end mode with default parameters
bigwig files were generated from bam files using Deeptools 2.0 suite (bamCompare)
Peak callings were performed using MACS2 (broad and paired-end mode) using inputs as controls
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files

source_name: KG1 cell line

growth_protocol: Human myeloblastic cell line KG1were maintained at exponential growth in RPMI with 10% foetal calf serum and 1% sodium pyruvate

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA or proteins-DNA complexes were isolated with antibody. DNA was purified using the i-Pure kit (Diagenode)
Libraries were prepared according to Illumina's instructions accompanying the Illumina's TruSeq ChIP sample Prep Kit Protocol

value: bone marrow


title: muscle from S1_postexercise_ 220min_male_1


title: Rnase_E_depletion_1


title: concentration_1 rep2


title: Homo shNC rep 2

source_name: 786O, shNC

value: control


title: Homo shNC rep 3


title: PNPase_depletion_3


title: muscle from S14_preexercise_ 0min_female_0

source_name: Vastus lateralis muscle at rest in female subject

value: pre-exercise


title: H3K4me1_ChIPSeq_KG1


title: H3K27ac_ChIPSeq_KG1


title: PNPase_depletion_2


title: PNPase_depletion_1


title: muscle from S2_postexercise_ 220 min_male_1

value: male


title: muscle from S12_preexercise_ 0min_female_0


title: muscle from S13_preexercise_ 0min_female_0


title: Homo shNC rep 1


title: Rnase_E_depletion_2


title: muscle from S10_preexercise_ 0min_female_0


title: muscle from S11_preexercise_ 0min_female_0


title: wild_type_no_target_Cas9_3

value: Cas9 control


title: microRNA NGS: hDF3 Oct4

city: Brno

first: Tomas

last: Barta

address: Kamenice 3

department: Faculty of Medicine

country: Czech Republic

institute: Masaryk University

data_processing:
Adapter trimming and basic length filtering - cutadapt
Quality filtering - FASTX-toolkit
Read length filtering - longer than 16 bp and shorter than 28 bp
mapped reads using miRBase 21
Genome_build: miRBase 21
Supplementary_files_format_and_content: mapped reads, raw counts

source_name: Neonatal fibroblasts

growth_protocol: Fibroblast cells were cultured in Knockout Dulbecco's modified Eagle's medium (DMEM), (Invitrogen, Life Technologies Ltd.) containing 10% foetal bovine serum (FBS), (PAA), 2 mM L-glutamine (Invitrogen, Life Technologies Ltd.), 1 × MEM non-essential amino acid solution, 1 ×  penicillin/streptomycin (PAA) and 10 ?M ? mercaptoethanol (Sigma-Aldrich). The cells were incubated at 37 °C/5 % CO2.

extract_protocol:
Cells were washed with phosphate-buffered saline (PBS), (pH 7.4) and lysed using RNA Blue reagent (Top-Bio). After 1-bromo-3-chloropropane (Sigma-Aldrich) addition and centrifugation (21.000 × g, 15 minutes, 4 °C), the cell lysates were separated into three layers. The top aqueous layer containing RNA was transferred to a new tube and precipitated by addition of isopropanol, followed by 10 minutes incubation on ice and centrifugation (18.000 × g, 10 minutes, 4 °C). RNA pellets were washed with 70% ethanol (8.500 × g, 10 minutes, 4 °C), air-dried, solubilized in PCR grade water (Top-Bio), and RNA integrity was analysed (RIN>8).
NEBNext Multiplex Small RNA Library Prep Set for Illumina (Set1, 2; New England Biolabs; Ipswich, MA, USA) was used to prepare libraries for further sequencing according to the manufacturer's instructions. Briefly, 800 ng of total RNA were used to create size selected small RNA library. The sequencing was performed with 2.0 pM library using the NextSeq® 500/550 High Output Kit v2 (75 cycles; Illumina; San Diego, CA, USA).

treatment_protocol: Fibroblasts were transduced by lentiviral particles containing GFP (PL-SIN-EF1α-EGFP; addgene #21320) or Oct4 (pSin-EF2-Oct4-Pur; addgene #16579), respectively. Cells were harvested 6 days upon transduction and selection in the presence of Puromycin

value: Neonatal fibroblasts


title: microRNA NGS: hDF2 Oct4


title: microRNA NGS: hDF1 Oct4


title: muscle from S9_preexercise_ 0min_female_0

value: female


title: wild_type_no_target_Cas9_2


title: wild_type_no_target_Cas9_1


title: microRNA NGS: hDF2 GFP

value: GFP


title: mutant_RNJ_2

value: mutant RNJ

value: grown to mid-exponential phase


title: SJ060607_Media-1

city: Chicago

first: Sundararajan

last: Jayaraman

state: IL

address: 909 South Wolcott Avenue

institute: University of Illinois at Chicago

description: Media control-1

scan_protocol: GeneChip ® Scanner 3000 (high resolution)

data_processing: Data were analyzed in ‘S-Plus’ 6.2 statistical package with the ‘S+ArrayAnalyzer’ v2.0.1 from Insightful.  Data were normalized by quantiles and summarized using the Robust Multi-array Average (RMA). ANOVA was used to identify statistically significant, differentially expressed transcripts. ANOVA-generated p-values were corrected for False Discovery Rate (FDR) by Benjamini-Hochberg procedure. Hierarchical clustering was performed using ‘Average' weighting method and Euclidean distance metric. Data clustered was filtered by a BH-adjusted p-Value less than 0.05, greater than 2-fold expression difference, and having a gene expression level of more than 10 in at least two hybridizations with a statistical significance threshold of pVal < 0.001.

label: Biotin

source_name: Jurkat cells

label_protocol: GeneChip ® IVT Labeling Kit)

growth_protocol: Jurkat cells were grown in RPMI media containing antibiotics and 10% fetal bovine serum.

extract_protocol: Phenol: chloroform method was used to extract total RNA from cells lysed in TRIzol.

treatment_protocol: Jurkat cells were treated with 50ng/ml of Trichostatin A dissolved in dimethyl sulfoxide and diluted in phosphate buffered saline. Controls included cells grown in media alone or with the vehicle, dimethyl sulfoxide.

value: Jurkat cells

value: media


title: SJ060607_DMSO-4

value: DMSO


title: OtC1047 AR-EK scrambled n4

city: Newcastle upon Tyne

first: Evangelia

last: Kounatidou

address: Framlington Place

department: Northern Institute for Cancer Research

country: United Kingdom

institute: Newcastle University

description: Scr 4

data_processing:
Illumina HiSeq 2500 Rapid Run v2 SBS  (sequencer)
Paired-end 100-125 nucleotide (nt) reads were generated and checked for data quality using FASTQC (Babraham Institute, Cambridge, UK).
2 reads x 15 million fragments = 30 million per sample
data has been mapped and filtered against the human reference genome (hg19) using STAR
DESeq2 package to perform differencial gene expression analysis using the HTSeq raw count data  .
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: tab-delimited text file contains raw read counts of each gene (row) for each sample (column)

source_name: prostate cancer cell line

growth_protocol: CWR22Rv1 AR-EK cells were routinely grown in RPMI 1640 media supplemented with 2mM L-glu and 10% FCS. Passaged every 48-72h. Regular mycoplasma testing was performed.

extract_protocol:
CWR22Rv1 AR-EK cells were harvested 48h post-transfection and total RNA was extracted using the RNeasy Mini kit (Qiagen). Illumina TruSeq RNA Sample Prep Kit was used with 500 ng of total RNA for the construction of sequencing libraries. Performed by Otogenetics, Atlanta, USA.
RNA libraries were prepared for sequencing using standard Illumina protocols. Performed by Otogenetics, Atlanta, USA.

treatment_protocol: CWR22Rv1 AR-EK cells were transfected with scrambled- and ARexon1-targeting siRNAs for 48h in steroid depleted media.

value: prostate

value: CWR22Rv1 AR-EK

tag: passage number

tag: transfection

value: scrambled


title: mutant_RNJ_3


title: SJ060607_DMSO-3

tag: cell type


title: muscle from S8_preexercise_ 0min_female_0

value: Skeletal muscle


title: muscle from S7_preexercise_ 0min_male_1

source_name: Vastus lateralis muscle at rest in male subject


title: mutant_RNJ_1


title: SJ060607_Media-2

description: Media control-2


title: SJ060607_TSA-6

value: 50ng/ml of Trichostatin A dissolved in dimethyl sulfoxide and diluted in phosphate buffered saline. Controls included cells grown in media alone or with the vehicle, dimethyl sulfoxide.


title: MAT

city: Nanjing

first: Xin

last: Liu

state: Jiangsu

department: College of Animal Science and Technology

institute: Nanjing Agricultural University

description: mesenteric adipose

data_processing:
Raw sequencing data was evaluated by FAST-QC
Raw reads after quality control testing were mapped to the reference pig genome version 11.1 (Sscrofa 11.1) using HiSAT2 program (V2.0.5) for mRNAs and lncRNAs, and BWA-MEM for circRNAs
The normalized expression level of each gene was measured by fragments per kilobase of transcript per million reads mapped (FPKM) for mRNAs and lncRNAs, and spliced reads per billion mapping (SRPBM) for circRNAs
Genome_build: Sscrofa 11.1
Supplementary_files_format_and_content: tab-delimited text files include FPKM (for mRNAs and lncRNAs) or SRPBM (for circRNAs) values for each gene

organism: Sus scrofa

source_name: mesenteric adipose

extract_protocol:
Four adipose tissue were subjected to total RNA extraction using TRIzol reagent (Invitrogen, Carlsbad, CA, USA). Total RNA from IAT, SAT, RPAT and MAT (3 individuals/group) was pooled in equal amounts to generate mixed sample respectively.
Sequencing libraries were prepared using NEB Next Ultra Directional RNA LibraryPrep Kit (NEB, Ispawich, MA, USA) after removing ribosomal RNA

treatment_protocol: IAT, SAT, RPAT, and MAT of pigs

tag: breed

value: Chinese Erhualian pigs

value: mesenteric adipose

tag: Sex


title: OtC1045 AR-EK scrambled n3

description: Scr 3


title: RPAT

description: retroperitoneal adipose

source_name: retroperitoneal adipose

value: retroperitoneal adipose

value: male


title: microRNA NGS: hDF3 GFP

value: Neonatal fibroblasts


title: OtC1048 AR-EK siARex1 n4

description: siEx1 4

value: ARexon1-targeting siRNA


title: microRNA NGS: hDF1 GFP

value: GFP


title: OtC1044 AR-EK siARex1 n2

description: siEx1 2


title: SAT

description: subcutaneous adipose

source_name: subcutaneous adipose

value: subcutaneous adipose


title: muscle from S4_preexercise_ 0min_male_1

value: pre-exercise


title: wild_type_2

value: wild type

value: grown to mid-exponential phase


title: OtC1046 AR-EK siARex1 n3

description: siEx1 3


title: wild_type_1


title: OtC1043 AR-EK scrambled n2

description: Scr 2


title: SJ060607_TSA-5

value: Jurkat cells

tag: treatment


title: muscle from S5_preexercise_ 0min_male_1


title: muscle from S3_preexercise_ 0min_male_1


title: IAT

description: intramuscular adipose

source_name: intramuscular adipose

value: intramuscular adipose


title: PDGFRa_I_3

status: Public on Feb 08 2019

city: Graz

first: Leigh

last: Marsh

address: Neue Stiftingtalstraße 6/VI

country: Austria

institute: Ludwig Boltzmann Institute  for Lung Vascular Research

data_processing:
NGS reads passing vendor quality filtering were aligned to the mm10 reference genome assembly provided by the UCSC Genome Browser based on Genome Reference Consortium GRCm38 with the TopHat2 (v2.1.1, http://genomebiology.com/2013/14/4/R36/abstract) splice junction mapper utilising the Bowtie2 short read aligner (v2.2.9 http://www.nature.com/nmeth/journal/v9/n4/full/nmeth.1923.html).
"basic" Ensembl transcript annotation from version e87 (December 2016) served as reference transcriptome. Cufflinks (v2.1.1, http://www.nature.com/nbt/journal/v31/n1/full/nbt.2450.html) allowed for transcriptome assembly, customary including novel transcript structures, on the basis of the reference transcriptome and spliced read alignments, as well as raw transcript quantification.
Before differential expression calling with Cuffdiff (included in Cufflinks v2.1.1, http://www.nature.com/nbt/journal/v28/n5/full/nbt.1621.html), transcriptome sets of each sample of each group to be compared were combined via the Cuffmerge algorithm.
Finally, the cummeRbund (https://bioconductor.org/packages/release/bioc/html/cummeRbund.html), biomaRt (https://bioconductor.org/packages/release/bioc/html/biomaRt.html) and rtracklayer (https://bioconductor.org/packages/release/bioc/html/rtracklayer.html) Bioconductor packages were utilised in custom R scripts to perform quality assessment and further refine analysis results.
Genome_build: GRCm38 (mm10) Reference Genome Assembly
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each gene and sample

source_name: sorted Td-tomato cells

extract_protocol:
The left lung lobe from tdTomato mice was mechanically separated and a single single cell suspension generated. tdTomato-positive cells were sorted directly into RNA lysis buffer (Qiagen, Venlo, Netherlands) using a FACSAria II cell sorter (BD Biosciences, San Jose, CA, USA). RNA was isolated with the RNeasy micro kit (Qiagen).
Library preparation used the SmartSeq2 protocol and sequenced on the Illumina HiSeq 3000 platform

tag: mouse strain

value: Pdgfra-CreERT2; tdTomatoflox

tag: organ

value: Lung

value: Saline 14 days (11 weeks of age)

value: 5x3mg ip. tamoxifen induction (at 6 weeks of age)


title: PDGFRa_II_5

tag: agent

value: Bleomycin 14 days  (11 weeks of age)


title: Acta2_II_8

value: Acta2-CreERT2; tdTomatoflox

value: 400 mg/Kg food tamoxifen induction(5 days after bleomycin treatment)


title: PDGFRa_I_1


title: Acta2_II_7


title: PDGFRa_II_7


title: PDGFRa_I_4


title: PDGFRa_I_2


title: Acta2_II_6


title: PDGFRa_II_8


title: PDGFRa_II_6


title: muscle from S1_preexercise_0min_male_1

tag: gender

value: male

tag: tissue

value: Skeletal muscle


title: Acta2_II_5


title: wild_type_3


title: Acta2_I_4

value: 400 mg/Kg food tamoxifen induction(5 days after saline treatment)


title: Acta2_I_2


title: Acta2_I_3


title: muscle from S2_preexercise_ 0min_male_1

tag: age


title: Acta2_I_1


title: 1_N2Control.GeneExp

city: Muenster

first: Ruediger

middle: J

last: Paul

address: Schlossplatz 8

department: Institute of Zoophysiology

country: Germany

institute: University of Muenster

data_processing:
Using Illumina HiSeq2000 technology, samples were sequenced at the BGI with a minimum of 10 megareads per sample and a sequencing quality of more than 98% clean reads. Sequences were mapped to Wormbase release WS257. Mean expression intensities of genes (i.e., means from the three biological replicates per experimental condition, after checking for substantial deviations between corresponding data; see below) and differential gene expression were calculated with the FPKM method (fragments per kilobase of exon per million fragments mapped) to normalize for sequencing depth and gene length. The NOISeq method was used to determine the threshold of P (diverge probability ≥ 0.8) for the differentially expressed genes (DEGs).
In case of nhr-69, the three biological replicates at each experimental condition showed a high degree of similarity with regard to the expression intensity of corresponding genes, and mean expression intensities were calculated using the data from all three biological replicates. In case of N2 Bristol variety, however, one biological replicate at each experimental condition differed significantly from the two others regarding the expression intensity of corresponding genes, and mean expression intensities were calculated here using the data from only two biological replicates.
Genome_build: Wormbase release WS257
Supplementary_files_format_and_content: Tab-delimited text files which include: GeneID: identity of gene; geneLength: gene length; Means: groupA: mean expression (FPKM) of groupA; Means: groupB: mean expression (FPKM) of groupB; Ratio(s2/s1): mean expression in two groups [Ratio(s2/s1)]; log2 Ratio(s2/s1): Log2(folds of mean expression in two groups); Probability: probability of significant differential gene expression between two experimental conditions (from NOISeq, diverge probability ≥ 0.8); KEGG Orthology: KEGG annotation; GO Component: GO Component annotation; GO Function: GO Function annotation; GO Process: GO Process annotation; Blast nr: NR annotation

organism: Caenorhabditis elegans

source_name: N2 Bristol variety under control conditions

growth_protocol: C. elegans worms (N2 Bristol variety) developed from the L1 larval stage to the adult stage under control conditions (without 5 µM of the ADD 7a-HADD in the NGM medium) on 5 NGM plates, each seeded with E. coli OP50 suspension.

extract_protocol:
RNAiso-G (Segenetic, Borken, Germany) was added to the samples, before they were frozen in liquid nitrogen. After thermal disruption of worms (liquid nitrogen, 35°C; three repetitions), chloroform extraction on ice (10 min), and centrifugation (12.000 × g, 4°C, 15 min), DNA was digested and RNA purified with a RNase-free DNase set and RNeasy® mini kit (Qiagen, Hilden, Germany). Quality control was performed using an Agilent Bioanalyzer® (Agilent Technologies, Böblingen, Germany). After adding the samples to RNAstableTM matrix (Biomatrica, San Diego, CA, USA) and a subsequent vacuum centrifigution for drying (2 h), the samples from three experimental approaches were sent to the Beijing Genomics Institute (BGI) for RNA-Seq analysis.
RNA libraries were prepared for sequencing using standard Illumina HiSeq2000 protocols.

treatment_protocol: After reaching adulthood, the worms of both strains were washed off from the 5 control or test plates and cleaned several times using purified water to get rid of bacteria. Five plates per strain and experimental condition were combined to one biological sample. Three biological samples (replicates) per strain and experimental condition were further prepared for RNA-Seq.

tag: strain background

value: N2 Bristol

value: control

tag: developmental stage

value: synchronized adult worms

value: whole worms


title: 3_nhr69Control.GeneExp

source_name: nhr-69 deletion mutant under control conditions

growth_protocol: C. elegans worms (nhr-69 deletion mutant, nhr-69(ok1926) I) developed from the L1 larval stage to the adult stage under control conditions (without 5µM of the ADD 7a-HADD in the NGM medium) on 5 NGM plates, each seeded with E. coli OP50 suspension.

value: nhr-69 deletion mutant


title: 4_nhr69Test.GeneExp

source_name: nhr-69 deletion mutant under test conditions

growth_protocol: C. elegans worms (nhr-69 deletion mutant, nhr-69(ok1926) I) developed from the L1 larval stage to the adult stage under test conditions (with 5µM of the ADD 7a-HADD in the NGM medium) on 5 NGM plates, each seeded with E. coli OP50 suspension.

value: 5 µM ADD 7a-HADD


title: 2_N2Test.GeneExp

source_name: N2 Bristol variety under test conditions

growth_protocol: C. elegans worms (N2 Bristol variety) developed from the L1 larval stage to the adult stage under test conditions (with 5 µM of the ADD 7a-HADD in the NGM medium) on 5 NGM plates, each seeded with E. coli OP50 suspension.


title: P90_5_H6

city: Uppsala

first: Asa

middle: Kristina

last: Bjorklund

address: Box 596

department: Cell and Molecular Biology

institute: Uppsala University

data_processing:
All reads were aligned to the mouse (mm10) genome plus EGFP sequence using STAR (Dobin et al. 2013)
Non-uniquely mapped reads were removed
Rpkmforgenes (available at http://sandberg.cmb.ki.se/rnaseq/), options -readcount -fulltranscript -mRNAnorm -rmnameoverlap -u, was used to generate RPKM values and read counts. We used a file with unique positions from Storvall et al. 2013 PLOS ONE. Gene annotations used were transcripts in Ensembl  (May 2014) and ERCC-spike in annotations.
Genome_build: mm10
Supplementary_files_format_and_content: gene expression values (tab-delimited text)

source_name: single cell

extract_protocol:
Single cells have been extracted from tissue using Neuronal Tissue Dissociation Kit (Miltenyi Biotec) for embryonic and early postnatal stages. Papain Dissociation System (Worthington) was used for the adult mice. cDNA was generated from FACS sorted single cells using Smart-seq2 protocol (Picelli et al. Nature Methods 2013). For some of the samples, ERCC spike-in RNA was added to the lysis buffer.
Nextera XT DNA sample preparation index kit, 96 indices (Illumina)

value: neuron

tag: genotype

value: Pitx3tm1Mli heterozygote

value: postnatal day 90

tag: spike-in

value: ERCC


title: P90_5_H4


title: P90_5_H2


title: P90_5_H3


title: P90_5_H5


title: P90_5_G5


title: P90_5_H1


title: P90_5_F1


title: P90_5_G6


title: P90_5_F4


title: P90_5_F5


title: P90_5_F3


title: P90_5_G4


title: P90_5_F6


title: P90_5_G1


title: P90_5_G3


title: P90_5_F2


title: P90_5_E6


title: P90_5_G2


title: P90_5_E5


title: P90_5_E4


title: P90_5_E1


title: P90_5_D6


title: P90_5_D3


title: P90_5_E3


title: P90_5_E2


title: P90_5_D5


title: P90_5_D2


title: P90_5_D4


title: P90_5_C6


title: P90_5_C5


title: P90_5_C2


title: P90_5_D1


title: P90_5_C4


title: P90_5_A5


title: P90_5_B6


title: P90_5_A1


title: P90_5_B3


title: P90_5_A6


title: P90_5_B2


title: P90_5_B1


title: P90_5_A4


title: P90_4_H9


title: P90_4_H7


title: P90_4_H5


title: P90_4_H6


title: P90_4_H4


title: P90_4_H8


title: P90_4_H11


title: P90_4_H12


title: P90_4_H3


title: P90_5_B5


title: P90_5_C1


title: P90_5_A2


title: P90_4_H1


title: P90_5_A3


title: P90_4_H10


title: P90_5_C3


title: P90_5_B4


title: P90_4_G2


title: P90_4_G10


title: P90_4_G3


title: P90_4_G11


title: P90_4_G8


title: P90_4_F7


title: P90_4_H2


title: P90_4_F6


title: P90_4_F3


title: P90_4_F9


title: P90_4_G6


title: P90_4_G9


title: P90_4_G4


title: P90_4_G5


title: P90_4_G7


title: P90_4_F5


title: P90_4_G1


title: P90_4_F12


title: P90_4_F2


title: P90_4_F4


title: P90_4_G12


title: P90_4_F10


title: P90_4_F11


title: P90_4_F1


title: P90_4_E7


title: P90_4_E5


title: P90_4_E4


title: P90_4_E8


title: P90_4_E12


title: P90_4_E11


title: P90_4_E10


title: P90_4_D9


title: P90_4_D7


title: P90_4_E3


title: P90_4_E1


title: P90_4_D4


title: P90_4_D5


title: P90_4_D3


title: P90_4_D12


title: P90_4_D1


title: P90_4_D10


title: P90_4_D2


title: P90_4_D11


title: P90_4_C8


title: P90_4_C9


title: P90_4_C6


title: P90_4_C7


title: P90_4_C5


title: P90_4_C2


title: P90_4_E2


title: P90_4_D6


title: P90_4_E9


title: P90_4_C3


title: P90_4_C4


title: P90_4_D8


title: P90_4_B9


title: P90_4_C11


title: P90_4_C1


title: P90_4_C10


title: P90_4_C12


title: P90_4_B8


title: P90_4_B7


title: P90_4_B2


title: P90_4_B4


title: P90_4_B5


title: P90_4_B6


title: P90_4_B3


title: P90_4_B12


title: P90_4_A9


title: P90_4_B10


title: P90_4_B11


title: P90_4_B1


title: P90_4_A8


title: P90_4_A7


title: P90_4_A6


title: muscle from S6_preexercise_ 0min_male_1

tag: individual

tag: time

value: pre-exercise


title: P90_4_A5


title: P90_4_A2


title: P90_4_A4


title: P90_4_A12


title: P90_4_A3


title: P90_4_A11


title: P90_2_H9


title: P90_4_A1


title: P90_4_A10


title: P90_2_H3


title: P90_2_H6


title: P90_2_H4


title: P90_2_H2


title: P90_2_H8


title: P90_2_H10


title: P90_2_H7


title: P90_2_H12


title: P90_2_G9


title: P90_2_G8


title: P90_2_G7


title: P90_2_H11


title: P90_2_G6


title: P90_2_G2


title: P90_2_G5


title: P90_2_G10


title: P90_2_G12


title: P90_2_G3


title: P90_2_G11


title: P90_2_G1


title: P90_2_F6


title: P90_2_F7


title: P90_2_F3


title: P90_2_H5


title: P90_2_F4


title: P90_2_F9


title: P90_2_F5


title: P90_2_F2


title: P90_2_F11


title: P90_2_E8


title: P90_2_E4


title: P90_2_E3


title: P90_2_G4


title: P90_2_E7


title: P90_2_E5


title: P90_2_E10


title: P90_2_D9


title: P90_2_D8


title: P90_2_F12


title: P90_2_D6


title: P90_2_D3


title: P90_2_D4


title: P90_2_E1


title: P90_2_D11


title: P90_2_D2


title: P90_2_F1


title: P90_2_D10


title: P90_2_E9


title: P90_2_F10


title: P90_2_E6


title: P90_2_D1


title: P90_2_D12


title: P90_2_C9


title: P90_2_E12


title: P90_2_E11


title: P90_2_E2


title: P90_2_C8


title: P90_2_C7


title: P90_2_C3


title: P90_2_C5


title: P90_2_C6


title: P90_2_C4


title: P90_2_C2


title: P90_2_C1


title: P90_2_C10


title: P90_2_B8


title: P90_2_C11


title: P90_2_C12


title: P90_2_B7


title: P90_2_B6


title: P90_2_B11


title: P90_2_B12


title: P90_2_B3


title: P90_2_B5


title: P90_2_B10


title: P90_2_B4


title: P90_2_B2


title: P90_2_A8


title: P90_2_B1


title: P90_2_A7


title: P90_2_A5


title: P90_2_A6


title: P90_2_A9


title: P90_2_A4


title: P90_2_A11


title: P90_2_A12


title: P90_2_A2


title: P90_1_H9


title: P90_2_A10


title: P90_2_B9


title: P90_2_A1


title: P90_1_H8


title: P90_1_H6


title: P90_1_H2


title: P90_1_H7


title: P90_1_H10


title: P90_1_H3


title: P90_1_H12


title: P90_1_H1


title: P90_1_H4


title: P90_1_H11


title: P90_1_H5


title: P90_1_G9


title: P90_2_A3


title: P90_1_G7


title: P90_1_G4


title: P90_1_G8


title: P90_1_G3


title: P90_1_G12


title: P90_1_G1


title: P90_1_F8


title: P90_1_F9


title: P90_1_F7


title: P90_1_F6


title: P90_1_F5


title: P90_1_F4


title: P90_1_F3


title: P90_1_F1


title: P90_1_F11


title: P90_1_F10


title: P90_1_G6


title: P90_1_G5


title: P90_1_E9


title: P90_1_E8


title: P90_1_E5


title: P90_1_F2


title: P90_1_F12


title: P90_1_E7


title: P90_1_E3


title: P90_1_E2


title: P90_1_E4


title: P90_1_E6


title: P90_1_G2


title: P90_1_E11


title: P90_1_G11


title: P90_1_E10


title: P90_1_E1


title: P90_1_D9


title: P90_1_D6


title: P90_1_D8


title: P90_1_D5


title: P90_1_D7


title: P90_2_F8


title: P90_1_D11


title: P90_1_D4


title: P90_1_D10


title: P90_1_C9


title: P90_1_D12


title: P90_1_D1


title: P90_1_D3


title: P90_1_C6


title: P90_1_C8


title: P90_1_C7


title: P90_1_E12


title: P90_1_C5


title: P90_1_C2


title: P90_2_H1


title: P90_1_C10


title: P90_1_C1


title: P90_1_C4


title: P90_1_C3


title: P90_1_C11


title: P90_1_C12


title: P90_1_B6


title: P90_1_B8


title: P90_1_B9


title: P90_1_B7


title: P90_1_B4


title: P90_1_B3


title: P90_1_B5


title: P90_1_B10


title: P90_1_B12


title: P90_1_B2


title: P90_1_B1


title: P90_1_B11


title: P90_1_A9


title: P90_1_A8


title: P90_1_A7


title: P90_1_A6


title: P90_1_A5


title: P90_1_A3


title: P90_1_A2


title: P7_99

value: postnatal day 7

value: no


title: P90_1_A12


title: P90_1_A4


title: P90_1_A10


title: P90_1_A1


title: P90_1_D2


title: P90_1_A11


title: P7_91


title: P7_85


title: P7_84


title: P7_93


title: P7_82


title: P7_76


title: P7_94


title: P7_92


title: P7_77


title: P7_86


title: P7_79


title: P7_70


title: P7_71


title: P7_69


title: P7_64


title: P7_97


title: P7_63


title: P7_61


title: P7_66


title: P90_2_D7


title: P7_6


title: P90_2_D5


title: P7_58


title: P7_56


title: P7_54


title: P7_75


title: P7_78


title: P7_53


title: P7_5


title: P7_73


title: P7_47


title: P7_52


title: P7_48


title: P7_46


title: P7_45


title: P7_68


title: P7_51


title: P7_62


title: P7_43


title: P7_44


title: P7_41


title: P7_60


title: P7_40


title: P7_39


title: P7_42


title: P7_37


title: P7_38


title: P7_32


title: P7_31


title: P7_7


title: P7_30


title: P7_3


title: P7_29


title: P7_27


title: P7_26


title: P7_270


title: P7_271


title: P7_258


title: P7_256


title: P7_251


title: P7_25


title: P7_250


title: P7_252


title: P7_28


title: P7_249


title: P7_247


title: P7_237


title: P7_231


title: P7_238


title: P7_241


title: P7_235


title: P7_244


title: P7_230


title: P7_242


title: P7_234


title: P7_236


title: P7_228


title: P7_227


title: P7_222


title: P7_221


title: P7_223


title: P7_272


title: P7_22


title: P7_257


title: P7_218


title: P7_219


title: P7_21


title: P7_209


title: P7_211


title: P7_208


title: P7_213


title: P7_212


title: P7_207


title: P7_203


title: P7_199


title: P7_196


title: P7_197


title: P7_20


title: P7_193


title: P7_204


title: P7_189


title: P7_185


title: P7_190


title: P7_187


title: P7_19


title: P7_220


title: P7_192


title: P7_186


title: P7_188


title: P7_191


title: P7_194


title: P7_183


title: P7_181


title: P7_18


title: P7_182


title: P7_174


title: P7_179


title: P7_184


title: P7_206


title: P7_176


title: P7_180


title: P7_177


title: P7_172


title: P7_170


title: P7_171


title: P7_17


title: P7_169


title: P7_167


title: P7_162


title: P7_158


title: P7_16


title: P7_156


title: P7_155


title: P7_153


title: P7_163


title: P7_173


title: P7_160


title: P7_164


title: P7_149


title: P7_166


title: P7_147


title: P7_151


title: P7_144


title: P7_157


title: P7_143


title: P7_152


title: P7_150


title: P7_140


title: P7_141


title: P7_142


title: P7_138


title: P7_136


title: P7_135


title: P7_134


title: P7_148


title: P7_124


title: P7_133


title: P7_131


title: P7_123


title: P7_132


title: P7_13


title: P7_130


title: P7_129


title: P7_15


title: P7_120


title: P7_121


title: P7_126


title: P7_128


title: P7_122


title: P7_113


title: P7_14


title: P7_114


title: P7_139


title: P7_115


title: P7_112


title: P7_110


title: P7_11


title: P7_117


title: P7_109


title: P7_137


title: P7_108


title: P7_12


title: P7_118


title: P7_100


title: P1_9

value: postnatal day 1


title: P7_101


title: P7_105


title: P7_104


title: P1_89


title: P1_90


title: P7_107


title: P7_116


title: P1_92


title: P1_86


title: P1_73


title: P1_71


title: P1_74


title: P1_82


title: P1_85


title: P1_87


title: P1_83


title: P1_77


title: P1_7


title: P1_69


title: P1_93


title: P1_94


title: P7_103


title: P1_65


title: P1_67


title: P1_64


title: P1_51


title: P1_54


title: P1_57


title: P1_5


title: P1_62


title: P1_6


title: P1_60


title: P1_40


title: P1_42


title: P1_47


title: P1_81


title: P1_49


title: P1_373


title: P1_380


title: P1_382


title: P1_372


title: P1_370


title: P1_68


title: P1_4


title: P1_39


title: P1_381


title: P1_365


title: P1_368


title: P1_37


title: P1_357


title: P1_369


title: P1_50


title: P1_367


title: P1_352


title: P1_366


title: P1_351


title: P1_356


title: P1_348


title: P1_344


title: P1_354


title: P1_355


title: P1_347


title: P1_360


title: P1_342


title: P1_34


title: P1_339


title: P1_335


title: P1_349


title: P1_334


title: P1_333


title: P1_358


title: P1_332


title: P1_327


title: P1_330


title: P1_33


title: P1_331


title: P1_350


title: P1_341


title: P1_318


title: P1_319


title: P1_317


title: P1_323


title: P1_316


title: P1_310


title: P1_32


title: P1_325


title: P1_311


title: P1_308


title: P1_31


title: P1_309


title: P1_302


title: P1_300


title: P1_303


title: P1_296


title: P1_295


title: P1_326


title: P1_294


title: P1_293


title: P1_301


title: P1_292


title: P1_315


title: P1_291


title: P1_287


title: P1_288


title: P1_277


title: P1_276


title: P1_285


title: P1_324


title: P1_274


title: P1_275


title: P1_273


title: P1_265


title: P1_261


title: P1_266


title: P1_259


title: P1_257


title: P1_262


title: P1_255


title: P1_254


title: P1_322


title: P1_252


title: P1_250


title: P1_248


title: P1_25


title: P1_286


title: P1_247


title: P1_245


title: P1_244


title: P1_26


title: P1_238


title: P1_236


title: P1_228


title: P1_229


title: P1_237


title: P1_232


title: P1_230


title: P1_227


title: P1_231


title: P1_253


title: P1_225


title: P1_220


title: P1_22


title: P1_224


title: P1_221


title: P1_21


title: P1_212


title: P1_209


title: P1_210


title: P1_208


title: P1_207


title: P1_213


title: P1_235


title: P1_203


title: P1_202


title: P1_1_H9


title: P1_201


title: P1_215


title: P1_1_H6


title: P1_1_H5


title: P1_1_H8


title: P1_1_H4


title: P1_1_H11


title: P1_223


title: P1_1_H10


title: P1_1_H3


title: P1_1_H1


title: P1_1_H2


title: P1_1_G8


title: P1_1_H12


title: P1_1_G9


title: P1_1_G7


title: P1_205


title: P1_204


title: P1_1_G6


title: P1_200


title: P1_233


title: P1_1_H7


title: P1_1_G10


title: P1_1_G5


title: P1_1_F8


title: P1_1_G2


title: P1_1_G3


title: P1_1_G4


title: P1_1_F6


title: P1_1_F5


title: P1_1_F12


title: P1_1_F3


title: P1_2


title: P1_1_G11


title: P1_1_F2


title: P1_1_F9


title: P1_1_G1


title: P1_1_F11


title: P1_1_F10


title: P1_1_E6


title: P1_1_F4


title: P1_1_E7


title: P1_1_G12


title: P1_1_E5


title: P1_1_E4


title: P1_1_E2


title: P1_1_E8


title: P1_1_E12


title: P1_1_F1


title: P1_1_E3


title: P1_1_F7


title: P1_1_E9


title: P1_1_E10


title: P1_1_D7


title: P1_1_D6


title: P1_1_E11


title: P1_1_D5


title: P1_1_D9


title: P1_1_E1


title: P1_1_D4


title: P1_1_D8


title: P1_1_D3


title: P1_1_D11


title: P1_1_D10


title: P1_1_D1


title: P1_1_C8


title: P1_1_C9


title: P1_1_C5


title: P1_1_D2


title: P1_1_C4


title: P1_1_C3


title: P1_1_D12


title: P1_1_C11


title: P1_1_C7


title: P1_1_C1


title: P1_1_B9


title: P1_1_C2


title: P1_1_B8


title: P1_1_B7


title: P1_1_C10


title: P1_1_B3


title: P1_1_B2


title: P1_1_B11


title: P1_1_B10


title: P1_1_B6


title: P1_1_B5


title: P1_1_B1


title: P1_1_B4


title: P1_1_A9


title: P1_1_B12


title: P1_1_C6


title: P1_1_A8


title: P1_1_A6


title: P1_1_A5


title: P1_1_A4


title: P1_1_C12


title: P1_1_A3


title: P1_1_A2


title: P1_1_A10


title: P1_1_A1


title: P1_1_A11


title: P1_1_A7


title: P1_196


title: P1_195


title: P1_199


title: P1_197


title: P1_191


title: P1_198


title: P1_192


title: P1_190


title: P1_181


title: P1_182


title: P1_184


title: P1_175


title: P1_176


title: P1_179


title: P1_172


title: P1_1_A12


title: P1_168


title: P1_17


title: P1_188


title: P1_18


title: P1_171


title: P1_167


title: P1_166


title: KO4

city: Houaton

first: Ali

last: Marian

state: Texas

address: 6770 Bertner Ave DAC C900a

department: Centre for Cardiovascular Genetics

institute: UTHSC, Houston

description:
LMNA-KO4-791_GTGAAA_L002
LMNA-KO4-791_GTGAAA_L003
LMNA-KO4-791_GTGAAA_L004

data_processing:
Data was mapped to the mouse geneome using TopHat2 and the UCSC mm10 mouse genome as reference.
Gene expression was quantified using Cufflinks 2 and the Genecode reference.
Differential gene expression was determined using EdgeR.
Genome_build: UCSC mm10
Supplementary_files_format_and_content: xlsx file contains the cpm for the Samples and the calculated log2ratio for the KO samples compared to the NTG samples along with the FDR and pvalue for the comparison.

source_name: Lmna Knockout_heart

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

value: post natal day 14

tag: genotype/variation

value: Lmna Knockout

value: Heart


title: KO3

description:
LMNA-KO3-719_GTCCGC_L002
LMNA-KO3-719_GTCCGC_L003
LMNA-KO3-719_GTCCGC_L004


title: KO5

description:
LMNA-KO5-718_GTGGCC_L002
LMNA-KO5-718_GTGGCC_L003
LMNA-KO5-718_GTGGCC_L004


title: P1_165

tag: cell type


title: KO1

description:
LMNA-KO1-716_ATGTCA_L002
LMNA-KO1-716_ATGTCA_L003
LMNA-KO1-716_ATGTCA_L004


title: NTG5

description:
NTG5-733_AGTTCC_L002
NTG5-733_AGTTCC_L003
NTG5-733_AGTTCC_L004

value: WT


title: P1_163


title: P1_187


title: P1_164


title: P1_180


title: NTG4

description:
NTG4-801_AGTCAA_L002
NTG4-801_AGTCAA_L003
NTG4-801_AGTCAA_L004


title: NTG3

description:
NTG3-786_CTTGTA_L002
NTG3-786_CTTGTA_L003
NTG3-786_CTTGTA_L004


title: P1_159


title: P1_173


title: P1_162


title: P1_157


title: NTG1

description:
NTG1-784_TAGCTT_L002
NTG1-784_TAGCTT_L003
NTG1-784_TAGCTT_L004


title: NTG2

description:
NTG2-785_GGCTAC_L002
NTG2-785_GGCTAC_L003
NTG2-785_GGCTAC_L004


title: P1_158


title: P1_154


title: AP2-G::AP2-I schizonts anti-HA, rep 2

city: University Park

first: Manuel

last: Llinas

state: PA

address: Millennium Science Complex

department: Biochemistry and Molecular Biology

institute: Pennsylvania State University

description: AP2-G::AP2-I schizonts anti HA ChIP, rep 2

data_processing:
Reads were trimmed using Trimmomatic 0.32.3.
Reads were mapped to the P. falciparum 3D7 genome (Pf 3D7 v28, obtained from PlasmoDB) using BWA-MEM 0.4.1.
Duplicate reads were removed using samtools 1.1.2.
MACS2 (version 2.1.1.20160309) was used to call peaks with a q value cutoff of 0.01.
Bam files were converted to bigwig files using bamCoverage from the deeptools suite 3.1.2.0.0.
Genome_build: Pf 3D7 v28
Supplementary_files_format_and_content: bigWig files

organism: Plasmodium falciparum

source_name: AP2-G-DD::AP2-I-GFP strain

growth_protocol: Parasites were cultured at 37°C in the presence of 5% oxygen and 7% carbon dioxide, in RPMI 1640 media supplemented with hypoxanthine, 0.5% Albumax II (Invitrogen), and 2.5 nM WR99210.

extract_protocol:
ChIP was performed as previously described (PMID:28618269) with minor modifications. Shld1 was added to AP2-G-DD::AP2-I-GFP cultures at 24 hpi to stabilize AP2-G and nuclei were harvested 12 hours later (committed schizonts). Crosslinked nuclei were then resuspended in Covaris shearing buffer (0.1% SDS, 10 mM Tris pH 8.1, 1 mM EDTA) and sonicated using an M220 ultrasonicator (Covaris) and the following conditions: 5% duty cycle, 75 W peak incident power, 200 cycles per burst, treatment time 300 seconds. The sonicated chromatin was diluted ten-fold with dilution buffer and precleared with Protein A/G magnetic beads (Pierce) for two hours. The pre-cleared material was then incubated with antibody and magnetic beads overnight, with a small volume of non-immunoprecipitated input material kept separately. For immunoprecipitations with AP2-G-DD, rat α HA (Roche 3F10) was used. For immunoprecipitations with AP2-I-GFP, rabbit α GFP (Abcam ab290) was used. The next day, beads were washed and the bound DNA eluted in elution buffer. Crosslinking was reversed by incubating overnight at 45°C and DNA was subsequently treated with RNase A at 37° for 30 minutes and Proteinase K at 45° for two hours. DNA was purified the Qiagen MinElute kit and quantified using the Qubit HS DNA assay.
Barcoded libraries for Illumina TruSeq single-end sequencing were constructed using NEBNext DNA library Prep reagents (New England Biolabs) by following the standard Illumina library preparation protocol. The DNA was first end-repaired for 30 min at 20°C, purified using Agencourt AMPure XP beads (Beckman Coulter) and then dA-tailed for 30 min at 37°C, and purified using Ampure XP beads. NEXTflex Illumina DNA barcodes (diluted 1/10) were then ligated to the DNA fragments using T4 DNA ligase at 20°C for 15 min. The resulting DNA was then size selected for 250 bp inserts using Ampure XP beads PCR-amplified (12 cycles) using Kapa HiFi (Kapa biosystems) and purified using AMPure XP beads.

treatment_protocol: 0.5 μM Shld1 was added at 24 hpi (12 hours prior to the schizont timepoint) to stabilise the AP2-G-DD protein.

tag: strain

tag: Stage

value: Schizonts

tag: chip antibody

value: anti-HA (Roche 3F10)


title: AP2-G::AP2-I schizonts Input, rep 2

description: AP2-G::AP2-I schizonts Input, rep 2


title: AP2-G::AP2-I schizonts Input, rep 1

description: AP2-G::AP2-I schizonts Input, rep 1


title: KO2

description:
LMNA-KO2-717_CCGTCC_L002
LMNA-KO2-717_CCGTCC_L003
LMNA-KO2-717_CCGTCC_L004


title: P1_150


title: P1_148


title: AP2-G gametocytes input, rep 2

description: AP2-G-DD gametocyte input, rep 2

data_processing:
Read were trimmed using Trimmomatic 0.32.3.
Reads were mapped to the P. falciparum 3D7 genome (Pf 3D7 v28, obtained from PlasmoDB) using BWA-MEM 0.4.1.
Duplicate reads were removed using samtools 1.1.2.
MACS2 (version 2.1.1.20160309) was used to call peaks with a q value cutoff of 0.01.
Genome_build: Pf 3D7 v28
Supplementary_files_format_and_content: Bam files were converted to bigwig files using bamCoverage from the deeptools suite  3.1.2.0.0.

source_name: AP2-G-DD strain

growth_protocol: Parasites were cultured at 37°C in the presence of 5% oxygen and 7% carbon dioxide, in RPMI 1640 media supplemented with hypoxanthine, 0.5% Albumax II (Invitrogen), and 2.5 nM WR99210

extract_protocol:
ChIP was performed as previously described (PMID:28618269) with minor modifications. Shld1 was added to AP2-G-DD cultures at 24 hpi to stabilize AP2-G and nuclei were harvested 12 (committed schizonts), 36 (sexual rings), or 60 (stage I gametocytes) hours later.  Crosslinked nuclei were then resuspended in Covaris shearing buffer (0.1% SDS, 10 mM Tris pH 8.1, 1 mM EDTA) and sonicated using an M220 ultrasonicator (Covaris) and the following conditions: 5% duty cycle, 75 W peak incident power, 200 cycles per burst, treatment time 300 seconds.  The sonicated chromatin was diluted ten-fold with dilution buffer and precleared with Protein A/G magnetic beads (Pierce) for two hours. The pre-cleared material was then incubated with antibody and magnetic beads overnight, with a small volume of non-immunoprecipitated input material kept separately. For immunoprecipitations with AP2-G-DD, rat α HA (Roche 3F10) was used. The next day, beads were washed and the bound DNA eluted in elution buffer. Crosslinking was reversed by incubating overnight at 45°C and DNA was subsequently treated with RNase A at 37° for 30 minutes and Proteinase K at 45° for two hours. DNA was purified the Qiagen MinElute kit and quantified using the Qubit HS DNA assay.
Barcoded libraries for Illumina TruSeq single-end sequencing were constructed using NEBNext DNA library Prep reagents (New England Biolabs) by following the standard Illumina library preparation protocol. The DNA was first end-repaired for 30 min at 20°C, purified using Agencourt AMPure XP beads (Beckman Coulter) and then dA-tailed for 30 min at 37°C, and purified using Ampure XP beads. NEXTflex Illumina DNA barcodes (diluted 1/10) were then ligated to the DNA fragments using T4 DNA ligase at 20°C for 15 min. The resulting DNA was then size selected for 250 bp inserts using Ampure XP beads PCR-amplified (12 cycles) using Kapa HiFi (Kapa biosystems) and purified using AMPure XP beads.

value: Stage I gametocytes

tag: antibody


title: AP2-G gametocytes anti HA, rep 2

description: AP2-G-DD gametocyte HA ChIP, rep 2

value: HA (Roche 3F10)


title: AP2-G::AP2-I schizonts anti-GFP, rep 2

description: AP2-G::AP2-I schizonts anti GFP ChIP, rep 2

value: anti-GFP (Abcam ab290)


title: P1_146

value: neuron


title: AP2-G gametocytes anti HA, rep 1

description: AP2-G-DD gametocyte HA ChIP, rep 1


title: AP2-G gametocytes input, rep 1

description: AP2-G-DD gametocyte input, rep 1


title: P1_147

value: Pitx3tm1Mli heterozygote


title: AP2-G::AP2-I schizonts anti-GFP, rep 1

description: AP2-G::AP2-I schizonts anti GFP ChIP, rep 1


title: P1_142


title: P1_155


title: AP2-G rings input, rep 2

description: AP2-G-DD ring input, rep 2

value: Rings


title: P1_139


title: AP2-G rings input, rep 1

description: AP2-G-DD ring input, rep 1


title: AP2-G rings anti HA, rep 2

description: AP2-G-DD ring HA ChIP, rep 2


title: P1_138


title: P1_152


title: P1_137


title: AP2-G::AP2-I schizonts anti-HA, rep 1

description: AP2-G::AP2-I schizonts anti HA ChIP, rep 1


title: P1_153


title: AP2-G rings anti HA, rep 1

description: AP2-G-DD ring HA ChIP, rep 1


title: P1_134


title: P1_132


title: AP2-G schizonts input, rep 2

description: AP2-G-DD schizont input, rep 2


title: AP2-G schizonts input, rep 1

description: AP2-G-DD schizont input, rep 1


title: AP2-G schizonts anti HA, rep 2

description: AP2-G-DD schizont HA ChIP, rep 2


title: AP2-G schizonts anti HA, rep 1

description: AP2-G-DD schizont HA ChIP, rep 1


title: P1_133


title: P1_15


title: AI012_T47D_24h_E2+DHT_rep3

first: Hari

last: Singhal

address: 929 E 57th St

department: Ben May Department for Cancer Research

institute: University of Chicago

data_processing:
RNA sequencing data analysis was performed using Artificial Intelligene’s (AI, www.artificialintelligene.com) RNAseq analysis platform. Briefly, short reads were aligned to the hg19 human genome using STAR. Subsequently cufflinks packages were used to perform transcript assemblies. Downstream differential gene expression calling on the reference and experimental groups of interest was performed using DESeq2. To perform clustering analyses on a group of samples, a union of all the genes and their expression RPKM values within that group was generated to build a read count matrix for the group of interest. Various unsupervised and other machine learning techniques were applied to this composite read count matrix of interest. The sample-sample correlation heatmaps represent the correlation observed between any two samples. The sample-feature heatmaps represent the signal intensity of a feature for any given sample. ggplot2, heatmap.2 and Pheatmap packages in R were used to build various heatmaps. Functional analysis was performed using gene set enrichment analyses.
Genome_build: HG19
Supplementary_files_format_and_content: AI012_T47D_ReadCounts.csv

source_name: T47D breast cancer cells

growth_protocol: Cells maintained in RPMI+10%FBS+L-Glutamine+Penn/Strep

extract_protocol:
Cells were scraped after 24 hour treatment, spun down, snap frozen. RNA extraction was performed using Quiagen Rneasy plus mini kit
KAPA stranded mRNA-Seq kit (KR0960-v3.15) was used

treatment_protocol: Cells were stripped (using RPMI complete medium with 10% Charcoal Stripped FBS for 48 hours, then treated with compound for 24 hours

tag: treatment

value: 10nM E2 + 10nM DHT

tag: replicate


title: P1_13


title: P1_141


title: P1_125


title: P1_129


title: P1_127


title: AI012_T47D_24h_E2+Dex_rep3

value: 10nM E2 + 10nM Dexamethasone


title: P1_118


title: AI012_T47D_24h_E2+Prog_rep3

value: 10nM E2 + 10nM Progesterone


title: P1_113

value: no


title: P1_126

value: postnatal day 1


title: P1_123


title: AI012_T47D_24h_E2_rep3

value: 10nM E2


title: AI012_T47D_24h_E2+DHT_rep2


title: P1_121


title: P1_116


title: AI012_T47D_24h_E2+Aldo_rep2

value: 10nM E2 + 10nM Aldosterone


title: AI012_T47D_24h_E2+Dex_rep2


title: P1_115


title: P1_11


title: AI012_T47D_24h_E2+Prog_rep2


title: AI012_T47D_24h_E2_rep2


title: AI012_T47D_24h_E2+DHT_rep1


title: AI012_T47D_24h_veh_rep3

value: Vehicle


title: P1_104


title: AI012_T47D_24h_E2+Aldo_rep3


title: AI012_T47D_24h_E2+Prog_rep1


title: P1_111


title: P1_109


title: P1_128


title: AI012_T47D_24h_veh_rep2


title: AI012_T47D_24h_E2_rep1


title: AI012_T47D_24h_E2+Dex_rep1


title: P1_101


title: P1H_2_H7

value: Pitx3tm1Mli homozygote

value: ERCC


title: P1H_2_H8


title: AI012_T47D_24h_E2+Aldo_rep1


title: P1_10


title: P1H_2_H6


title: P1H_2_H9


title: P1H_2_H5


title: WT RPF, replicate 1

city: Barcelona

first: Juana

last: Díez

state: Barcelona

address: Carrer del Dr. Aiguader 88

department: Department of Experimental and Health Sciences

institute: Universitat Pompeu Fabra

description:
Sample_lib54_WTC1_R
MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0
Ribosome footprints
Replicate 1
processed data file: raw_counts_RPF.tsv

data_processing:
Library strategy: Ribo-Seq
Raw sequencing reads were processed using FASTX-Toolkit to remove adapter sequences via “fastx_clipper -Q 33 -a CTGTAGGCACCATCAAT -v -c -l 25”. Subsequently, all surviving reads were mapped to sacCer3 rRNA sequences to filter out rRNA contaminations. All non-mapping reads were then used for mapping to the sacCer3 SGD transcriptome (CDS+18 nt UTR sequence on either end) using bowtie 1.0.0 with settings “-S -t -p 30 -n 1 -m 1 -l 25 –norc”. Reads mapping within the first 63 nt of a gene (=15 codons) were excluded from further analyses to remove possible CHX induced artifacts.
Differential expression testing was performed using DESeq2 v1.14.1 and riborex v1.2.3.
Genome_build: sacCer3 (R64)
Supplementary_files_format_and_content: raw_counts_mRNA.tsv: Tab-separated text file contains raw mRNA read counts.
Supplementary_files_format_and_content: raw_counts_RPF.tsv: Tab-separated text file contains raw ribosome footprint counts. Each column represents one sample in lexicographical order.

organism: Saccharomyces cerevisiae

source_name: whole cell

growth_protocol: Xrn1-AID cells were grown to log-phase on YPD medium at 30ºC (no stress) and then subjected to auxin (500 µM) for 30 minutes (t30) or not subjected to auxin (t0). The same protocol (without auxin addition) was used for BY4741 wild-type and mutant strains.

extract_protocol:
Total RNA was extracted by a hot-phenol protocol and then mRNA was isolated with Poly(A)Purist MAG kit (Ambion). RPF were isolated from the monosomal pic (80S) coming from digestion of polysomes with RNaseI. Next, a denaturing urea gel was used to isolate the RNA fragments corresponding to ribosome footprints (Ingolia, 2009) and (Nedialkova, 2015).
Libraries were prepared using the protocol described in (Ingolia, 2009) and (Nedialkova and Leidel, 2015). For RNA-seq libraries, RNA integrity was assessed using a denaturing formaldehyde gel and mRNA isolated using the Poly(A) purist MAG kit (Ambion). For RPF libraries, ribosome footprints were size-selected and purified from a TBE-urea denaturing gel. Libraries were sequenced with Illumina HiScanSQ.

treatment_protocol: Untreated (no auxin, t0) / Xrn1 depletion (500 µM auxin for 30 minutes, t30).

value: MATa his3<delta>1 leu2<delta>0 met15<delta>0 ura3<delta>0


title: WT RPF, replicate 2

description:
Sample_lib55_WTC2_R
MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0
Ribosome footprints
Replicate 2
processed data file: raw_counts_RPF.tsv


title: Xrn1-degron T30 RPF, replicate 1

description:
Sample_lib9Xrn1Degc301R
BY25598; MATa ura3-1::ADH1-OsTIR1-9Myc(URA3) ade2-1 his3-11,15 leu2-3,112 trp1-1 can1-100 XRN1-AID (HIS)
Ribosome footprints
Replicate 1
processed data file: raw_counts_RPF.tsv


title: P1H_2_H4


title: Xrn1-degron T30 RPF, replicate 2

description:
Sample_lib10Xrn1Degc302R
BY25598; MATa ura3-1::ADH1-OsTIR1-9Myc(URA3) ade2-1 his3-11,15 leu2-3,112 trp1-1 can1-100 XRN1-AID (HIS)
Ribosome footprints
Replicate 2
processed data file: raw_counts_RPF.tsv


title: P1H_2_H3


title: P1_112


title: Xrn1-degron T0 RPF, replicate 1

description:
Sample_lib7Xrn1Degc01R
BY25598; MATa ura3-1::ADH1-OsTIR1-9Myc(URA3) ade2-1 his3-11,15 leu2-3,112 trp1-1 can1-100 XRN1-AID (HIS)
Ribosome footprints
Replicate 1
processed data file: raw_counts_RPF.tsv


title: P1H_2_H12


title: P1H_2_H2


title: AI012_T47D_24h_veh_rep1


title: WT mRNA, replicate 3

description:
Sample_lib116_WTC3_m
MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0
mRNA
Replicate 3
processed data file: raw_counts_mRNA.tsv

data_processing:
Raw sequencing reads were processed using FASTX-Toolkit to remove adapter sequences via “fastx_clipper -Q 33 -a CTGTAGGCACCATCAAT -v -c -l 25”. Subsequently, all surviving reads were mapped to sacCer3 rRNA sequences to filter out rRNA contaminations. All non-mapping reads were then used for mapping to the sacCer3 SGD transcriptome (CDS+18 nt UTR sequence on either end) using bowtie 1.0.0 with settings “-S -t -p 30 -n 1 -m 1 -l 25 –norc”. Reads mapping within the first 63 nt of a gene (=15 codons) were excluded from further analyses to remove possible CHX induced artifacts.
Differential expression testing was performed using DESeq2 v1.14.1 and riborex v1.2.3.
Genome_build: sacCer3 (R64)
Supplementary_files_format_and_content: raw_counts_mRNA.tsv: Tab-separated text file contains raw mRNA read counts.
Supplementary_files_format_and_content: raw_counts_RPF.tsv: Tab-separated text file contains raw ribosome footprint counts. Each column represents one sample in lexicographical order.


title: Xrn1 (D208A) RPF, replicate 2

description:
Sample_lib5Xrn1DcD2R
MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 xrn1D208A (HIS marker)
Ribosome footprints
Replicate 2
processed data file: raw_counts_RPF.tsv

value: MATa his3<delta>1 leu2<delta>0 met15<delta>0 ura3<delta>0 xrn1D208A (HIS marker)


title: Xrn1 (D208A) RPF, replicate 3

description:
Sample_lib6Xrn1DcD3R
MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 xrn1D208A (HIS marker)
Ribosome footprints
Replicate 3
processed data file: raw_counts_RPF.tsv


title: Xrn1 (D208A) RPF, replicate 1

description:
Sample_lib4Xrn1DcD1R
MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 xrn1D208A (HIS marker)
Ribosome footprints
Replicate 1
processed data file: raw_counts_RPF.tsv


title: P1H_2_H10


title: P1H_2_H1


title: P1H_2_H11


title: WT mRNA, replicate 2

description:
Sample_lib65_WTC2_m
MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0
mRNA
Replicate 2
processed data file: raw_counts_mRNA.tsv


title: P1H_2_G9


title: WT RPF, replicate 3

description:
Sample_lib97_WTC3_R
MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0
Ribosome footprints
Replicate 3
processed data file: raw_counts_RPF.tsv


title: WT mRNA, replicate 1

description:
Sample_lib64_WTC1_m
MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0
mRNA
Replicate 1
processed data file: raw_counts_mRNA.tsv


title: Xrn1-degron T30 mRNA, replicate 2

description:
Sample_lib28_Xrn1Deg_c_302_M
BY25598; MATa ura3-1::ADH1-OsTIR1-9Myc(URA3) ade2-1 his3-11,15 leu2-3,112 trp1-1 can1-100 XRN1-AID (HIS)
mRNA
Replicate 2
processed data file: raw_counts_mRNA.tsv


title: P1H_2_G7


title: P1H_2_G6


title: Xrn1-degron T0 mRNA, replicate 2

description:
Sample_lib26_Xrn1Deg_c_02_M
BY25598; MATa ura3-1::ADH1-OsTIR1-9Myc(URA3) ade2-1 his3-11,15 leu2-3,112 trp1-1 can1-100 XRN1-AID (HIS)
mRNA
Replicate 2
processed data file: raw_counts_mRNA.tsv


title: Xrn1-degron T0 RPF, replicate 2

description:
Sample_lib8Xrn1Degc02R
BY25598; MATa ura3-1::ADH1-OsTIR1-9Myc(URA3) ade2-1 his3-11,15 leu2-3,112 trp1-1 can1-100 XRN1-AID (HIS)
Ribosome footprints
Replicate 2
processed data file: raw_counts_RPF.tsv


title: Xrn1-degron T0 mRNA, replicate 1

description:
Sample_lib25_XrnDeg_c_01_M
BY25598; MATa ura3-1::ADH1-OsTIR1-9Myc(URA3) ade2-1 his3-11,15 leu2-3,112 trp1-1 can1-100 XRN1-AID (HIS)
mRNA
Replicate 1
processed data file: raw_counts_mRNA.tsv


title: P1H_2_G8


title: Xrn1-degron T30 mRNA, replicate 1

description:
Sample_lib27_Xrn1Deg_c_301_M
BY25598; MATa ura3-1::ADH1-OsTIR1-9Myc(URA3) ade2-1 his3-11,15 leu2-3,112 trp1-1 can1-100 XRN1-AID (HIS)
mRNA
Replicate 1
processed data file: raw_counts_mRNA.tsv


title: Xrn1 (D208A) mRNA, replicate 2

description:
Sample_lib17_Xrn1D_c_D2_M
MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 xrn1D208A (HIS marker)
mRNA
Replicate 2
processed data file: raw_counts_mRNA.tsv


title: Xrn1 (D208A) mRNA, replicate 1

description:
Sample_lib16_Xrn1D_c_D1_M
MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 xrn1D208A (HIS marker)
mRNA
Replicate 1
processed data file: raw_counts_mRNA.tsv


title: P1H_2_G5


title: P1H_2_G2


title: P1H_2_G3


title: freeze_Mg

city: Baltimore

first: Allen

middle: R

last: Buskirk

address: 725 N. Wolfe St

department: Molecular Biology and Genetics

institute: Johns Hopkins University School of Medicine

description: mRNA: ribosome footprints

data_processing:
Reads with N bases or Phred < 10 were dropped. The linker sequence was trimmed and reads mapping to rRNA or tRNA sequences were discarded. The remaining reads were mapped to the E. coli K-12 MG1655 genome version 2 with bowtie allowing two mismatches.
Genome_build: NC_000913ver2
Supplementary_files_format_and_content: WIG files of ribosome occupancy, assigned to the 3'-end of reads, normalized by the total number of reads in the library.

organism: Escherichia coli str. K-12 substr. MG1655

source_name: cell cultures

growth_protocol: Cultures were grown in MOPS complete synthetic media to mid log phase and harvested by filtration (200 mL) or direct freezing (50 mL)

extract_protocol:
Cell pellets were cryogenically pulverized in a Spex 6870 freezer mill; 5 cycles of 1 min at 5 Hz with 1 min cooling. Cell lysates were clarified, digested with nucleases, and monosomes were purified over a sucrose gradient.
Ribosome footprints and total RNA fragments were PAGE purified, ligated to a linker using RNA ligase T2, converted to DNA using RT, circularized, and PCR amplified.
OTHER (ribosome profiling)

value: freeze Mg

tag: drug treatment in culture

tag: harvesting method

value: direct freeze

value: lysis buffer containing:150 mM MgCl2


title: P1H_2_G12

value: neuron

tag: age


title: freeze_Mg_MPC

description: mRNA: ribosome footprints

value: freeze Mg MPC

value: mupirocin


title: freeze_Mg_ctrl

description: mRNA: ribosome footprints

value: freeze Mg ctrl


title: P1H_2_G11


title: P1H_2_G10


title: P1H_2_G1


title: P1H_2_F8


title: filter_Cm_MPC

description: mRNA: ribosome footprints

value: filter Cm MPC

value: filtration

value: lysis buffer containing:Cm


title: P1H_2_F7

value: postnatal day 1


title: P1H_2_F9


title: filter_Mg_ctrl

description: mRNA: ribosome footprints

value: filter Mg ctrl


title: filter_Mg_MPC

description: mRNA: ribosome footprints

value: filter Mg MPC


title: P1H_2_F6

value: Pitx3tm1Mli homozygote


title: filter_Mg

description: mRNA: ribosome footprints

value: filter Mg


title: P1H_2_G4

value: ERCC


title: media_Cm

description: mRNA: ribosome footprints

value: media Cm

value: chloramphenicol


title: P1H_2_F4


title: P1H_2_F5


title: P1H_2_F3


title: P1H_2_F12


title: P1H_2_F2


title: MRNAi4_16S rRNA Seq

city: Nanjing City

first: Xingyin

state: Jiangsu Province

address: Long Mian Street No.1

institute: Nanjing Medical University

description:
processed data file:
KDM5_RNAi_OTU_assignment_and_abundance.new.txt
KDM5_RNAi_OTU_new.fasta

data_processing:
Raw fastq files were quality-filtered by Trimmomatic and merged by FLASH according to the following criteria: (i) The reads were truncated at any site receiving an average quality score <20 over a 50 bp sliding window. (ii) Sequences whose overlap being longer than 10 bp were merged according to their overlap with mismatch no more than 2 bp. (iii)Sequences of each sample were separated according to barcodes (exactly matching) and Primers (allowing 2 nucleotide mismatching), and reads containing ambiguous bases were removed.
Operational taxonomic units (OTUs) were subtract to negative controls to prevent any potential contaminant 16S reads. clustered with 97% similarity cutoff using UPARSE（version 7.1 http://drive5.com/uparse/) with a novel ‘greedy’ algorithm that performs chimera filtering and OTU clustering simultaneously.
The taxonomy of each 16S rRNA gene sequence was analyzed by RDP Classifier algorithm (http://rdp.cme.msu.edu/) against the Silva (SSU123) 16S rRNA database using confidence threshold of 70%.
To subtracted potential contenminates existed in kit and water, only genera OTU with an average relative abundance ≥10-4 and existed in at least 10% subjects were considered in the analyses.
Supplementary_files_format_and_content: The sequences of each OTU are in "OTU.fasta.new". The assignment and abundance of OTU in each sample are shown in "OTU assignment and abundance.txt.new", the number in “OTU assignment and abundance.txt.new” is the abundance of OTU in each sample.

organism: Drosophila melanogaster

source_name: Gut_kdm5 RNAi

growth_protocol: Flies were reared and maintained at 25°C, 50% relative humidity and a 12-hour light/dark cycle

extract_protocol:
Total genome DNA from 30 adult fly midguts was extracted using the kit (Tiangen, Beijing, China). DNA concentration and purity was assessed on the Qubit@ 2.0 Fluorometer (Thermo Scientific).  The V3-V4 region of the bacterial 16S rRNA gene was amplified with the common primer pair (Forward primer, 5'- ACTCCTACGGGAGGCAGCA-3'; reverse primer, 5'- GGACTACHVGGGTWTCTAAT-3')  combined with adapter sequences and barcode sequences. PCR amplification was performed in a total volume of 50 μl, which contained 10 μl Bμffer, 0.2 μl Q5 High-Fidelity DNA Polymerase, 10 μl High GC Enhancer, 1 μl dNTP, 10μM of each primer and 60 ng genome DNA. Thermal cycling conditions were as follows: an initial denaturation at 95 °C for 5 min, followed by 15 cycles at 95 °C for 1 min, 50 °C for 1 min and 72 °C for 1 min, with a final extension at 72 °C for 7 min. The PCR products from the first step PCR were purified through VAHTSTM DNA Clean Beads. A second round PCR was then performed in a 40μl reaction which contained 20 μl 2×Phμsion HF MM, 8 μl ddH2O, 10μM of each primer and 10μl PCR products from the first step. Thermal cycling conditions were as follows: an initial denaturation at 98 °C for 30s, followed by 10 cycles at 98 °C for 10s, 65 °C for 30s min and 72 °C for 30s, with a final extension at 72 °C for 5 min. Finally, all PCR products were quantified by Quant-iT™ dsDNA HS Reagent and pooled together. High-throughput sequencing analysis of bacterial rRNA genes was performed on the purified, pooled sample using the Illumina Hiseq 2500 platform(2×250 paired ends) at Biomarker Technologies Corporation, Beijing, China.
Purified amplicons were pooled in equimolar and paired-end sequenced (2 × 250) on an Illumina Hiseq 2500 platform.

tag: tissue

value: intestine

tag: condition

value: mutant

tag: Sex

value: female


title: MRNAi5_16S rRNA Seq

tag: genotype


title: MRNAi2_16S rRNA Seq


title: MRNAi3_16S rRNA Seq


title: MRNAi1_16S rRNA Seq


title: P1H_2_F10

value: neuron

tag: spike-in


title: P1H_2_F1


title: MWT5_16S rRNA Seq

value: control


title: filter_Cm_ctrl

description: mRNA: ribosome footprints

value: filter Cm ctrl


title: P1H_2_E9


title: MWT4_16S rRNA Seq


title: MWT3_16S rRNA Seq


title: filter_NaCl

description: mRNA: ribosome footprints

value: filter NaCl

value: lysis buffer containing:1 M NaCl


title: P1H_2_E8


title: MWT2_16S rRNA Seq


title: MWT1_16S rRNA Seq


title: P1H_2_E6


title: P1H_2_E7


title: KD.LP2_16S rRNA Seq

description:
processed data file:
OTU assignment and abundance of kdm5 flies feeding LP.txt

data_processing:
Raw fastq files were quality-filtered by Trimmomatic and merged by FLASH according to the following criteria: (i) The reads were truncated at any site receiving an average quality score <20 over a 50 bp sliding window. (ii) Sequences whose overlap being longer than 10 bp were merged according to their overlap with mismatch no more than 2 bp. (iii)Sequences of each sample were separated according to barcodes (exactly matching) and Primers (allowing 2 nucleotide mismatching), and reads containing ambiguous bases were removed.
Operational taxonomic units (OTUs) were subtract to negative controls to prevent any potential contaminant 16S reads. clustered with 97% similarity cutoff using UPARSE?version 7.1 http://drive5.com/uparse/) with a novel ?greedy? algorithm that performs chimera filtering and OTU clustering simultaneously.
The taxonomy of each 16S rRNA gene sequence was analyzed by RDP Classifier algorithm (http://rdp.cme.msu.edu/) against the Silva (SSU123) 16S rRNA database using confidence threshold of 70%.
To subtracted potential contaminates existed in kit and water, only genera OTU with an average relative abundance of greater or equal to 10^-4 and existed in at least 10% subjects were considered in the analyses.

source_name: Gut_feeding with Lactobacillus plantarum

growth_protocol: Flies were reared and maintained at 25°C, 50% relative humidity and a 12-hour light/dark cycle.

extract_protocol:
Total genome DNA of gut samples was extracted using the kit (Tiangen Company, Beijing, China). The DNA concentration was performed using Qubit@ 2.0 Fluorometer (Thermo Scientific). DNA quality was also monitored on 1% agarose gels. PCR was performed to produce V4 regions of the 16S rDNA gene using the conserved primers 515F (5’-GTGCCAGCMGCCGCGGTAA-3’) and 806R (5’-GGACTACHVGGGTWTCTAAT-3’). PCR products and operate electrophoresis on 2% agarose gel for detection. Samples with bright main strip between 400-450bp were chosen for purifing with GeneJET Gel Extraction Kit (Thermo Scientific). PCR fragments were sequenced by Novogene Bioinformatics Technology Co., Ltd. (Tianjin, China).
Libraries was sequenced on an Illumina HiSeq platform and 250 bp paired-end reads were generated.

treatment_protocol: Since Lactobacillus is resistant to vancomycin, to abolish other pathogenic bacteria effects, newborn kdm5 mutant flies were transferred to a new diet containing vancomycin (30 μg/mL) 2 days before feeding with food supplemented with L. plantarum (OD＝600) or normal food. DNA was extracted after flies feeding with L. plantarum or normal food for 3 days. L. plantarum culture was prepared freshly every day.

tag: feeding condition

value: Feeding with Lactobacillu plantarum


title: P1H_2_E5

value: postnatal day 1


title: KD.LP1_16S rRNA Seq


title: KD.LP3_16S rRNA Seq


title: KD3_16S rRNA Seq

source_name: Gut_normal food

value: Normal food


title: P1H_2_F11


title: P1H_2_E3


title: P1H_2_E4


title: P1H_2_E2


title: P1H_2_E11


title: P1H_2_E10


title: KD1_16S rRNA Seq


title: KD2_16S rRNA Seq


title: W5_16S rRNA Seq

description:
processed data file:
OTUs.tax_assignments_update.xls.gz

source_name: Female whole animal

extract_protocol:
Total genome DNA from 30 adult fly midguts was extracted using the kit (Tiangen, Beijing, China). DNA concentration and purity was assessed on the Qubit@ 2.0 Fluorometer (Thermo Scientific). 16S rRNA genes were amplified used the specific V4 primers 515F-806R. All PCR products and operate electrophoresis on 2% agarose gel for detection. Samples with bright main strip between 400-450bp were chosen for further experiments.
Libraries was sequenced on an Illumina HiSe platform and 250 bp paired-end reads were generated.

tag: passages

value: 1-3 days


title: W4_16S rRNA Seq


title: P1H_2_E1

tag: cell type

value: Pitx3tm1Mli homozygote


title: P1H_2_D8


title: P1H_2_D9


title: P1H_2_D7


title: W3_16S rRNA Seq

tag: strain


title: W2_16S rRNA Seq


title: K4_16S rRNA Seq


title: W1_16S rRNA Seq


title: K2_16S rRNA Seq


title: P1H_2_D6


title: K5_16S rRNA Seq


title: P1H_2_D5


title: K1_16S rRNA Seq


title: P1H_2_E12


title: P1H_2_D2


title: K3_16S rRNA Seq


title: P1H_2_D11


title: P1H_2_D10


title: P1H_2_D1


title: P1H_2_C9


title: P1H_2_C8


title: P1H_2_C7


title: Jan30_Cell_16

city: Cincinnati

first: Yael

last: Haberman

state: OH

address: 3333 Burnet Ave

department: Gastroenterology

institute: Cincinnati Children's Hospital

data_processing:
Basecalling was performed with Illumina's bcl2fastq v2.15.0
Identifying information was removed from the fastqs with desnp v1.0 (manuscript in preparation)
kallisto v0.42.5 was used to quantify transcripts from two different models: Gencode v26 and the UCSC knownGenes table (Dec 2014).  Parameters: --bias
Genome_build: GRCh38
Supplementary_files_format_and_content: Abundance.tsv files from kallisto: tab-separated, containing abundance estimates in TPM

source_name: esophagus

extract_protocol:
Single cells were isolated on the Fluidigm C1 system using the 7-10 uM capture chip and manually examined to remove empty chambers and chambers with multiple cells
Libraries were constructed using the SMARTer Ultra Low RNA Kit for the Fluidigm C1 system (CloneTech)

tag: disease

value: Remission

tag: cell isolation batch

tag: cluster


title: Feb29_Cell_96

value: ActiveEOE


title: Feb29_Cell_95


title: Jan30_Cell_17


title: Feb29_Cell_94


title: P1H_2_D4

value: ERCC


title: Feb29_Cell_92


title: Feb29_Cell_93


title: P1H_2_C6


title: P1H_2_C4


title: Feb29_Cell_90


title: P1H_2_D3


title: Feb29_Cell_9


title: P1H_2_C5


title: Feb29_Cell_91


title: P1H_2_C3


title: Feb29_Cell_89


title: P1H_2_D12


title: Feb29_Cell_88


title: Jan30_Cell_14


title: P1H_2_C12


title: Jan30_Cell_13


title: Feb29_Cell_87


title: P1H_2_C10


title: P1H_2_C1


title: Feb29_Cell_85


title: Feb29_Cell_84


title: P1H_2_B8


title: Feb29_Cell_82


title: P1H_2_B5


title: P1H_2_B9


title: Feb29_Cell_86


title: P1H_2_B6


title: Feb29_Cell_80


title: P1H_2_B7


title: P1H_2_B2


title: P1H_2_C2


title: P1H_2_C11


title: Feb29_Cell_81


title: Feb29_Cell_78


title: Feb29_Cell_79


title: Feb29_Cell_8


title: P1H_2_B12


title: P1H_2_B4


title: P1H_2_B11


title: Feb29_Cell_83


title: Feb29_Cell_76


title: P1H_2_B3


title: Feb29_Cell_75


title: Feb29_Cell_77


title: P1H_2_A9


title: P1H_2_B1


title: P1H_2_B10


title: P1H_2_A8


title: P1H_2_A7


title: P1H_2_A6


title: Feb29_Cell_71


title: Feb29_Cell_73


title: Feb29_Cell_72


title: P1H_2_A5


title: Feb29_Cell_7


title: P1H_2_A4


title: P1H_2_A2


title: Feb29_Cell_69


title: Feb29_Cell_70


title: Feb29_Cell_64


title: Feb29_Cell_65


title: Feb29_Cell_68


title: Feb29_Cell_66


title: P1H_2_A12


title: Feb29_Cell_67


title: P1H_2_A11


title: P1H_2_A10


title: Feb29_Cell_63


title: Feb29_Cell_74


title: P1H_2_A1


title: Feb29_Cell_6


title: P1H_1_H9


title: P1H_1_H7


title: P1H_1_H6


title: Feb29_Cell_4


title: P1H_1_H5


title: P1H_1_H3


title: Feb29_Cell_2


title: P1H_1_H4


title: Feb29_Cell_20


title: Feb29_Cell_3


title: P1H_1_H2


title: Feb29_Cell_19


title: Feb29_Cell_18


title: P1H_2_A3


title: P1H_1_H8


title: Feb29_Cell_17


title: P1H_1_H11


title: Feb29_Cell_5


title: P1H_1_G9


title: P1H_1_G8


title: Feb29_Cell_16


title: Feb29_Cell_12


title: Feb29_Cell_14


title: Feb29_Cell_15


title: P1H_1_H1


title: Feb29_Cell_13


title: P1H_1_G7


title: Feb29_Cell_11


title: P1H_1_G6


title: P1H_1_G5


title: Feb29_Cell_10


title: P1H_1_G4


title: P1H_1_G3


title: Feb22_Cell_8


title: P1H_1_G2


title: P1H_1_G11


title: P1H_1_G12


title: Feb29_Cell_1


title: Feb22_Cell_62


title: Feb22_Cell_61


title: P1H_1_G1


title: P1H_1_G10


title: Feb22_Cell_58


title: Feb22_Cell_59


title: Feb22_Cell_60


title: Feb22_Cell_6


title: P1H_1_F9


title: P1H_1_F8


title: Feb22_Cell_57


title: P1H_1_F7


title: P1H_1_F5


title: P1H_1_F4


title: P1H_1_F3


title: P1H_1_F6


title: Feb22_Cell_55


title: P1H_1_F2


title: Feb22_Cell_51


title: P1H_1_F11


title: Feb22_Cell_9


title: Feb22_Cell_56


title: Feb22_Cell_7


title: P1H_1_F1


title: Feb22_Cell_50


title: Feb22_Cell_54


title: P1H_1_F10


title: Feb22_Cell_5


title: Feb22_Cell_53


title: P1H_1_E7


title: P1H_1_E9


title: Feb22_Cell_48


title: P1H_1_E8


title: P1H_1_E4


title: P1H_1_E3


title: P1H_1_E6


title: P1H_1_E5


title: Feb22_Cell_47


title: Feb22_Cell_52


title: P1H_1_E2


title: P1H_1_F12


title: Feb22_Cell_49


title: P1H_1_E12


title: P1H_1_E10


title: P1H_1_E11


title: Feb22_Cell_44


title: Feb22_Cell_42


title: Feb22_Cell_43


title: Feb22_Cell_46


title: Feb22_Cell_45


title: P1H_1_E1


title: Feb22_Cell_4


title: Feb22_Cell_39

value: Low Del


title: P1H_1_D9


title: Feb22_Cell_38


title: P1H_1_D8


title: Feb22_Cell_36


title: P1H_1_D7


title: P1H_1_D5


title: P1H_1_D4


title: Feb22_Cell_35


title: Feb22_Cell_40


title: Feb22_Cell_32


title: P1H_1_D3


title: P1H_1_D6


title: Feb22_Cell_33


title: Feb22_Cell_41


title: Feb22_Cell_31


title: Feb22_Cell_37


title: Feb22_Cell_3


title: Feb22_Cell_30


title: P1H_1_D11


title: P1H_1_D10


title: Feb22_Cell_28


title: P1H_1_D1


title: P1H_1_C8


title: Feb22_Cell_26


title: Feb22_Cell_27


title: P1H_1_D2


title: Feb22_Cell_25


title: P1H_1_C7


title: P1H_1_D12


title: P1H_1_C9


title: Feb22_Cell_24


title: Feb22_Cell_34


title: P1H_1_C6


title: Feb22_Cell_23


title: P1H_1_C5


title: P1H_1_C4


title: Feb22_Cell_29


title: P1H_1_C3


title: Feb22_Cell_21


title: Feb22_Cell_22


title: P1H_1_C12


title: Feb22_Cell_2


title: Feb22_Cell_19


title: P1H_1_C11


title: Feb22_Cell_16


title: Feb22_Cell_15


title: P1H_1_B8


title: Feb22_Cell_14


title: Feb22_Cell_18


title: P1H_1_B6


title: Feb22_Cell_13


title: Feb22_Cell_12


title: P1H_1_B4


title: P1H_1_C2


title: P1H_1_B3


title: P1H_1_C10


title: P1H_1_H10


title: Feb13_Cell_96


title: P1H_1_B7


title: P1H_1_B10


title: Feb13_Cell_92


title: P1H_1_B1


title: Feb13_Cell_93


title: P1H_1_B9


title: P1H_1_B5


title: Feb13_Cell_91


title: Feb13_Cell_90


title: Feb22_Cell_20


title: Feb22_Cell_10


title: P1H_1_A8


title: Feb22_Cell_1


title: P1H_1_B12


title: P1H_1_A5


title: Feb13_Cell_88


title: P1H_1_H12


title: P1H_1_B2


title: Feb22_Cell_17


title: Feb13_Cell_87


title: Feb13_Cell_95


title: P1H_1_B11


title: P1H_1_A3


title: P1H_1_A2


title: Feb13_Cell_86


title: Feb13_Cell_85


title: P1H_1_A12


title: Feb22_Cell_11


title: P1H_1_A9


title: P1H_1_A7


title: Feb13_Cell_9


title: P1H_1_A6


title: P1H_1_A10


title: Feb13_Cell_82


title: Feb13_Cell_83


title: Feb13_Cell_89


title: P1H_1_A4


title: Feb13_Cell_81


title: 18_2_H9

value: Pitx3tm1Mli heterozygote

value: embryonic day 18.5


title: 18_2_H7


title: Feb13_Cell_79


title: P1H_1_A1


title: Feb13_Cell_94


title: 18_2_H8


title: 18_2_H6


title: 18_2_H5


title: Feb13_Cell_77


title: Feb13_Cell_78


title: Feb13_Cell_76


title: 18_2_H3


title: 18_2_H2


title: P1H_1_A11


title: Feb13_Cell_84


title: 18_2_H12


title: Feb13_Cell_7


title: Feb13_Cell_5


title: 18_2_H1


title: Feb13_Cell_50


title: 18_2_H10


title: Feb13_Cell_6


title: Feb13_Cell_80


title: Feb13_Cell_49


title: Feb13_Cell_51


title: 18_2_G9


title: Feb13_Cell_8


title: Feb13_Cell_48


title: Feb13_Cell_47


title: P1H_1_C1


title: 18_2_G7


title: 18_2_H4


title: 18_2_G3


title: 18_2_G6


title: Feb13_Cell_46


title: Feb13_Cell_45


title: Feb13_Cell_42


title: Feb13_Cell_43


title: 18_2_G5


title: Feb13_Cell_40


title: 18_2_G11


title: 18_2_G10


title: 18_2_G2


title: 18_2_G4


title: 18_2_G12


title: Feb13_Cell_38


title: 18_2_G8


title: 18_2_F9


title: Feb13_Cell_41


title: 18_2_F7


title: 18_2_H11


title: 18_2_F8


title: Feb13_Cell_35


title: Feb13_Cell_44


title: Feb13_Cell_37


title: 18_2_F5


title: Feb13_Cell_34


title: Feb13_Cell_33


title: Feb13_Cell_32


title: 18_2_F3


title: 18_2_F6


title: Feb13_Cell_31


title: 18_2_F2


title: 18_2_F4


title: Feb13_Cell_4


title: Feb13_Cell_39


title: Feb13_Cell_30


title: 18_2_F11


title: 18_2_F12


title: Feb13_Cell_3


title: 18_2_F10


title: Feb13_Cell_28


title: 18_2_F1


title: Feb13_Cell_29


title: 18_2_E9


title: Feb13_Cell_26


title: Feb13_Cell_27


title: Feb13_Cell_25


title: 18_2_E8


title: 18_2_E7


title: 18_2_E5


title: Feb13_Cell_22


title: 18_2_E6


title: 18_2_E3


title: Feb13_Cell_23


title: Feb13_Cell_20


title: 18_2_E2


title: 18_2_E12


title: Feb13_Cell_2


title: 18_2_E11


title: Feb13_Cell_18


title: Feb13_Cell_19


title: 18_2_E10


title: Feb13_Cell_17


title: 18_2_E1


title: 18_2_D9


title: 18_2_D8


title: Feb13_Cell_15


title: Feb13_Cell_16


title: Feb13_Cell_14


title: 18_2_D6


title: 18_2_D7


title: Feb13_Cell_13


title: Feb13_Cell_12


title: Feb13_Cell_11


title: 18_2_D5


title: 18_2_D4


title: Feb13_Cell_1


title: Feb13_Cell_21


title: 18_2_D3


title: 18_2_E4


title: Feb13_Cell_10


title: Dec8_Cell_96


title: 18_2_D12


title: Dec8_Cell_94


title: 18_2_D10


title: Dec8_Cell_95


title: 18_2_D11


title: Dec8_Cell_93


title: 18_2_D1


title: Dec8_Cell_92


title: 18_2_C9


title: 18_2_C8


title: 18_2_C7


title: Dec8_Cell_9


title: Dec8_Cell_91


title: Dec8_Cell_90


title: Dec8_Cell_89


title: 18_2_C4


title: Dec8_Cell_88


title: 18_2_C6


title: 18_2_C5


title: 18_2_C3


title: Dec8_Cell_85


title: 18_2_C2


title: Dec8_Cell_84


title: 18_2_C11


title: 18_2_C12


title: Dec8_Cell_86


title: 18_2_C10


title: Dec8_Cell_83


title: 18_2_C1


title: Dec8_Cell_87


title: Dec8_Cell_81


title: 18_2_B9


title: 18_2_D2


title: 18_2_B8


title: Dec8_Cell_8


title: 18_2_B7


title: Dec8_Cell_79


title: 18_2_B6


title: Dec8_Cell_78


title: 18_2_B5


title: 18_2_B4


title: Dec8_Cell_76


title: Dec8_Cell_77


title: 18_2_B3


title: Dec8_Cell_74


title: Dec8_Cell_72


title: Dec8_Cell_82


title: 18_2_B1


title: 18_2_A9


title: 18_2_B12


title: Dec8_Cell_80


title: 18_2_B10


title: 18_2_A8


title: 18_2_A7


title: Dec8_Cell_75


title: Dec8_Cell_6


title: Dec8_Cell_73


title: Dec8_Cell_71


title: 18_2_B11


title: 18_2_A6


title: 18_2_B2


title: 18_2_A5


title: 18_2_A3


title: 18_2_A4


title: Dec8_Cell_2


title: Dec8_Cell_4


title: Dec8_Cell_3


title: Dec8_Cell_7


title: Dec8_Cell_12


title: 18_2_A2


title: 18_2_A12


title: Dec8_Cell_11


title: 18_2_A10


title: Dec5_Cell_9


title: Dec8_Cell_10


title: Dec5_Cell_8


title: 18_2_A11


title: Dec8_Cell_1


title: Dec5_Cell_69


title: Dec8_Cell_5


title: 18_1_H6


title: Dec5_Cell_67


title: Dec5_Cell_66


title: 18_1_H5


title: Feb13_Cell_24


title: 18_2_A1


title: Dec5_Cell_65


title: 18_1_H7


title: Dec5_Cell_63


title: Dec8_Cell_70


title: 18_1_H9


title: 18_1_H8


title: Feb13_Cell_36


title: Dec5_Cell_61


title: Dec5_Cell_68


title: Dec5_Cell_62


title: 18_1_H11


title: Dec5_Cell_64


title: 18_1_H4


title: 18_1_H1


title: Dec5_Cell_58


title: Dec5_Cell_59


title: 18_1_H10


title: Dec5_Cell_60


title: 18_1_H12


title: 18_1_G9


title: Dec5_Cell_57


title: Dec5_Cell_56


title: Dec5_Cell_54


title: 18_1_G8


title: Dec5_Cell_53


title: 18_1_G5


title: 18_1_G6


title: 18_1_H2


title: 18_1_G4


title: 18_1_G3


title: Dec5_Cell_52


title: Dec5_Cell_51


title: Dec5_Cell_50


title: 18_1_G11


title: 18_1_G2


title: 18_1_G12


title: 18_1_G10


title: Dec5_Cell_48


title: 18_1_G1


title: 18_1_F9


title: 18_1_G7


title: 18_1_F8


title: Dec5_Cell_45


title: Dec5_Cell_44


title: Dec5_Cell_55


title: Dec5_Cell_46


title: 18_1_F4


title: Dec5_Cell_43


title: 18_1_F7


title: 18_1_F6


title: Dec5_Cell_41


title: 18_1_F3


title: Dec5_Cell_42


title: Dec5_Cell_49


title: 18_1_F5


title: Dec5_Cell_39


title: Dec5_Cell_37


title: Dec5_Cell_38


title: Dec5_Cell_34


title: 18_1_F2


title: 18_1_F12


title: Dec5_Cell_47


title: 18_1_F11


title: Dec5_Cell_33


title: Dec5_Cell_40


title: Dec5_Cell_36


title: 18_1_E9


title: Dec5_Cell_31


title: 18_1_E7


title: 18_1_E5


title: 18_1_E4


title: Dec5_Cell_29


title: 18_1_F10


title: Dec5_Cell_25


title: Dec5_Cell_26


title: 18_1_E11


title: Dec5_Cell_22


title: 18_1_E12


title: Dec5_Cell_21


title: 18_1_E1


title: 18_1_D9


title: Dec5_Cell_24


title: 18_1_D8


title: Dec5_Cell_35


title: 18_1_E10


title: 18_1_E8


title: Dec5_Cell_19


title: 18_2_G1


title: 18_1_D5


title: 18_1_D4


title: 18_1_H3


title: Dec5_Cell_16


title: Dec5_Cell_20


title: 18_1_D12


title: 18_1_D2


title: 18_1_D11


title: Dec5_Cell_13


title: Dec5_Cell_15


title: Dec5_Cell_14


title: Dec5_Cell_32


title: 18_1_E3


title: Dec5_Cell_27


title: Dec5_Cell_28


title: 18_1_E6


title: 18_1_E2


title: 18_1_D1


title: Dec5_Cell_12


title: 18_1_F1


title: 18_1_C9


title: Dec1_Cell_96


title: 18_1_C8


title: 18_1_D7


title: Dec5_Cell_23


title: Dec5_Cell_30


title: Dec1_Cell_94


title: 18_1_C5


title: Dec1_Cell_93


title: Dec5_Cell_18


title: Dec1_Cell_92


title: 18_1_C4


title: Dec5_Cell_17


title: 18_1_D3


title: 18_1_D6


title: 18_1_D10


title: Dec5_Cell_11


title: 18_1_C3


title: 18_1_C12


title: Dec5_Cell_10


title: 18_1_C7


title: Dec1_Cell_87


title: 18_1_C6


title: 18_1_B9


title: 18_1_C2


title: Dec1_Cell_85


title: Dec1_Cell_84


title: Dec1_Cell_89


title: Dec1_Cell_90


title: 18_1_C10


title: 18_1_B8


title: Dec1_Cell_88


title: Dec1_Cell_83


title: 18_1_B7


title: Dec1_Cell_91


title: Dec1_Cell_86


title: 18_1_C1


title: 18_1_B4


title: Dec1_Cell_79


title: 18_1_B3


title: Dec1_Cell_78


title: Dec1_Cell_95


title: Dec1_Cell_81


title: 18_1_B5


title: 18_1_C11


title: Dec1_Cell_76


title: 18_1_B6


title: 18_1_B12


title: Dec1_Cell_82


title: Dec1_Cell_75


title: 18_1_B11


title: 18_1_B10


title: Dec1_Cell_73


title: 18_1_B2


title: Dec1_Cell_80


title: 18_1_A9


title: Dec1_Cell_74


title: Dec1_Cell_72


title: Dec1_Cell_71


title: 18_1_B1


title: 18_1_A7


title: 18_1_A8


title: Dec1_Cell_70


title: 18_1_A6


title: Dec1_Cell_7


title: 18_1_A5


title: Dec1_Cell_77


title: 18_1_A2


title: Dec1_Cell_69


title: 18_1_A11


title: Dec1_Cell_64


title: 18_1_A12


title: 18_1_A4


title: 18_1_A3


title: 18_1_A10


title: Dec1_Cell_63


title: Dec1_Cell_67


title: Dec1_Cell_65


title: Dec1_Cell_66


title: Dec1_Cell_62


title: 18_1_A1


title: Dec1_Cell_60


title: Dec1_Cell_6


title: 15_95

value: embryonic day 15.5

value: no


title: 15_96

value: neuron


title: Dec1_Cell_68


title: 15_93


title: 15_94


title: Dec1_Cell_59


title: Dec1_Cell_58


title: Dec1_Cell_56


title: 15_92


title: Dec1_Cell_57


title: 15_87


title: 15_90


title: 15_88


title: 15_9


title: Dec1_Cell_55


title: Dec1_Cell_54


title: Dec1_Cell_52


title: Dec1_Cell_53


title: Dec1_Cell_51


title: 15_85


title: Dec1_Cell_50


title: 15_84


title: Dec1_Cell_61


title: 15_8


title: Dec1_Cell_45


title: 15_80


title: 15_91


title: Dec1_Cell_47


title: 15_83


title: Dec1_Cell_5


title: Dec1_Cell_44


title: 15_75


title: Dec1_Cell_49


title: Dec1_Cell_4


title: Dec1_Cell_48


title: 15_78


title: 15_72


title: 15_79


title: Dec1_Cell_46


title: 15_69


title: 15_86


title: 15_76


title: Dec1_Cell_1


title: 15_77


title: 15_63


title: 15_71


title: Dec1_Cell_43


title: 15_68


title: Dec1_Cell_3


title: 15_7


title: Aug29_Cell_81


title: Aug29_Cell_83


title: Aug29_Cell_79


title: Aug29_Cell_82


title: Aug29_Cell_78


title: Dec1_Cell_2


title: 15_62


title: 15_56


title: Aug29_Cell_76


title: Aug29_Cell_75


title: Aug29_Cell_80


title: 15_61


title: 15_60