title: Mirlet7d_Input

data_processing:
Raw  reads  were  visualized  by  FastQC  to  determine  the  quality  of  the  sequencing.  Trimming  was  performed  using  trimmomatic  with  the  following  parameters  LEADING:3  TRAILING:3  SLIDINGWINDOW:4:15 MINLEN
:17 CROP:60 HEADCROP:6.
High quality reads were mapped  to the NONCODE V4.0 for  the  ncRNAs  and  to  the    GENECODE  M1  version  for   the   protein   coding   genes using bowtie2 with  (-D  15  -R  3  -N  0  -L  20  -i  S,  1,  0.56  -p8.  After  mapping,  the  sam  files  were  converted  to bam  format  by  using  samtools  view (-Sb)  followed  by  samtools  sort.  The sorted bam  files  were  further  converted  to  fastq  files  with  SamToFastq.jar  from  picard-tools-1.119  and  remapped  to  mm9  (UCSC reference genome). The tag libraries were created by using MakeTaglibrary from HOMER (-format  sam).  The  makeUCSCfile command  was  used  for  visual
izing  the  mapped  sequence  tag  density  after  normalizing  the  samples  to  10  million.  For  the  ncRNAs  and  for  protein  coding  RNAs, samples were  quantified by using analyzeRepeats.pl with   the   parameters   (analyzeRepeats.pl database.gtf mm9 -count genes -s trand both and -rpkm; reads per kilobase per millions mapped). The  NONCODE_V.4.gtf  file  was  used  to  quantify  ncRNAs  and the  GENECODE_M1.gtf  file  was used to quantify protein coding RNAs.
Mirlet7d bound ncRNAs and protein coding RNAs were identified by calculating the enrichment of the RNA-seq mapped reads (RPKM) after Mirlet7d-Pd over the input reads. KNIME 2.9.1 platform (Konstanz, Germany) was used to filter more than 2.5 times (FC>2.5) enriched ncRNAs and coding RNAs in the Mirlet7d-Pd compared to the input, by using the column filter, numeric binner and row filter nodes.
 The distribution of the different ncRNA to the gene areas (Introns, Exons and 3’-UTRs) and promoter (TSS, Transcriptional Start Site, +/- 2.5 Kb) was analyzed using Bedtools v2.15  (intersect -wa -wb), crossing the  two bed files, one was the bed file obtained from UCSC table browser from the mm9 promoter Refseq database track and the other file was the bed coordinate from the ncRNA, where the  Mirlet7d -Pd was enriched (FC>2.5) over the input. The classification of the ncRNA was made by NONCODE name per region.
Supplementary_files_format_and_content: Bedgraph_UCSC files to load in the UCSC genome Browser

value: Input for Pull_Down

tag: protocol


title: Mirlet7d_Pull_Down

status: Public on Apr 06 2018

type: SRA

city: Nancy Cedex

first: Guillermo

last: Barreto

address: 9, Avenue de la Forêt de Haye ‐ BP 20199

department: Campus Biologie-Santé. Faculté de Médecine

country: France

institute: CNRS Director of Research

description: Custom LNA oligonucleotide from EXIQON

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

growth_protocol: MLE-12 cells were kept at 37°c in DMEM medium containing 10 % Fetal Calf Serum, and 1% P/S/G (penicillin/Streptomycin/L-glutamine)

extract_protocol:
Total RNA was isolated with TRIzol(R)  (Invitrogen)
[Nuclear_RNA_seq] Libraries were prepared according to SMARTer Stranded Total RNA Sample Prep Kit - HI Mammalian (including rRNA depletion RiboGone)
[Pull_Down_Input_Mirlet7d] Libraries were treated the Kit  for rRNA depletion by RiboGone™ - Mammalian and Pre-amplification step was performed with pre-amplification using SMARTer® Universal Low Input RNA Kit for Sequencing

treatment_protocol: MLE-12 cells were transfected with 25nM of Biotinylated microRNA (Random or Mirlet7d) and harsvested after 48 h

tag: cell line

tag: sample type

value: pull down experiment (Mirlet7d_Biotinylated was used for the pull down with streptavidin beads)


title: trans input 1

city: Barcelona

first: Guillaume

last: Diss

address: C/ Dr. aiguader, 88

country: Spain

institute: CRG

description:
from plasmid library
TableS1.xlsx

library_source: genomic

data_processing:
trans library filtering (sample 1-6): Paired reads for which one of the two variable regions had an average Phred score below or equal to 20 were also discarded. Additionally, paired reads were also filtered-out if they had i) one or more non-resolved bases (Ns) in the variable or UMI regions, ii) more than one mutated codon in each gene’s variable region or iii) if the mutated codon ended in an A or T (since these were not encoded by the NNS mutagenic primers). (custom perl script)
cis library (sample 7-12): Paired-end reads, which were overlapping over the full length of the variable region, were assembled using PEAR version 0.9.6 38 with a p-value threshold for correct assembly of 0.05, a maximum and minimum fragment length of 150 nt, and a minimum overlap size of 100 nt. These parameters force the assembly of sequences of the unique expected length. An average of 30% and 20% of the paired end reads from the three input and output libraries, respectively, were not assembled and filtered out. These included the adapter sequences and indels (resulting from the <100% coupling efficiency inherent to DNA synthesis). Additionally, assembled reads with Ns in any part of the sequence were filtered out.
variant calling (custom perl script)
UMIs counting (custom perl script)
Supplementary_files_format_and_content: Excel file with read count for each variants in each sample

molecule: other

organism: synthetic construct

source_name: deep mutational scanning

growth_protocol: Yeast was grown in synthetic complete media -HIS at 30ºC (for input samples) and SC -HIS 1M NaCl at 37ºC (output samples). Cells were harvest, centrifuged and pellets saved at -20ºC for DNA extraction

extract_protocol: The sequencing libraries were constructed by two consecutive PCR reactions using a method adapted from Levy et al 35. The first PCR was designed to amplify the region of interest, i.e. from directly upstream of the first mutated codon in FOS to directly upstream of the first mutated codon in JUN (the two genes are in head-to-tail orientation). The first PCR also added Unique Molecular Barcodes (UMIs) and the first half of the illumina adapter sequences. A small number of cycles of the first PCR would limit the number of differently barcoded molecules that derive from the same template molecule. The second PCR would then add the remainder of the Illumina adapter sequences. Plasmid concentrations in the total DNA extractions were first quantified by qPCR using primer pair OGD241-OGD242 that bind in ori region of the plasmid. For each six samples of each of the cis and trans libraries, respectively 4 and 48 PCRs were performed using Q5 Hot Start High-Fidelity DNA Polymerase (New England Biolabs) according to manufacturer’s protocol in 50 μL reactions with 4.2 x 107 molecules of plasmid from the DNA extraction, 25 pmol of primers OGD237 and OGD238, and a melting temperature of 66˚C (previously determined by temperature gradient), an extension time of 30 sec or 1 min, respectively, for 4 cycles. A total of 2 x 109 molecules of plasmids were then used to prepare the sequencing libraries from each sample. Excess primers were removed by adding 2 μL of ExoSAP-IT (Affymetrix) and incubating for 20 min at 37˚C followed by an inactivation for 15 min at 80˚C. This step was necessary because these 60 nt primers are not efficiently removed by the following column purification step. The 48 PCRs of each sample of the trans library were then pooled and purified using eight Qiagen PCR purification kit (Qiagen) columns per sample. According to manufacturer’s protocol, one column is able to bind 10 μg of DNA, which corresponds to ~8 x 108 genomes. Eight columns were then used to ensure that they are not saturated by the genomic DNA carried over from the DNA extraction. The DNA was eluted in 2 x 50 μL of EB buffer (provided by the manufacturer) and pooled for each sample. The eluted DNA was then split into 24 PCR reactions per, which were performed using Kapa HiFi HotStart DNA polymerase (Kapa Biosystems) according to manufacturer’s protocol in 50 μL with 15 pmol of illumina adapter primers. The reverse primers carried a different index for each of the six samples of the same library. For this PCR step, Kapa was chosen over Q5 because it was less efficient in the first PCR reactions (higher optimal melting temperature) and thus would lead to a lower re-barcoding of amplicons with new UMIs present on primers from the first PCR reaction that would have been carried over. Each sample was loaded on an agarose gel to check for correct amplification. A strong non-specific band of lower size was observed, which seemed to gradually disappear as the number of cycles in the first PCR was increased. However, increasing the number of cycles would increase the probability of producing amplicons with different UMIs that derived from the same original template molecule. The number of cycles in the first PCR was thus kept to four and the band of correct size was extracted by gel purification from each sample. To this end, the 24 PCRs of each sample were pooled, concentrated on four Qiagen PCR purification kit (Qiagen) columns per sample and each eluted with 2 x 50 μL of EB buffer (provided by the manufacturer). The bands of correct size were then purified on 2% agarose gel starting from 100 μL of each sample using 10 μL QIAEX II beads (Qiagen) according to manufacturer’s protocol and eluted in 20 μL EB buffer. DNA concentration was determined by picogreen in triplicates and the six samples were pooled at equimolar ratio. The pooled sample was sequenced in a single lane of an Illumina HiSeq2500 with 125 bp paired-end reads at the EMBL Genomics Core Facilities in Heidelberg, Germany.

tag: molecule

value: PCR amplicon


title: input DNA

city: Copenhagen SV

first: Shizuka

last: Uchida

email: heart.lncrna@gmail.com, suc@dcm.aau.dk

address: Frederikskaj 10B, 2. (building C)

department: Department of Clinical Medicine

country: Denmark

institute: Aalborg University

data_processing:
The sequencing reads were analyzed and mapped to the mouse genome assembly mm10 via Ion PGM Torrent Server (Life Technologies).
The BAM files were used as inputs to HOMER (Heinz et al., 2010) for peak calling and further analysis for motif discoveries.
Genome_build: mm10
Supplementary_files_format_and_content: Text files generated by HOMER.

molecule: genomic DNA

source_name: C2C12 cells, input DNA

growth_protocol: Murine myoblast cell line C2C12 cells were cultured in the growth medium containing 20% FBS (Life Technologies, #10270106) in DMEM with high glucose, pyruvate (Life Technologies, # 41966-029) supplemented with antibiotics (penicillin and streptomycin, Sigma-Aldrich, #P4333) at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol:
After two days of differentiation, C2C12 cells were detached with trypsin-EDTA and fixed with 1% formaldehyde. Shearing of chromatin was carried out through Bioruptor Plus (Diagenode) using the following sonication steps: 20 cycles at the low intensity for 30 sec ON / 30 sec OFF; 40 cycles at the high intensity for 30 sec ON / 30 sec OFF; and 50 cycles at the high intensity for 30 sec ON / 30 sec OFF. The efficiency of shearing was assessed by running the sheared chromatin on an 2% agarose gel. Using this sheared chromation, ChIP was performing with EZ-Magna ChIP A/G Kit (Millipore, #17-10086) following manufacturer’s protocol. For each ChIP experiment, 10 μg of an antibody were used.
For each library preparation, 100 ng of immunoprecipitated DNA were used as a starting template following manufacturer’s protocol. Briefly, immunoprecipitated DNA was end-repaired, adapter-ligated and amplified using Ion Plus Fragment Library Kit (Life Technologies, #4471252). The adapter-ligated DNA was size selected through E-Gel Electrophoresis System (Life Technologies) to obtain the optimal size for 200bp read sequencing. Then, size selected DNA was amplified for 18 cycles of PCR. After amplification, the fragments size of the library was assessed through High Sensitivity DNA Analysis Kit (Agilent, # 5067-4626). To calculate a dilution factor, Ion Library Quantitation Kit (Life Technologies, #4468802) was used. Using this dilution factor, template-positive Ion-Sphere particles were prepared using Ion PGM™ Template OT2 200 Kit (Life Technologies,  #4480974) via Ion OneTouch 2 System (Life Technologies). The quality of template-positive Ion-Sphere particles was assessed via Ion-Sphere™ Quality Control Assay (Life Technologies, #4468656). Particles were subsequently enriched according to manufacturer’s protocols. The enriched template-positive Ion-Sphere particles were sequenced using Ion 318™ Chip Kit v2 (Life Technologies, #4484355) and Ion PGM™ Hi-Q™ Sequencing Kit (Life Technologies, #A25592) via Ion PGM™ System (Life Technologies).

treatment_protocol: Transient siRNA transfection (10nM final concentration) was carried out using RNAiMax (Life Technologies) according to the manufacturer’s protocol. To induce the differentiation process (initiated 24 hours after the transfection), C2C12 cells were cultured in the differentiation medium containing 2% horse serum (Sigma-Aldrich, #H1270) in DMEM with low glucose, pyruvate (Life Technologies, #31885-023) supplemented with antibiotics (penicillin and streptomycin, Sigma-Aldrich, #P4333).

value: myoblast cell line C2C12

tag: time

value: Day 2 of differentiation

tag: chip antibody


title: Nuclear_RNA_seq_Mirlet7d_GOF

data_processing:
Raw reads was done using FastQC, trimmed of the raw reads using Trimmomatic (Bolger et al. 2014) with the following parameters( ILLUMINACLIP:adapters/TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:17 CROP:60 HEADCROP:6)
RNA_seq reads were aligned to the mm9 genome.
 After mapping, the sam files were converted to bam format by using samtools view (-Sb) followed by samtools sort. Mapping was performed using bowtie2 following the Parameters (bowtie2 -D 15 -R 3 -N 0 -L 20 -i S,1,0.56 -p8). For the
MakeTaqlibrary -format sam; was used to create the taq library
to quantify the libraries ;
 analyzeRepeats.pl mm9 -count genes -strand both was used for the Protein-coding whereas for the ncRNAs (analyzeRepeats.pl  NONCODE_v4.gtf mm9 -count genes -strand both and -rpkm) was used.
homer makeUCSC (normalized to 10 millions) was used to obtain bedgraph files to Visualize in UCSC genome browser
Genome_build: Mouse mm9
Supplementary_files_format_and_content: Bedgraph_UCSC files to load in the UCSC genome Browser

tag: genotype/variation

value: Mirlet7d GOF

value: gain-of-function


title: Zpbp2 KO Rep 3

status: Public on Apr 05 2018

city: Montreal

first: Anna

middle: K.

last: Naumova

state: Quebec

address: 1001 Decarie Blvd, Bloc E, Room EM03226

department: Department of Obstetrics and Gynecology

country: Canada

institute: McGill University

description: Zpbp2 KO

data_processing:
trimomatic adapter removal
star alignment
picard rna metrics, merging, sorting and duplicate removal
ht-seq raw count generation
Genome_build: mm9
Supplementary_files_format_and_content: Gene Count Data Set in .tsv format

source_name: Liver

extract_protocol:
For RNA-seq analysis, livers were collected from  3 C57BL/6J and 3 B6.Zpbp2-/- 12-week old adult males.  Total RNA was isolated using TRIzol® Reagent (Thermo Fisher Scientific) and purified using the RNeasy® MinElute® Cleanup Kit (Qiagen, Inc).
Total RNA was quantified using a NanoDrop Spectrophotometer ND-1000 (NanoDrop Technologies, Inc.) and its integrity was assessed on a 2100 Bioanalyzer (Agilent Technologies). Libraries were generated from 250 ng of total RNA as following: mRNA enrichment was performed using the NEBNext Poly(A) Magnetic Isolation Module (New England BioLabs). cDNA synthesis was achieved with the NEBNext RNA First Strand Synthesis and NEBNext Ultra Directional RNA Second Strand Synthesis Modules (New England BioLabs). The remaining steps of library preparation were done using and the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabs). Adapters and PCR primers were purchased from New England BioLabs. Libraries were quantified using the Quant-iT™ PicoGreen® dsDNA Assay Kit (Life Technologies) and the Kapa Illumina GA with Revised Primers-SYBR Fast Universal kit (Kapa Biosystems). Average size fragment was determined using a LabChip GX (PerkinElmer) instrument.   The libraries were normalized, denatured in 0.05N NaOH and then were diluted to 200pM and neutralized using HT1 buffer. The clustering was done on a  Illumina cBot and the flowcell was ran on a HiSeq 4000 for 2x100 cycles (paired-end mode) following the manufacturer’s instructions.

tag: strain

tag: tissue

value: liver

tag: genotype

value: Zpbp2 KO


title: Zpbp2 KO Rep 2

description: Zpbp2 KO


title: WT Rep 3

description: WT

value: WT


title: MyoD

source_name: C2C12 cells, MyoD

value: MyoD (Santa Cruz, catalog# sc-304; lot# C0812)


title: Zpbp2 KO Rep 1

description: Zpbp2 KO


title: WT Rep 2

description: WT


title: WT Rep 1

description: WT


title: LI_Adult2_T2-V-2

city: Beijing

first: Rui

last: WANG

address: No.5 Yiheyuan Road, Haidian District

department: Biodynamics Optical Imaging Center (BIOPIC)

country: China

institute: Peking University

data_processing:
For data from Illumina, Illumina CASAVA version 1.8 were used to the basecalling
Read 2 was used to obtain the cell barcodes to further split the reads according to the cell IDs(barcode) and the same time recorded the UMI sequences
Read 1 was picked in each cell according to the cell ID in read2 and the UMI information was aligned to it,and then these raw reads were trimmed to remove TSO or polyA sequence
Adaptor contamination and low-quality reads were discarded from the trimmed Read 1 raw data
TopHat(version 2.0.14) with default settings were used for sequence alignment and uniquely mapped reads were kept.
Paired end raw fastq data firstly separated by cell barcode that attached in read2. UMIs information were aligned to the coressponding read1,which was then trimed to remove the template switch oligo(TSO) sequence and polyA tail sequence. Trimed Read1 fastq data were keep for further analysis. TPM(transcripts-per-million mapped reads) data were calculated as the total UMIs for a genes to be divided by the sum of UMIs from each cell and then multiply by 1,000,000
Genome_build: Reference sequence and transcript annotation files were from UCSC genome assembly hg19
Supplementary_files_format_and_content: All_Merge_umi_tpm_gene.txt

molecule: polyA RNA

organism: Homo sapiens

extract_protocol:
After pick single cells using mouth pipette, they were transferred to cold scRNA-seq lysis buffer immediately. Subsequently, the lysis buffer were shocked for 3min at 72℃ to make sure the release of RNA.
We use a modified STRT-Seq protocol to construct our library. In brief, we use single cell-specific barcodes to ensure the protocol was applicable to a large number of cells. After cDNA amplification, the single cells labeled with different barcodes as many as 44-88 cells can be pooled together for subsequent library construction and sequencing. What’s more, we add biotin in our indexed primers which can pair with 3’ cDNA primers, so after additional amplifying of pooled cDNAs following shearing to about 300bp , we use Dynabeads® MyOne™ Streptavidin C1 beads to enrich for the 3’

treatment_protocol: The large intestine (LI) from two adults were dissected.The mesenterium of large intestine were torn off carefully under a microscope. The middle section of dissected LI was used to collect single cells. The selected tissue pieces were washed by PBS for several times. Then the selected tissue pieces were minced to small pieces by surgical scissors, after which the minced tissues were digested to single cells by using 2mg/mL Collagenase/Dispase for 30-40 min at 37℃. 40µm strainer was used to filter large tissue debris. Then the cell suspension in the solution of Collagenase/Dispase was centrifuged at 800g for 5min at 4℃ and the cell pellet was re-suspended in 1% HSA.

tag: individual

tag: developmental stage

value: Adult

value: large intestine

tag: tissue region

value: Villus


title: LI_Adult2_T2-V-1


title: LI_Adult2_T2-C-1

value: Crypt


title: LI_Adult2_T1-M-2

value: Mix


title: LI_Adult2_T2-C-2


title: LI_Adult2_T1-V-1


title: LI_Adult2_T1-V-2


title: LI_Adult2_T1-C-1


title: LI_Adult1_T2-V-1


title: LI_Adult2_T1-C-2


title: LI_Adult1_T2-C-2


title: LI_Adult2_T1-M-1


title: LI_Adult1_T2-M-2


title: LI_Adult1_T2-M-1


title: LI_Adult1_T1-V-2


title: LI_Adult1_T1-C-2


title: LI_Adult1_T1-V-1


title: LI_Adult1_T1-C-1


title: LI_Adult1_T2-C-1


title: LI_9w_embryo1_90

description:
polyA RNA
Paired end raw data firstly separated by cell barcode that attached in read2. UMI information was aligned to the coressponding read1,which was then trimmed to remove the template switch oligo(TSO) sequence and polyA tail sequence. Trimed Read1 fastq data uploaded to SRA

data_processing:
For data from Illumina, Illumina CASAVA version 1.8 were used to the basecalling
Read 2 was used to abtain the cell barcodes to further split the reads according to the cell IDs(barcode) and the same time recorded the UMI sequences
Read 1 was picked in each cell according to the cell ID in read2 and the UMI information was aligned to it,and then these raw reads were trimmed to remove TSO or polyA sequence
Adaptor contamination and low-quality reads were discarded from the trimmed Read 1 raw data
TopHat(version 2.0.14) with default settings were used for sequence alignment and uniquely mapped reads were kept.
Paired end raw data firstly separated by cell barcode that attached in read2. UMI information was aligned to the coressponding read1,which was then trimmed to remove the template switch oligo(TSO) sequence and polyA tail sequence. Trimed Read1 fastq data uploaded to SRA
Genome_build: Reference sequence and transcript annotation files were from UCSC genome assembly hg19
Supplementary_files_format_and_content: TPM table : TPM(transcripts-per-million mapped reads) data was calculated as the total UMIs for a genes to be divided by the sum of UMIs from each cell and then multiply by 1,000,000

extract_protocol:
After pick single cells using mouth pipette, they were transferred to cold scRNA-seq lysis buffer immediately. Subsequently, the lysis buffer were shocked for 3min at 72℃ to make sure the release of RNA.
We use a modified Smart-seq2 protocol to construct our library. In brief, we use single cell-specific barcodes to insure the protocol was applicable to a large number of cells. After cDNA amplification, the single cells labeled with different barcodes as many as 44-88 cells can be pooled together for subsequent library construction and sequencing. What’s more, we add biotin in our indexed primers which can pair with 3’ cDNA primers, so after additional amplifying of pooled cDNAs following shearing to about 300bp , we use Dynabeads® MyOne™ Streptavidin C1 beads to enrich for the 3’ terminal of cDNAs. Then the library was constructed by using Kapa Hyper Prep Kit(Thermo Fither) and run on illumina Illumina HiSeq 4000 for 150bp pair-end reads.

treatment_protocol: For every embryo, the main organs of digest system, including esophagus, stomach, small intestine (SI), large intestine (LI), were dissected. For 11W to 25W small intestine, the villi and crypt were separated by shaving off the villi carefully with a surgical blade. The mesenterium of small intestine and large intestine were torn off carefully under a microscope. The middle section of dissected esophagus, SI and LI was used to collect single cells. And the corpus of stomach was used to collect single cells. The selected tissue pieces were washed by PBS for several times considering there many microorganisms and mucus in digest system even in the early development stage. Then the selected tissue pieces were minced to small pieces by surgical scissors, after which the minced tissues were digested to single cells by using 2mg/mL Collagenase/Dispase for 30-40 min at 37℃. When digest intestine crypt, 2mM EDTA was firstly used to insure the release of the cells from intestine crypt. 40µm strainer was used to filter large tissue debris. Then the cell suspension in the solution of Collagenase/Dispase was centrifuged at 800g for 5min at 4℃ and the cell pellet was re-suspended in 1% HSA.

value: 9 week gestation


title: LI_9w_embryo1_85


title: LI_9w_embryo1_82


title: LI_9w_embryo1_88


title: LI_Adult1_T2-V-2


title: LI_9w_embryo1_81


title: LI_9w_embryo1_79


title: LI_9w_embryo1_78


title: LI_9w_embryo1_77


title: LI_9w_embryo1_76


title: LI_9w_embryo1_75


title: LI_9w_embryo1_73


title: LI_9w_embryo1_70


title: LI_9w_embryo1_89


title: LI_9w_embryo1_71


title: LI_9w_embryo1_87


title: LI_9w_embryo1_69


title: LI_9w_embryo1_80


title: LI_9w_embryo1_84


title: LI_9w_embryo1_66


title: LI_9w_embryo1_74


title: LI_9w_embryo1_65


title: LI_9w_embryo1_72


title: LI_9w_embryo1_86


title: LI_9w_embryo1_67


title: LI_9w_embryo1_83


title: LI_9w_embryo1_68


title: LI_9w_embryo1_63


title: LI_9w_embryo1_61


title: LI_9w_embryo1_62


title: LI_9w_embryo1_60


title: LI_9w_embryo1_58


title: LI_9w_embryo1_55


title: LI_9w_embryo1_57


title: LI_9w_embryo1_56


title: LI_9w_embryo1_59


title: LI_9w_embryo1_54


title: LI_9w_embryo1_64


title: LI_9w_embryo1_51


title: LI_9w_embryo1_53


title: LI_9w_embryo1_50


title: LI_9w_embryo1_45


title: LI_9w_embryo1_47


title: LI_9w_embryo1_49


title: LI_9w_embryo1_40


title: LI_9w_embryo1_42


title: LI_9w_embryo1_39


title: LI_9w_embryo1_46


title: LI_9w_embryo1_48


title: LI_9w_embryo1_44


title: LI_9w_embryo1_36


title: LI_9w_embryo1_43


title: LI_9w_embryo1_37


title: LI_9w_embryo1_32


title: LI_9w_embryo1_31


title: LI_9w_embryo1_35


title: LI_9w_embryo1_33


title: LI_9w_embryo1_29


title: LI_9w_embryo1_52


title: LI_9w_embryo1_27


title: LI_9w_embryo1_41


title: LI_9w_embryo1_38


title: LI_9w_embryo1_26


title: LI_9w_embryo1_25


title: LI_9w_embryo1_24


title: LI_9w_embryo1_22


title: LI_9w_embryo1_21


title: LI_9w_embryo1_19


title: LI_9w_embryo1_20


title: LI_9w_embryo1_18


title: LI_9w_embryo1_17


title: LI_9w_embryo1_11


title: LI_9w_embryo1_30


title: LI_9w_embryo1_7


title: LI_9w_embryo1_9


title: LI_9w_embryo1_10


title: LI_9w_embryo1_12


title: LI_9w_embryo1_13


title: LI_9w_embryo1_14


title: LI_9w_embryo1_15


title: LI_9w_embryo1_8


title: LI_9w_embryo1_16


title: LI_9w_embryo1_5


title: LI_9w_embryo1_2


title: LI_9w_embryo1_28


title: LI_9w_embryo1_3


title: LI_9w_embryo1_6


title: LI_9w_embryo1_4


title: SI_9w_embryo1_85

value: small intestine


title: SI_9w_embryo1_90


title: SI_9w_embryo1_89


title: LI_9w_embryo1_1


title: SI_9w_embryo1_84


title: SI_9w_embryo1_82


title: SI_9w_embryo1_83


title: SI_9w_embryo1_87


title: SI_9w_embryo1_80


title: SI_9w_embryo1_76


title: SI_9w_embryo1_78


title: SI_9w_embryo1_73


title: SI_9w_embryo1_75


title: SI_9w_embryo1_72


title: SI_9w_embryo1_69


title: SI_9w_embryo1_77


title: SI_9w_embryo1_71


title: SI_9w_embryo1_68


title: SI_9w_embryo1_67


title: SI_9w_embryo1_88


title: SI_9w_embryo1_65


title: SI_9w_embryo1_63


title: SI_9w_embryo1_62


title: SI_9w_embryo1_64


title: SI_9w_embryo1_66


title: SI_9w_embryo1_86


title: SI_9w_embryo1_61


title: SI_9w_embryo1_60


title: SI_9w_embryo1_81


title: SI_9w_embryo1_57


title: SI_9w_embryo1_56


title: SI_9w_embryo1_58


title: SI_9w_embryo1_74


title: SI_9w_embryo1_54


title: SI_9w_embryo1_55


title: SI_9w_embryo1_70


title: SI_9w_embryo1_53


title: SI_9w_embryo1_79


title: SI_9w_embryo1_52


title: SI_9w_embryo1_50


title: SI_9w_embryo1_48


title: SI_9w_embryo1_47


title: SI_9w_embryo1_49


title: SI_9w_embryo1_51


title: SI_9w_embryo1_45


title: SI_9w_embryo1_46


title: SI_9w_embryo1_44


title: SI_9w_embryo1_42


title: SI_9w_embryo1_40


title: SI_9w_embryo1_41


title: SI_9w_embryo1_43


title: SI_9w_embryo1_59


title: SI_9w_embryo1_38


title: SI_9w_embryo1_37


title: SI_9w_embryo1_36


title: SI_9w_embryo1_31


title: SI_9w_embryo1_32


title: SI_9w_embryo1_33


title: SI_9w_embryo1_29


title: SI_9w_embryo1_28


title: SI_9w_embryo1_30


title: SI_9w_embryo1_25


title: SI_9w_embryo1_27


title: SI_9w_embryo1_24


title: SI_9w_embryo1_26


title: SI_9w_embryo1_20


title: SI_9w_embryo1_19


title: SI_9w_embryo1_22


title: SI_9w_embryo1_39


title: SI_9w_embryo1_21


title: SI_9w_embryo1_18


title: SI_9w_embryo1_16


title: SI_9w_embryo1_17


title: SI_9w_embryo1_13


title: SI_9w_embryo1_10


title: SI_9w_embryo1_11


title: SI_9w_embryo1_14


title: SI_9w_embryo1_8


title: SI_9w_embryo1_7


title: SI_9w_embryo1_12


title: SI_9w_embryo1_9


title: SI_9w_embryo1_6


title: SI_9w_embryo1_35


title: SI_9w_embryo1_5


title: SI_9w_embryo1_2


title: SI_9w_embryo1_3


title: SI_9w_embryo1_4


title: SI_9w_embryo1_15


title: SI_9w_embryo1_1


title: stomach_9w_embryo1_88

value: stomach


title: stomach_9w_embryo1_84


title: stomach_9w_embryo1_85


title: stomach_9w_embryo1_81


title: stomach_9w_embryo1_83


title: stomach_9w_embryo1_89


title: stomach_9w_embryo1_79


title: stomach_9w_embryo1_77


title: stomach_9w_embryo1_80


title: stomach_9w_embryo1_82


title: stomach_9w_embryo1_76


title: stomach_9w_embryo1_78


title: stomach_9w_embryo1_75


title: stomach_9w_embryo1_74


title: stomach_9w_embryo1_73


title: stomach_9w_embryo1_72


title: stomach_9w_embryo1_70


title: stomach_9w_embryo1_71


title: stomach_9w_embryo1_67


title: stomach_9w_embryo1_68


title: stomach_9w_embryo1_66


title: stomach_9w_embryo1_62


title: stomach_9w_embryo1_90


title: stomach_9w_embryo1_63


title: stomach_9w_embryo1_65


title: stomach_9w_embryo1_64


title: stomach_9w_embryo1_61


title: stomach_9w_embryo1_60


title: stomach_9w_embryo1_87


title: stomach_9w_embryo1_59


title: stomach_9w_embryo1_58


title: stomach_9w_embryo1_54


title: stomach_9w_embryo1_51


title: stomach_9w_embryo1_52


title: stomach_9w_embryo1_53


title: stomach_9w_embryo1_49


title: stomach_9w_embryo1_48


title: stomach_9w_embryo1_57


title: stomach_9w_embryo1_44


title: stomach_9w_embryo1_45


title: stomach_9w_embryo1_46


title: stomach_9w_embryo1_42


title: stomach_9w_embryo1_40


title: stomach_9w_embryo1_32


title: stomach_9w_embryo1_35


title: stomach_9w_embryo1_36


title: stomach_9w_embryo1_33


title: stomach_9w_embryo1_56


title: stomach_9w_embryo1_39


title: stomach_9w_embryo1_38


title: stomach_9w_embryo1_37


title: stomach_9w_embryo1_55


title: stomach_9w_embryo1_29


title: stomach_9w_embryo1_30


title: stomach_9w_embryo1_47


title: stomach_9w_embryo1_50


title: stomach_9w_embryo1_27


title: stomach_9w_embryo1_26


title: stomach_9w_embryo1_43


title: stomach_9w_embryo1_22


title: stomach_9w_embryo1_25


title: stomach_9w_embryo1_21


title: stomach_9w_embryo1_24


title: stomach_9w_embryo1_28


title: stomach_9w_embryo1_41


title: stomach_9w_embryo1_17


title: stomach_9w_embryo1_19


title: stomach_9w_embryo1_20


title: stomach_9w_embryo1_16


title: stomach_9w_embryo1_18


title: stomach_9w_embryo1_31


title: stomach_9w_embryo1_10


title: stomach_9w_embryo1_13


title: stomach_9w_embryo1_8


title: stomach_9w_embryo1_14


title: stomach_9w_embryo1_12


title: stomach_9w_embryo1_15


title: stomach_9w_embryo1_11


title: stomach_9w_embryo1_9


title: stomach_9w_embryo1_3


title: stomach_9w_embryo1_4


title: stomach_9w_embryo1_2


title: stomach_9w_embryo1_7


title: stomach_9w_embryo1_5


title: esophagus_9w_embryo1_86

value: esophagus


title: esophagus_9w_embryo1_87


title: esophagus_9w_embryo1_90


title: esophagus_9w_embryo1_84


title: esophagus_9w_embryo1_85


title: esophagus_9w_embryo1_83


title: esophagus_9w_embryo1_89


title: esophagus_9w_embryo1_88


title: esophagus_9w_embryo1_82


title: esophagus_9w_embryo1_80


title: stomach_9w_embryo1_6


title: esophagus_9w_embryo1_81


title: esophagus_9w_embryo1_78


title: esophagus_9w_embryo1_79


title: stomach_9w_embryo1_1


title: esophagus_9w_embryo1_76


title: esophagus_9w_embryo1_73


title: esophagus_9w_embryo1_74


title: esophagus_9w_embryo1_77


title: esophagus_9w_embryo1_72


title: esophagus_9w_embryo1_71


title: esophagus_9w_embryo1_70


title: esophagus_9w_embryo1_69


title: esophagus_9w_embryo1_67


title: esophagus_9w_embryo1_66


title: esophagus_9w_embryo1_68


title: esophagus_9w_embryo1_64


title: esophagus_9w_embryo1_62


title: esophagus_9w_embryo1_65


title: esophagus_9w_embryo1_61


title: esophagus_9w_embryo1_75


title: esophagus_9w_embryo1_57


title: esophagus_9w_embryo1_63


title: esophagus_9w_embryo1_58


title: esophagus_9w_embryo1_55


title: esophagus_9w_embryo1_52


title: esophagus_9w_embryo1_56


title: esophagus_9w_embryo1_59


title: stomach_9w_embryo1_86


title: esophagus_9w_embryo1_53


title: esophagus_9w_embryo1_54


title: esophagus_9w_embryo1_51


title: esophagus_9w_embryo1_50


title: esophagus_9w_embryo1_60


title: esophagus_9w_embryo1_45


title: esophagus_9w_embryo1_43


title: esophagus_9w_embryo1_48


title: esophagus_9w_embryo1_46


title: esophagus_9w_embryo1_44


title: esophagus_9w_embryo1_47


title: esophagus_9w_embryo1_39


title: esophagus_9w_embryo1_42


title: esophagus_9w_embryo1_37


title: esophagus_9w_embryo1_40


title: esophagus_9w_embryo1_41


title: esophagus_9w_embryo1_35


title: esophagus_9w_embryo1_33


title: esophagus_9w_embryo1_49


title: esophagus_9w_embryo1_31


title: esophagus_9w_embryo1_30


title: esophagus_9w_embryo1_26


title: esophagus_9w_embryo1_27


title: esophagus_9w_embryo1_29


title: esophagus_9w_embryo1_28


title: esophagus_9w_embryo1_24


title: esophagus_9w_embryo1_21


title: esophagus_9w_embryo1_20


title: esophagus_9w_embryo1_22


title: esophagus_9w_embryo1_36


title: esophagus_9w_embryo1_19


title: esophagus_9w_embryo1_38


title: esophagus_9w_embryo1_17


title: esophagus_9w_embryo1_32


title: esophagus_9w_embryo1_25


title: esophagus_9w_embryo1_16


title: esophagus_9w_embryo1_14


title: esophagus_9w_embryo1_18


title: esophagus_9w_embryo1_7


title: esophagus_9w_embryo1_9


title: esophagus_9w_embryo1_12


title: esophagus_9w_embryo1_15


title: esophagus_9w_embryo1_13


title: esophagus_9w_embryo1_11


title: esophagus_9w_embryo1_10


title: esophagus_9w_embryo1_8


title: esophagus_9w_embryo1_5


title: esophagus_9w_embryo1_3


title: esophagus_9w_embryo1_4


title: esophagus_9w_embryo1_2


title: LI_EM1_25w_9-16_51-74_83-90

description: polyA RNA

value: 25 week gestation


title: esophagus_9w_embryo1_1


title: SI_EM1_Villus_25w_43-90

description: polyA RNA


title: LI_EM1_25w_1-8_17-50_75-82

description: polyA RNA


title: SI_EM1_25w_1-33

description: polyA RNA


title: SI_EM1_Villus_25w_1-42

description: polyA RNA


title: stomach_EM1_25w_1-42

description: polyA RNA


title: esophagus_EM1_25w_67-90

description: polyA RNA


title: LI_EM1.2_24w_51-90

description: polyA RNA

value: 24 week gestation


title: esophagus_9w_embryo1_6


title: stomach_EM1_25w_43-90

description: polyA RNA


title: esophagus_EM1_25w_35-66

description: polyA RNA


title: SI_EM1.2_24w_1-90

description: polyA RNA


title: LI_EM1_Villus_24w_1-90

description: polyA RNA


title: esophagus_EM1.2_24w_1-82

description: polyA RNA


title: stomach_EM1.2_24w_1-90

description: polyA RNA


title: stomach_9w_embryo1_69


title: LI_EM1_24w_51-90

description: polyA RNA


title: LI_EM1_24w_1-50

description: polyA RNA


title: esophagus_EM1_24w_51-90

description: polyA RNA


title: stomach_EM1_24w_51-90

description: polyA RNA


title: stomach_EM1_24w_1-50

description: polyA RNA


title: SI_EM1_Villus_24w_1-50

description: polyA RNA


title: LI_EM2_21w_51-90

description: polyA RNA

value: 21 week gestation


title: SI_EM1_24w_51-90

description: polyA RNA


title: esophagus_EM2_21w_51-90

description: polyA RNA


title: LI_EM1_21w_1-50

description: polyA RNA


title: SI_EM2_21w_51-90

description: polyA RNA


title: SI_EM2_Villus_21w_51-90

description: polyA RNA


title: SI_EM1_21w_9-50

description: polyA RNA


title: stomach_EM1_21w_1-50

description: polyA RNA


title: SI_EM1_24w_1-50

description: polyA RNA


title: esophagus_EM1_21w_1-50

description: polyA RNA


title: LI_EM1_19w_1-50

description: polyA RNA

value: 19 week gestation


title: SI_EM1_19w_51-90

description: polyA RNA


title: SI_EM1_19w_1-50

description: polyA RNA


title: esophagus_EM1_19w_51-90

description: polyA RNA


title: stomach_EM1_19w_51-90

description: polyA RNA


title: esophagus_EM1_19w_1-50

description: polyA RNA


title: stomach_EM1_19w_1-50

description: polyA RNA


title: esophagus_EM1_24w_1-50

description: polyA RNA


title: esophagus_EM1_16w_51-90

description: polyA RNA

value: 16 week gestation


title: stomach_EM1_16w_51-90

description: polyA RNA


title: LI_EM1_16w_1-50

description: polyA RNA


title: SI_EM1_16w_51-90

description: polyA RNA


title: SI_EM1_16w_1-50

description: polyA RNA


title: stomach_EM1_16w_1-50

description: polyA RNA


title: LI_EM1_14w_1-90

description: polyA RNA

value: 14 week gestation


title: SI_EM1_Villus_21w_1-50

description: polyA RNA


title: esophagus_EM1_14w_1-90

description: polyA RNA


title: LI_EM1_11w_1-42

description: polyA RNA

value: 11 week gestation


title: LI_EM1_11w_43-90

description: polyA RNA


title: SI_EM1_11w_43-90

description: polyA RNA


title: stomach_EM1_11w_51-90

description: polyA RNA


title: stomach_EM1_11w_1-50

description: polyA RNA


title: SI_EM2_8w_1-50

description: polyA RNA

value: 8 week gestation


title: esophagus_EM1_11w_51-90

description: polyA RNA


title: esophagus_EM1_11w_9-50

description: polyA RNA


title: esophagus_EM2_8w_51-90

description: polyA RNA


title: stomach_EM1_8w_51-90

description: polyA RNA


title: LI_EM2_8w_43-90

description: polyA RNA


title: SI_EM2.2_7w_1-90

description: polyA RNA

value: 7 week gestation


title: esophagus_EM1_8w_51-90

description: polyA RNA


title: LI_EM1_8w_1-50

description: polyA RNA

value: large intestine


title: stomach_EM1_14w_1-90

description: polyA RNA


title: SI_EM1_14w_1-90

description: polyA RNA


title: SI_EM2_7w_1-90

description: polyA RNA


title: esophagus_EM2_7w_1-90

description: polyA RNA


title: esophagus_EM2.2_7w_1-90

description: polyA RNA


title: LI_EM2_7w_1-90

description: polyA RNA


title: LI_EM2.2_7w_1-90

description: polyA RNA


title: SI_EM1_7w_43-90

description: polyA RNA


title: stomach_EM2_8w_1-42

description: polyA RNA


title: stomach_EM2.2_7w_1-90

description: polyA RNA


title: SI_EM1_7w_1-42

description: polyA RNA


title: stomach_EM1_6w_43-90

description: polyA RNA

value: 6 week gestation


title: LI_EM1_6w_1-90

description: polyA RNA


title: SI_EM1_6w_43-90

description: polyA RNA


title: stomach_EM1_7w_1-42

description: polyA RNA


title: stomach_EM2_6w_1-90

description: polyA RNA


title: stomach_EM1_6w_1-42

description: polyA RNA


title: LI_EM2_6w_1-90

description: polyA RNA


title: esophagus_EM2_6w_1-90

description: polyA RNA


title: SI_EM2_6w_1-90

description: polyA RNA


title: OCI/AML-3_JQ1+6nM_NVP-2_rep-3

city: Vienna

first: Matthias

last: Muhar

address: Campus-Vienna-Biocenter 1

country: Austria

institute: Research Institute for Molecular Pathology

description: Shallow sequencing for observation of global effects on transcription.

data_processing:
Library strategy: SLAM-seq
Raw reads were adapter trimmed using cutadapt through the trim_galore (v0.3.7) wrapper tool with adapter overlaps set to 3bp for trimming (--stringency 3).
Trimmed reads were processed using SlamDunk v0.2.4 running the full analysis procedure (slamdunk all) and aligning against the human genome (UCSC version GRCh38), trimming 12 bp from the 5’ end (-5 12), reporting up to 100 alignments for multimappers (-n 100) and activating multimapper retainment strategy (-m), filtering for variants with a variant fraction of 0.2 (-mv 0.2), filtering with a base-quality cutoff of 27 (-mbq 27) and stringency filter set to 2 (requiring ≥ 2 T>C conversions per read).
Genome_build: GRCh38
Supplementary_files_format_and_content: *tsv: Tab-delimited text files; SlamDunk v0.2.4 output containing UTR coordinates named by EntrezID, raw and normalized read counts, as well as T>C conversion statistics. For details see: http://t-neumann.github.io/slamdunk/docs.html
Supplementary_files_format_and_content: hg38_refseq_062016_ensemblv84_3UTR.bed

extract_protocol:
Total RNA was extracted using a commercial column purification kit and treated with iodoacetamide for alkylation of 4-thiouridine.
3'UTR sequencing libraries were generated from 500ng of alkylated total RNA using a commercial kit (QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina, Lexogen).

tag: treatment

value: 200nM JQ1 + 6nM NVP-2, 90 min

tag: 4su labeling time before harvest (min)


title: OCI/AML-3_JQ1+6nM_NVP-2_rep-1


title: esophagus_EM1_6w_1-42

description: polyA RNA


title: OCI/AML-3_60nM_NVP-2_rep-2

value: 60nM NVP-2, 90 min


title: OCI/AML-3_60nM_NVP-2_rep-3


title: OCI/AML-3_60nM_NVP-2_rep-1


title: OCI/AML-3_6nM_NVP-2_rep-3

value: 6nM NVP-2, 90 min


title: LI_EM1_16w_51-90

description: polyA RNA


title: OCI/AML-3_6nM_NVP-2_rep-1


title: OCI/AML-3_JQ1_rep-3

value: 200nM JQ1, 90 min


title: OCI/AML-3_JQ1_rep-2


title: OCI/AML-3_DMSO_rep-2


title: MOLM-13_JQ1+6nM_NVP-2_rep-3_exp-2


title: OCI/AML-3_DMSO_rep-1


title: MOLM-13_JQ1+6nM_NVP-2_rep-2_exp-2


title: OCI/AML-3_JQ1_rep-1


title: OCI/AML-3_JQ1+6nM_NVP-2_rep-2


title: MOLM-13_60nM_NVP-2_rep-2_exp-2


title: MOLM-13_60nM_NVP-2_rep-1_exp-2


title: MOLM-13_6nM_NVP-2_rep-3_exp-2


title: MOLM-13_6nM_NVP-2_rep-1_exp-2


title: MOLM-13_JQ1_rep-1_exp-2


title: MOLM-13_JQ1_rep-2_exp-2


title: MOLM-13_DMSO_rep-2_exp-2


title: MOLM-13_unlabeled_rep-3

description: PolyA RNA


title: MOLM-13_DMSO_rep-1_exp-2


title: MOLM-13_unlabeled_rep-2

description: PolyA RNA


title: MOLM-13_unlabeled_rep-1

description: PolyA RNA


title: Pali_dKO_EB_D4_rep1

city: Dublin 2

first: Darren

middle: John

last: Fitzpatrick

state: Ireland

address: College Green

department: Smurfit Institute of Genetics

country: Ireland

institute: Trinity College Dublin

description:
Ribo Zero RNA
ESCs that have been maintained in a pluripotent state through culturing with LIF on gelatinised plates

data_processing: Sequencing reads were aligned to the mouse reference genome (mm10) using kallisto v0.43.1. Aligned reads were aggregated into a count for each gene using tximport and normalised using DESeq2. Sequence tracks were generated by aligning reads to the mm10 reference using HISAT v2.0.5. Resulting bedGraph files were converted to bigWig format and scaled using hits per billion with the bamTobw.sh utility.

source_name: Embryoid Bodies

growth_protocol: Embryonic stem cells (ESCs) were grown on gelatinised culture dishes in GMEM (sigma) supplemented with 10% ES cell qualified FBS (Millipore), 100 U/mL penicillin (Gibco), 100 U/mL streptomycin (Gibco), 50µM β-mercaptoethanol (sigma), 1:100 Glutamax (Gibco), 1:100 non-essential amino acids (Gibco), 1mM sodium pyruvate (Gibco) and 1:500 homemade leukemia inhibitory factor (LIF). For Embryoid body differentiation, 2-3x106 million ESCs were washed three times with PBS (Lonza) and seeded to non-adherent petri-dishes in ESC media without LIF. The media was changed every 2 days. RNA was harvested after 4 days.

extract_protocol:
RNA was extracted using Rneasy Kit (Qiagen) according to manufacturers instructions.
Libraries were prepared using the Truseq Stranded Total RNA library prep kit Ribo-Zero Human/ Mouse/ Rat (Illumina) according to manufacturer’s instructions. Sequencing was performed on an Illumina HiSeq 2500 sequencer using HiSeq v4 chemistry following the manufacturers protocols.

tag: cell type

value: Embryoid Bodies


title: Pali_dKO_EB_D4_rep2

description:
Ribo Zero RNA
ESCs that have been induced to differentiate by removal of LIF from culture media and growth on non-adherent plates


title: Pali_dKO_EB_D8_rep2

growth_protocol: Embryonic stem cells (ESCs) were grown on gelatinised culture dishes in GMEM (sigma) supplemented with 10% ES cell qualified FBS (Millipore), 100 U/mL penicillin (Gibco), 100 U/mL streptomycin (Gibco), 50µM β-mercaptoethanol (sigma), 1:100 Glutamax (Gibco), 1:100 non-essential amino acids (Gibco), 1mM sodium pyruvate (Gibco) and 1:500 homemade leukemia inhibitory factor (LIF). For Embryoid body differentiation, 2-3x106 million ESCs were washed three times with PBS (Lonza) and seeded to non-adherent petri-dishes in ESC media without LIF. The media was changed every 2 days. RNA was harvested after 8 days.


title: Pali_dKO_ES_rep2

source_name: Embryonic Stem Cell

growth_protocol: Embryonic stem cells (ESCs) were grown on gelatinised culture dishes in GMEM (sigma) supplemented with 10% ES cell qualified FBS (Millipore), 100 U/mL penicillin (Gibco), 100 U/mL streptomycin (Gibco), 50µM β-mercaptoethanol (sigma), 1:100 Glutamax (Gibco), 1:100 non-essential amino acids (Gibco), 1mM sodium pyruvate (Gibco) and 1:500 homemade leukemia inhibitory factor (LIF).

value: Embryonic Stem Cell


title: MOLM-13_6nM_NVP-2_rep-2_exp-2


title: Pali_dKO_ES_rep1


title: Pali_WT_EB_D8_rep1

value: Wild type


title: LI_EM1.2_24w_1-50

description: polyA RNA

value: 24 week gestation


title: Pali_WT_EB_D4_rep2


title: SI_EM1_Villus_24w_51-90

description: polyA RNA

value: small intestine


title: Pali_WT_EB_D4_rep1


title: MOLM-13_DMSO_rep-3_exp-2


title: Pali_WT_EB_D8_rep2


title: Pali_WT_ES_rep2


title: Pali_dKO_EB_D8_rep1


title: Pali_WT_ES_rep1


title: esophagus_EM1_6w_43-90

description: polyA RNA

value: esophagus


title: LI_EM1_19w_51-90

description: polyA RNA

value: 19 week gestation


title: Pali1_sKO_ES_rep1


title: C129_WT_EB_D8_rep2


title: C129_WT_EB_D8_rep1


title: Pali1_sKO_EB_D4_rep1


title: Pali1_sKO_ES_rep2


title: C129_WT_EB_D4_rep2


title: C129_WT_EB_D4_rep1


title: C129_WT_ES_rep2


title: Aebp2_Gt_EB_D8_rep2


title: Pali1_sKO_EB_D8_rep1


title: Pali1_sKO_EB_D8_rep2


title: Aebp2_Gt_EB_D4_rep2


title: C129_WT_ES_rep1


title: Aebp2_Gt_EB_D4_rep1


title: Aebp2_Gt_EB_D8_rep1


title: Aebp2_Gt_ES_rep2


title: SI_EM1_11w_1-42

description: polyA RNA


title: Pali1_sKO_EB_D4_rep2


title: MOLM-13_JQ1+6nM_NVP-2_rep-1_exp-2


title: PolII_72h_ctrl_1

first: Thomas

middle: Rainer

last: Burkard

address: Dr. Bohrgasse 7

institute: IMBA

data_processing:
Basecalling RTA 1.13.48.0
The reads were aligned with bowtie to the Mus musculus genome (mm9). Options are set to 3 mismatches, 1 max multihit, tryhard and best strata.
Duplicates are removed with picard-tools (1.82).
Deduplicated ChIP-seq alignments are converted to bigWigs and replicates are merged with the kent tools.
Tracks were normalized with RseQC to a wigsum of 200000000.
Promotor regions were defined from -30 to +300 and gene body is the remaining gene (UCSC RefSeq). Density of promotor and body was summarized with bigWigAverageOverBed.
The traveling ratio was calculated for the average over bases with non-covered bases counting as zeroes for promotor over body.
Genome_build: mm9
Supplementary_files_format_and_content: tab separated text file containing the traveling ratios

source_name: tatsf1floxCreERT2 embryonic stem cells

growth_protocol: Mouse ESCs derived from tatsf1 flox/flox CreERT2 mice were grown on MEFs in conventional ESC medium.

extract_protocol:
Chromatin IP was performed using anti-Polymerase II (Pol II N-20 (Santa Cruz sc-899) ) antibody. Precipitated genomic DNA or whole genomic DNA was used for library preparation.
Library preparation was done using Kapa Library Preparation Kit (Roche). Barcoded samples were multiplexed and sequenced 50bp SE on a HighSeq2500 (Illumina).

treatment_protocol: Mouse ESCs derived from tatsf1floxCreERT2 mice were treated with Ethanol (ctrl) or Tamoxifen to induce recombination and deletion of HTATSF1.

value: Ethanol (ctrl)

tag: barcode

tag: treatment time

value: anti-Polymerase II (Clone:N20; Vendor:Santa Cruz Biotechnology, catalogue number:SC-899 X, type:rabbit polyclonal IgG)


title: PolII_72h_tam_2

value: Tamoxifen


title: PolII_72h_ctrl_2


title: tat_tam_input_1


title: tat_tam_PolII_1


title: tat_ctrl_PolII_1


title: tat_ctrl_input_1


title: tat_tam_PolII_2


title: PolII_72h_tam_1


title: tat_tam_input_2


title: MOLM-13_JQ1_rep-3_exp-2

tag: cell line


title: stomach_EM2_7w_1-90

description: polyA RNA

value: 7 week gestation

value: stomach


title: Input_2

data_processing:
Basecalling RTA 1.17.20.0
The reads were aligned with bowtie to the Mus musculus genome (mm9). Options are set to 3 mismatches, 1 max multihit, tryhard and best strata.
Duplicates are removed with picard-tools (1.82).
BED files of the reads are generated with bedtools.
Peaks are called with Macs 1.4. (tat chip vs. input of same replicate number)
Genome_build: mm9
Supplementary_files_format_and_content: BED file of called peaks

extract_protocol:
Chromatin-IP was performed with rabbit anti mouse HTATSF1 antibody.
Library preparation was done using Kapa Library Preparation Kit (Roche). Barcoded samples were multiplexed and sequenced 50bp SE on a HighSeq2500 (Illumina).

value: no treatment


title: Input_1


title: tat_Chip_2

value: anti-HTATSF1 (produced in rabbit against mouse HTATSF1 peptide SGNNLSGNDEFDEQLR-C)


title: Aebp2_Gt_ES_rep1


title: tat_Chip_1


title: Pod-cre-GFP

city: Bukgu

first: Jihwan

last: Park

state: Gwangju

address: 123 Cheomdangwagi-ro

country: South Korea

institute: GWANGJU INSTITUTE OF SCIENCE /TECHNOLOGY

description:
Sample 7
processed file is combined into single data matrix

data_processing:
Cell Ranger 1.3 (http://10xgenomics.com) was used to process Chromium single cell 3’ RNA-seq output.
“cellranger count” aligned the Read2 to the mouse reference genome (mm10) using STAR
Aligned reads were used to generate data matrix only when they have valid barcodes and UMI, map to exons (Ensembl GTFs GRCm38.p4)
The output files for 7 batches were aggregated into one gene-cell matrix using “cellranger aggr” without read depth normalization option
Once the gene-cell data matrix was generated, poor quality cells were excluded, such as cells with <300 genes detected or with >3,000 unique expressed genes (as they are potentially cell duplets). Only genes expressed in 10 or more cells were used for further analysis. Cells were also discarded if their mitochondrial gene percentages were over 50%.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data file is a sparsematrix in R: each row corresponds to genes (first row is the cluster number), and each column corresponds to single cell, number in the matrix is the UMI count data

source_name: whole kidney tissue

extract_protocol:
10X Genomics Chromium Prep. Barcoding and cDNA synthesis were performed according to the manufacturer's instructions.
The cDNA libraries were constructed using the 10x ChromiumTM Single cell 3’ Library Kit according to the manufacturer’s original protocol.

value: adult kidney

tag: age

value: 4-8 weeks


title: Scl-cre-GFP

description:
Sample 6
processed file is combined into single data matrix

value: SclCremTmG


title: stomach_EM2_21w_51-90

description: polyA RNA

value: 21 week gestation


title: Ksp-cre-GFP

description:
Sample 5
processed file is combined into single data matrix


title: normal2

description:
Sample 2
processed file is combined into single data matrix

value: WT


title: normal4

description:
Sample 4
processed file is combined into single data matrix


title: normal3

description:
Sample 3
processed file is combined into single data matrix


title: WT PBS8

city: Tübingen

first: Jonas

middle: J

last: Neher

address: Otfried Mueller Str. 23

department: Experimental Neuroimmunology

country: Germany

institute: German Center for Neurodegenerative Diseases (DZNE) Tübingen

data_processing:
Base calling from raw images and file conversion to fastq files were achieved by Illumina standard pipeline scripts. Quality control was then performed using FASTQC program (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), eliminating one sample which had less than 20 million reads.
Reads were trimmed off for sequencing adaptor and were mapped to mouse reference transcriptome (mm10) using STAR aligner v2.3.060 with non-default parameters. Unique read counts were obtained for each sample using HOMER software (http://homer.salk.edu/homer/) and ‘maketagdirectory -tbp 1’ command, followed by ‘analyzeRepeats.pl rna mm10 -count exons -noadj -condenseGenes’.
Raw read counts were imported into R and normalized using the Bioconductor package DESeq2 package61 using default parameter.  After normalization, all transcripts having a maximum overall group mean lower than 10 were removed. Unwanted or hidden sources of variation, such as batch and preparation date, were removed using the sva package62. The normalized rlog transformed expression values were adjusted according to the surrogate variables identified by sva using the function removeBatchEffect from the limma package63.
To determine gene clusters associated with wildtype or APP23 animals following i.p. injections of 1x or 4xLPS at 3 months of age, we then used the 13,627 present genes and applied the R implementation of the Weighted Gene Correlation Network Analysis (WGCNA). We then performed WGCNA clustering using the ‘1-TOMsimilarityFromExpr’ function with the network type "signed hybrid", a power parameter of 7, and a minimum module size of 50 dissecting the data into 10 modules.
Genome_build: mm10

source_name: microglia from 9 month-old animals

growth_protocol: For all experiments, 3 month-old hemizygous APP23 transgenic (C57BL/6J-Tg(Thy1-APPK670N;M671L)23) or wildtype littermates were used. Only female mice were used for this study. APP23 mice express a transgene consisting of human amyloid-β precursor protein (APP) with the KM670/671NL mutation under the Thy-1 promoter, and have been backcrossed with C57BL/6J mice for >20 generations.

extract_protocol:
10k microglia were directly sorted (using a Sony SH800 cell sorter) into RNAse-free PCR strips containing 30 μl of H2O with 0.2% Triton-X and 0.8 U/μl RNAse inhibitor (Clontech) and samples were immediatedly frozen on dry ice. . RNA was isolated using NucleoSpin RNA XS kit (Macherey-Nagel) according to the manufacturer’s instructions.
3ng total RNA was used as input material for cDNA synthesis. cDNA synthesis and enrichment was performed following the Smart-seq2 v4 protocol as described by the manufacturers (Clontech). Sequencing Library was prepared with 1 ng of cDNA using the Nextera XT library preparation kit (Illumina) as described59. Multiplexing of samples was achieved using 3 different index-primers in each lane. For sequencing, samples from each group (APP and WT) were pooled to rule out amplification and sequencing biases.

treatment_protocol: 3 month-old mice were randomly assigned to treatment groups and were injected intraperitoneally (i.p.) with bacterial lipopolysaccharides (LPS from salmonella enterica serotype typhimurium, Sigma) at a dose of 500 µg/kg bodyweight. Animals received either four LPS injections at 500 µg LPS/kg bodyweight on four consecutive days (4xLPS), a single LPS injection at the same concentration followed by three vehicle injections on the following three days (1xLPS) or four vehicle injections (PBS). Animals were sacrifised at 9 months of age and microglia were isolated.

value: wildtype

value: PBS i.p.

tag: gender

value: female

tag: background strain

value: microglia


title: tat_ctrl_PolII_2

tag: chip antibody


title: WT PBS7


title: WT PBS6


title: normal1

description:
Sample 1
processed file is combined into single data matrix


title: WT PBS5


title: WT PBS3


title: stomach_EM1_7w_43-90

description: polyA RNA


title: WT PBS1


title: WT PBS4


title: tat_ctrl_input_2


title: esophagus_EM1_16w_1-50

description: polyA RNA

value: 16 week gestation

value: esophagus


title: WT 4xLPS6

value: 4xLPS i.p.


title: WT 4xLPS5


title: WT 4xLPS4


title: WT 1xLPS9

value: 1xLPS i.p.


title: WT 4xLPS1


title: WT 4xLPS3


title: WT 4xLPS2


title: WT 1xLPS8


title: WT PBS9


title: WildBoar3_Brain

city: Wen’jiang,Chengu

first: long

middle: ke

last: ren

state: Sichuan

address: Huimin road, 211#

department: 1	Institute of Animal Genetics & Breeding

institute: sichuan agriculture university

data_processing:
High-quality reads were obtained by discarding reads that contained over 10% Ns (uncalled bases), had at least 10 bp that overlapped with adaptor sequences at mismatch rate equal to or less than 10%, or included over 50% of bases with base quality scores less than five. The remaining reads were mapped to the pig reference genome 10.2 using Tophat version 2.0.11[11]. Cufflinks version 2.2.1 [12] was used to quantify gene expression and obtain FPKM expression values (denoted as fragments per kb of transcript per Mb of mapped reads). We carried out read alignment and expression quantification separately for each sample. Only genes with FPKM values greater than 0.05 were considered reliable and used in subsequent analyses.
We applied Cuffquant (part of Cufflinks) to read mapping results for generating abundance files, which were further used in Cuffdiff (part of Cufflinks) to detect DEGs between wild boar and Rongchang pig. Genes with fold changes ≥ 2 and adjusted P values ≤ 0.05 were identified as DEGs.
identified mRNA in each library with reads and normalized data
Genome_build: sus scrofa 10.2
Supplementary_files_format_and_content: .txt file represents normalized reads

organism: Sus scrofa

source_name: WildBoar, Brain

extract_protocol:
Total RNA was extracted using the TRIzol (Life Technologies, Beijing, China) method following manufacturer’s protocol. RNA quality was confirmed using gel electrophoresis and visual spectrophotometry using a Nanodrop spectrophotometer. All samples had a 260/280 nm absorbance ratios between 1.8 and 2.0.
Sequencing libraries were constructed according to the manufacturer's standard procedures (Illumina, San Diego, USA). In brief, the poly(A) mRNA was extracted from total RNA using poly-T-attached magnetic beads, further fragmented, and used as templates for cDNA generation. The first-strand was synthesized using reverse transcriptase and random hexamer primers. Second-strand cDNA was synthesized based on the first strand with dNTP (here, dTTP was replaced by dUTP), buffer solution, DNA polymerase I, and RNase H. Double-stranded cDNA was then purified by AMPure XP beads, and the second strands containing U were degraded using the USER enzyme. Purified double-stranded cDNA was end-repaired, an A tail was added, and ligated to paired-end Illumina sequencing adaptors. About 320-bp cDNA fragments were size-selected by AMPure XP beads and amplified using PCR. The high-quality libraries were sequenced on the Illumina HiSeq 2000 platform and 100-bp paired-end reads were obtained. Bases were called using the Illumina CASAVA software.

value: brain


title: WildBoar2_Brain


title: WT 1xLPS7


title: OCI/AML-3_6nM_NVP-2_rep-2

value: 6nM NVP-2, 90 min


title: Placenta_inner_maternal_region

city: Davis

first: Janine

last: LaSalle

state: CA

address: Medical Microbiology and Immunology

country: USA

institute: UC Davis

description: Placenta was not a part of the MARBLES study and had no known pathologies

data_processing:
100 bp reads were trimmed at the 3' end to 85 bp for BS Seeker alignment.  BS Seeker parameters:  -e 85 -m 3 -a adapter2
Custom Perl scripts were used to calculate percent methylation for each genomic CpG site with read coverage.  Methylation data for both DNA strands were combined.  Only one read starting at a given genomic coordinate was kept to eliminate clonal replicates.  Red=80-100% methylation, green=60-80%, blue=1-60%, black=0%.
Genome_build: hg19
Supplementary_files_format_and_content: BED file with the name fields giving the % methylation at that CpG site.

source_name: placenta

extract_protocol: Samples of the placenta were frozen immediately after birth.  DNA was purified using Qiagen's Puregene kit and bisulfite converted with Zymo's EZ DNA Methylation Lightning kit.  Library was prepared with Epicentre's EpiGnome Methyl-Seq kit using indexed adapters, amplified for 14 cycles, and purified with AMPure beads.

tag: developmental timepoint

value: full term birth

tag: diagnosis

value: normal

tag: location in tissue

value: inner maternal side of the placenta


title: Placenta_middle_maternal_region

value: middle maternal side of the placenta


title: WildBoar1_Brain

tag: tissue


title: WT 1xLPS6

tag: genotype


title: WT PBS2


title: RongchangPig3_Brain

source_name: RongchangPig, Brain

tag: breed

value: Rongchang


title: Placenta_inner_fetal_region

value: inner fetal side of the placenta


title: RongchangPig2_Brain


title: WT 1xLPS5


title: SI_EM1_8w_1-50

description: polyA RNA

tag: developmental stage

value: 8 week gestation

value: small intestine


title: Autism_placenta_083

extract_protocol:
Samples of the placenta were frozen immediately after birth.  DNA was purified using Qiagen's Puregene kit and sonicated to about 200 bp.
Methylated adapters were added with the NEBNext DNA library prep kit.  Libraries were bisulfite converted with the Zymo EZ DNA Methylation Lightning kit, amplified for 14 cycles with PfuTurbo Cx, and purified with AMPure beads.

tag: Sex

value: male

value: autism


title: RongchangPig1_Brain


title: Autism_placenta_081


title: Autism_placenta_082


title: Autism_placenta_080


title: WT 1xLPS1

value: wildtype

tag: treatment

value: female

value: microglia


title: RNASeq_Htz1_OE_caffeine-30-min_rep2

city: Cambridge

first: Muxin

last: Gu

email: muxingu@gmail.com, mg445@cam.ac.uk

address: Jeffrey Cheah Biomedical Centre, Puddicombe Way

department: Haematology

country: United Kingdom

institute: University of Cambridge

data_processing:
ChIP-seq and RNA-seq reads were mapped to the S. cerevisiae genome assembly sacCer1 using Bowtie2 and Tophat2 respectively, allowing up to 2 mismatches per sequence and no ambiguously mapped reads.
Normalisation for ChIP-seq (wild-type (WT) and 4KR samples) was performed based on the assumption that the genomic background is constant over the time course. Background signal was set to 1.2 standard deviations above the mean of the ChIP:input ratios and then subtracted from the ChIP-seq signal.
Genome_build: sacCer1

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae cells grown in caffeine

growth_protocol: Cells were grown to mid-log phase in drug-free medium (SD-Ura) and then caffeine (Sigma) was added to 10 mM. MG-132 (Merck) 150 mM treatment was carried out in medium containing 0.006% SDS to facilitate drug uptake. For histone deacetylase inhibition, 75mM VPA was added to cells for 45 minutes.

extract_protocol:
Cultures were crosslinked with 1% (v/v) formaldehyde, quenched with glycine, and cells were lysed with beads in a FastPrep-24 (MP Biomedicals) cell homogeniser. Sonicated, clarified extracts were immunoprecipitated with anti-Htz1 antibodies before washing and DNA extraction, or were used directly to prepare input DNA.
Illumina TruSeq ChIP Sample Prep Kit were used for ChIP-seq library preparation. RNA library was prepared using the Illumina TruSeq stranded mRNA sample preparation kit.

value: YDS2 + bar1::HIS htz1::TRP + p[HTZ1]-2u-URA


title: APP PBS6

value: PBS i.p.


title: APP PBS5


title: RNASeq_Htz1_OE_caffeine-120-min_rep2


title: RNASeq_Htz1_OE_caffeine-30-min_rep1


title: HCT116_MYC-AID_IAA_rep-3

value: 100µM indole-3-acetic acid, 90 min

tag: genetic modification

value: MYC-AID / SFFV-OsTir1-T2A-BlastR

tag: 4su labeling time before harvest (min)


title: APP PBS4


title: RNASeq_Htz1_OE_caffeine-0-min_rep2


title: RNASeq_Htz1_OE_caffeine-120-min_rep1


title: HCT116_MYC-AID_IAA_rep-2


title: RNASeq_Htz1_OE_caffeine-0-min_rep1


title: APP PBS3


title: Placenta_outer_fetal_region

value: full term birth

value: outer fetal side of the placenta


title: Autism_placenta_078


title: WT 1xLPS4

value: 1xLPS i.p.


title: RNASeq_Htz1_4KR_caffeine-120-min_rep2

value: bar1::HIS htz1::TRP + p[htz1K3,8,10,14R-URA3]


title: HCT116_MYC-AID_IAA_rep-1


title: Typical_placenta_075

value: typical


title: RNASeq_Htz1_4KR_caffeine-120-min_rep1


title: WT 1xLPS3


title: WT 1xLPS2


title: Typical_placenta_076


title: HCT116_MYC-AID_DMSO_rep-3


title: APP PBS2


title: Typical_placenta_074


title: Autism_placenta_079


title: APP PBS1


title: HCT116_MYC-AID_DMSO_rep-2


title: RNASeq_Htz1_4KR_caffeine-30-min_rep2


title: APP 4xLPS4

value: 4xLPS i.p.


title: Autism_placenta_077


title: Typical_placenta_073


title: RNASeq_Htz1_4KR_caffeine-30-min_rep1


title: RNASeq_Htz1_4KR_caffeine-0-min_rep2


title: K562_MYC-AID_IAA_rep-3


title: K562_MYC-AID_IAA_rep-2


title: RNASeq_Htz1_4KR_caffeine-0-min_rep1


title: APP 4xLPS2


title: RNASeq_Htz1_WT_caffeine-120-min_rep2

value: YDS2 + bar1::HIS htz1::TRP + p[HTZ1]


title: APP 4xLPS1


title: APP 1xLPS5


title: APP 4xLPS3


title: Typical_placenta_072


title: Typical_placenta_067


title: K562_MYC-AID_DMSO_rep-3


title: APP 1xLPS4


title: APP 1xLPS3


title: Typical_placenta_068


title: Typical_placenta_071


title: RNASeq_Htz1_WT_caffeine-30-min_rep2


title: K562_MYC-AID_DMSO_rep-1


title: RNASeq_Htz1_WT_caffeine-30-min_rep1


title: K562_MYC-AID_IAA_rep-1


title: Typical_placenta_066


title: HCT116_MYC-AID_DMSO_rep-1


title: APP 1xLPS2


title: Typical_placenta_065


title: APP 1xLPS1


title: RNASeq_Htz1_WT_caffeine-0-min_rep2


title: Typical_placenta_070


title: RNASeq_Htz1_WT_caffeine-0-min_rep1


title: MOLM-13_JQ1_rep-2_exp-1

value: 200nM JQ1, 90 min


title: Typical_placenta_064


title: 48h +T Rep 2

data_processing:
Basecalling RTA 1.13.48.0
The strand specific paired-end reads were screened for ribosomal RNA by aligning with BWA (v0.6.1) against known rRNA sequences (RefSeq).
The rRNA subtracted reads were aligned with TopHat (v1.4.1) against the Mus musculus genome (mm9) and a maxiumum of 6 missmatches. Maximum multihits was set to 1 and InDels as well as Microexon-search was enabled. Additionally, a gene model was provided as GTF (UCSC, 2013_02_21, mm9).
Aligned reads are subjected to FPKM estimation with Cufflinks (v1.3.0). In this step bias detection and correction was performed. Furthermore, only those fragments compatible with RefSeq annotation (mm9) were allowed and counted towards the number of mapped hits used in the FPKM denominator. The aligned reads were counted with HTSeq.
The polyA containing transcripts were subjected to differential expression analysis with DESeq. DESeq parameters were chosen to match the DESeq publication (Anders S, Huber W., 2010).
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample (Standard output cufflinks); tab-delimited text file with differentially expressed genes for the whole analysis (standard output DESeq).

extract_protocol:
RNA was isolated using Trizol (ThermoFisher Scientific).
mRNA was enriched using beads, first and second strand cDNA synthesis (+Actinomycin D). Library preparation was done using Kapa Library Preparation Kit (Roche). Barcoded samples were multiplexed and sequenced 100bp PE on a HighSeq2000 (Illumina).

value: Tamoxifen

tag: barcode

tag: time of treatment


title: ChIPSeq_Input-DNA


title: Typical_placenta_063


title: MOLM-13_JQ1_rep-3_exp-1

tag: cell line


title: MOLM-13_JQ1_rep-1_exp-1


title: 48h +T Rep 1


title: 48h -T Rep 2

value: Ethanol (ctrl)


title: Autism_placenta_058

value: autism


title: MOLM-13_DMSO_rep-3_exp-1


title: ChIPSeq_Htz1_OE_caffeine-120-min_rep2


title: 48h -T Rep 1


title: MOLM-13_DMSO_rep-2_exp-1


title: Autism_placenta_057

value: male


title: ChIPSeq_Htz1_OE_caffeine-30-min_rep2


title: MOLM-13_DMSO_rep-1_exp-1


title: Autism_placenta_055


title: ChIPSeq_Htz1_OE_caffeine-120-min_rep1


title: MV4-11_JQ1_rep-3


title: Autism_placenta_056


title: ChIPSeq_Htz1_OE_caffeine-30-min_rep1


title: 72h +T Rep 2


title: 72h +T Rep 1


title: ChIPSeq_Htz1_OE_caffeine-0-min_rep2


title: MV4-11_JQ1_rep-2


title: Autism_placenta_053


title: ChIPSeq_Htz1_OE_caffeine-0-min_rep1


title: 72h -T Rep 2


title: MV4-11_JQ1_rep-1


title: Typical_placenta_052


title: ChIPSeq_Htz1_4KR_caffeine-120-min_rep2


title: MV4-11_DMSO_rep-3


title: 72h -T Rep 1


title: ARX_WT_178_E7

first: giovanni

last: iacono

state: Spain

address: Baldiri Reixac, 4

department: single cell sequencing

institute: CNAG,Centro Nacional de Análisis Genómico

data_processing:
alignment was done with GSNAP-gmap-2015-06-23
read counting was performed with custom C++ script
DEseq2 was used to call the expression changes
Genome_build: mm9
Supplementary_files_format_and_content: Normalized read counts for RNAseq data (ARX_rnaseq.xlsx)

source_name: embryonic forebrain_ARX_dup24/0

extract_protocol:
Total RNA was Trizol extracted. RNA was treated with DNase (Qiagen, 79254) and purified on the RNeasy MinElute Cleanup Kit (Qiagen, 74204). 2000 ng of total RNA were treated with the Ribo-Zero rRNA Removal Kit (Human/Mouse/Rat; Illumina MRZH11124). Depleted RNA was precipitated 1 h at -80°C in three volumes of ethanol plus 1 µg of glycogen. RNA was then washed and resuspended in 36 µl of RNase free water. RNA fragmentation buffer (NEBNext® Magnesium RNA Fragmentation Module, E6150S) was added to the solution and the RNA was fragmented by incubation at 95°C for 3 minutes. For reverse transcription, cDNA first strand synthesis was performed with random examer primers. cDNA second strand synthesis was performed with dUNTPs, to ensure strand specificity.
The RNA-seq library was synthetized with KAPA Hyper prep kit (KK8504), a treatment with USER enzyme (NEB, M5505L) was added to digest the unspecific strand. The libraries were pooled (4/lane) and sequenced on the illumina HiSeq, which yielded approximately 40 million single-end reads per sample.

tag: age

value: forebrain

tag: strain


title: Autism_placenta_051


title: ARX_178E10_wt


title: MV4-11_DMSO_rep-2


title: ChIPSeq_Htz1_4KR_caffeine-120-min_rep1


title: MV4-11_DMSO_rep-1


title: Autism_placenta_054

value: female


title: RNASeq_Htz1_WT_caffeine-120-min_rep1


title: ARX_179E1_wt


title: ChIPSeq_Htz1_4KR_caffeine-30-min_rep1


title: Typical_placenta_047


title: ChIPSeq_Htz1_4KR_caffeine-0-min_rep2


title: K562_JQ1_rep-3_exp-3


title: Typical_placenta_046


title: K562_JQ1_rep-2_exp-3


title: ARX_KO_178_E2

source_name: embryonic forebrain_ARX_wt/0


title: ChIPSeq_Htz1_4KR_caffeine-0-min_rep1


title: ChIPSeq_Htz1_WT_caffeine-120-min_rep2


title: Autism_placenta_045


title: K562_JQ1_rep-1_exp-3


title: Autism_placenta_049


title: ARX_178E6_ko


title: APP_4xLPSH3K27ac

data_processing:
Base calling from raw images and file conversion to fastq files was achieved by standard Illumina pipeline scripts. Sequencing reads were then mapped to mouse reference genome (mm10) using rna-STAR aligner v2.3.0 with non-default parameters.
Tag directories were created using ‘makeTagDirectory’ for individiual samples and inputs, and peak calling was performed using ‘findpeaks -style histone’ with 4-fold enrichment over background and input, a Poisson p-value of 0.0001, and a peak width of 500 bp for H3K4me1 and 250 bp for H3K27ac.
Peaks common to both replicates were determined using ‘mergepeaks’ (-prefix) function and to focus analysis on enhancers, peaks within ±2.5 kb of known TSS were filtered out. Union peak files for H3K4me1 and H3K27ac marks were then created for comparisons using ‘mergepeaks’ function (-d given).
Active enhancers, i.e. genomic regions containing both H3K4me1 and H3K27ac peaks, were identified using the ‘window’ function of bedtools, requiring peaks of both marks to be located in a genomic region of 4 kb
Union peak files of active enhancers were then used for comparisons between groups using the ‘getDifferentialPeaks’ function (using a fold-change cut-off of 1.5 and a cumulative Poisson p-value of 0.0001).
Differential peaks were annotated using the ‘annotatepeaks.pl’ function, including gene ontology analysis
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph files are merged replicates (for the generation of UCSC browser files, the ‘makeUCSCfile’ function was used uncluding normalisation to respective input and library size, with a resolution of 10 bp)

extract_protocol:
CD11bhigh/CD45low microglia were sorted by Fluorescence-activated cell sorting on a BD FACS Aria. For microglia isolation for chromatin purification, 1 mM sodium butyrate, an inhibitor of histone deacetylases, was added to the dissection medium and FACS buffers, and after staining, microglia were fixed in 1 % PFA for 10 minutes at room temperature, followed by addition of glycine (final concentration: 125 mM) for 5 minutes and washing in HBSS. Microglia were then sorted into homogenization buffer (0.32 M sucrose, 5 mM CaCl2, 5 mM MgAc2, 50 mM HEPES, 0.1 mM EDTA, 1 mM DTT, 0.1% vol/vol Triton-X-100) and centrifuged at 950 g for 5 minutes at 4 °C. The pellet was resuspended in 100 μl Nelson buffer (50 mM Tris, 150 mM NaCl, 20 mM EDTA, 1% vol/vol Triton-X-100, 0.5% vol/vol NP-40) and frozen on dry ice. The cross-linked chromatin was sheared for 3x7 cycles (30 sec. On/Off) in a BioruptorPlus (Diagenode) to achieve an average fragment size of 350 bps. Proper shearing and chromatin concentration was validated by DNA isolation and quantification using a small amount of each sample individually. Samples were split in half and 1 µg of ChiP-graded antibody (H3K4me1: Abcam ab8895; H3K27ac: Abcam ab4729) was added respectively and incubated overnight at 4ºC. From each sample, 1% of the total volume was taken as input prior to antibody binding. Immunoprecipitation was done by incubating samples with 30 µl BSA-blocked protein A magnetic beads (Dynabeads, Invitrogen) for 1hr at 4ºC.
After purifying the precipitated chromatin and isolating the DNA, DNA libraries were generated using the NEB Next Ultra DNA Library Prep Kit for Illumina and the NEB Q5 polymerase (both from New England Biolabs). Multiplexing of samples was done using 6 different index-primers from the Library Prep Kit. One sample from each condition (genotype and treatment) was pooled for that purpose to rule out amplification and sequencing biases within the final data. Input samples were pooled and processed accordingly. The ideal number of amplification cycles was estimated via RealTime PCR to avoid over-amplification. Accordingly, samples were amplified for 13-15 cycles and the DNA was isolated afterwards. Individual libraries were pooled whereby each pool represented one whole batch of samples for each condition and targeted histone modification and was set to a final DNA concentration of 2 nM before sequencing (50 bp) on a HiSeq 2000 (Illumina) according to the manufacturer's instructions.

tag: chip antibody

value: H3K27ac:Abcam ab4729


title: K562_DMSO_rep-3_exp-3


title: Autism_placenta_043

tag: developmental timepoint


title: APP_1xLPSH3K27ac


title: K562_DMSO_rep-1_exp-3


title: K562_DMSO_rep-2_exp-3


title: Autism_placenta_050

tag: diagnosis


title: ChIPSeq_Htz1_4KR_caffeine-30-min_rep2


title: Typical_placenta_042


title: ChIPSeq_Htz1_WT_caffeine-30-min_rep2


title: ARX_178E3_ko


title: ChIPSeq_Htz1_WT_caffeine-120-min_rep1


title: Autism_placenta_041


title: ChIPSeq_Htz1_WT_caffeine-30-min_rep1


title: K562_AID-BRD4_clone-2_IAA_rep-3

value: 100µM indole-3-acetic acid, 90 min

value: AID-BRD4 / SFFV-OsTir1-T2A-BlastR


title: ChIPSeq_Htz1_WT_caffeine-0-min_rep2


title: APP_PBSH3K27ac

value: PBS i.p.


title: WT_4xLPSH3K27ac

value: wildtype


title: Typical_placenta_040

value: full term birth


title: WT_1xLPSH3K27ac

value: 1xLPS i.p.


title: Autism_placenta_039


title: K562_AID-BRD4_clone-2_IAA_rep-2


title: ChIPSeq_Htz1_WT_caffeine-0-min_rep1


title: K562_AID-BRD4_clone-2_IAA_rep-1


title: Typical_placenta_038

value: typical


title: K562_AID-BRD4_clone-2_DMSO_rep-3


title: K562_AID-BRD4_clone-2_DMSO_rep-2


title: WT_PBSH3K27ac


title: Typical_placenta_036


title: APP_1xLPSH3K4me1

value: H3K4me1:Abcam ab8895


title: APP_4xLPSH3K4me1

value: 4xLPS i.p.


title: K562_AID-BRD4_clone-2_DMSO_rep-1


title: Typical_placenta_037


title: APP_PBSH3K4me1


title: Typical_placenta_035


title: Autism_placenta_034


title: K562_nilotinib_exp-2

description: PolyA RNA

value: 100nM nilotinib, 90 min


title: WT_4xLPSH3K4me1


title: Typical_placenta_033


title: WT_1xLPSH3K4me1


title: WT_PBSH3K4me1


title: K562_trametinib_exp-2

description: PolyA RNA

value: 10nM trametinib, 90 min


title: Autism_placenta_029


title: K562_mk2206_exp-2

description: PolyA RNA


title: APP_inputDNA

value: equal mixture of DNA from all treatment groups

value: none (input)


title: Autism_placenta_028

value: male

value: autism


title: WT_inputDNA


title: Autism_placenta_027


title: K562_flavopiridol_exp-1

description: PolyA RNA

value: 300nM flavopiridol, 60 min


title: K562_DMSO_exp-1

description: PolyA RNA

value: DMSO, 60 min


title: xylose rep2

city: Utrecht

first: Ronald

last: de Vries

address: Uppsalalaan 8

department: fungal physiology

country: Netherlands

institute: Centre of fungal biodiversity

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and removed for low-quality sequence, then mapped to Dichomitus squalens CBS464.89 (http://genome.jgi.doe.gov/Dicsqu464_1) using Bowtie2 (Langmead B et al., Genome Biology, 2009) and HISAT software (KimD, Langmead B and Salzberg SL, Nature Methods, 2015).
Fragments per kilobase of exon model per million mapped reads (FPKM) was calculated using RSEM tool (Li B & Dewey CN, BMC bioinformatics, 2011).
The gene_ids in the FPKM tables are from the gff3 file of JGI Dichomitus squalens CBS464.89 which is linked as supplementary file Dicsqu464_1_GeneCatalog_20151220.gff3.gz on the Series record or available at this link:
https://genome.jgi.doe.gov/Dicsqu18370_1/download/Dicsqu18370_1_GeneCatalog_20151202.gff3.gz
File Dicsqu464_JGI_gene_transcrip_protein_ids.txt can be used to convert the Gene_IDs to the normal JGI ID.
Genome_build: Dichomitus squalens CBS464.89 (http://genome.jgi.doe.gov/Dicsqu464_1)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Dichomitus squalens

source_name: Mycelium sample, xylose

growth_protocol: Strains were grown at 28°C for 5 days on low-nitrogen asparagine-succinate medium (LN-AS) 1.5% (w/v) agar plates supplemented with 25 mM of monosaccharides  L-rhamnose,  D-xylose, and a disaccharide cellobiose.

extract_protocol:
RNA was extracted from ground mycelia (Tissuelyser II, Qiagen) using a A combination of Trizol method and Nucleo spin RNA extraction kit from Macherey-Nagel. The RNA quantity and quality was checked with a RNA6000 Nano Assay using the Agilent 2100 Bioanalyser (Agilent Technologies, Santa Clara, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: sampling time

value: 5 days

value: wild type

tag: monomeric carbon source

value: xylose

value: mycelium


title: L-rhamnose rep2

source_name: Mycelium sample, L-rhamnose

tag: genotype

value: L-rhamnose

tag: tissue


title: L-rhamnose rep1


title: 17_MK5

city: Budapest

first: <Up loaded by Bioinformatics core  facility>

last: <PI shown in the article>

address: Szigony st 43.

country: Hungary

institute: HUN-REN Institute of Experimental Medicine

description: other (small RNA fracture)

data_processing:
Reads were trimmed with Trimmomatic program and their quality was checked by FastQC
Reads were stacked (identical sequences were counted)
Libraries were normalised to 1 million reads
Genome_build: None, Viral contigs were de novo assembled
Supplementary_files_format_and_content: Processed files are tab separated files, first column is the sequence the second is the normalised read count

organism: Vitis vinifera

source_name: shoot tips, young leaves, older leaves, tendrils and flowers

growth_protocol: Samples were collected from the field or from forced canes.

extract_protocol:
CTAB
Illumina TruSeq Small RNA Library Preparation Kits, according to the manufacturers instructions

tag: vine region

value: Tokaj, Mad

tag: cultivar

value: Teleki-Kober 125


title: 16_MK4

description: other (small RNA fracture)

value: Sargamuskotaly


title: 18_MK7

description: other (small RNA fracture)

value: Teleki-Kober 5C


title: 15_MK3

description: other (small RNA fracture)

value: K3 Harslevelu


title: K562_mk2206+trametinib_exp-2

description: PolyA RNA

tag: treatment

value: 300nM mk2206 + 10 nM trametinib, 90 min


title: 14_MK1

description: other (small RNA fracture)

value: Furmint T85


title: cellobiose rep1

source_name: Mycelium sample, cellobiose

value: cellobiose


title: 13_BV

description: other (small RNA fracture)

value: Tokaj, Bodrogkisfalud

value: Purcsin, Balafant, Sarga Ortliebi, Kek Bakator, Feher Jardovany


title: xylose, rep1

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and removed for low-quality sequence, then mapped to Dichomitus squalens CBS464.89 (http://genome.jgi.doe.gov/Dicsqu464_1) using Bowtie2 (Langmead B et al., Genome Biology, 2009) and BWA software (Li H. & Durbin R, Bioinformatics, 2009).
“Fragments per kilobase of exon model per million mapped reads” (FPKM) was calculated using RSEM tool (Li B & Dewey CN, BMC bioinformatics, 2011).
Genome_build: Dichomitus squalens CBS464.89 (http://genome.jgi.doe.gov/Dicsqu464_1)
Supplementary_files_format_and_content: *gene.FPKM.txt: Tab-delimited text files include FPKM values for each Sample.

growth_protocol: Strains were grown at 28°C for 5 days on low-nitrogen asparagine-succinate medium (LN-AS) 1.5% (w/v) agar plates supplemented with 25 mM of monosaccharides D-glucose, D-glucuronic acid, D-galacturonic acid, L-rhamnose, D-galactose, D-xylose, D-mannose and L-arabinose, and the disaccharide cellobiose.

extract_protocol:
RNA was extracted from grinded mycelia (Tissuelyser II, Qiagen) using a combination of Trizol method and Nucleo spin RNA extraction kit from Macherey-Nagel. The RNA quantity and quality were checked with a RNA6000 Nano Assay using the Agilent 2100 Bioanalyser (Agilent Technologies, Santa Clara, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain/background

tag: genotype/variation

tag: carbon source


title: K562_DMSO_exp-2

description: PolyA RNA

tag: 4su labeling time before harvest (min)


title: mannose, rep1

source_name: Mycelium sample, mannose

value: mannose


title: 11_SZHU

description: other (small RNA fracture)

value: Tokaj, Szegilong

value: Furmint


title: galactose, rep2

source_name: Mycelium sample, galactose

value: wild type

value: galactose

value: 5 days


title: 9_SZHT

description: other (small RNA fracture)


title: galactose, rep1

value: mycelium


title: mannose, rep2


title: L-rhamnose, rep2

value: L-rhamnose


title: L-rhamnose, rep1


title: 8_ET

description: other (small RNA fracture)

value: Eger

value: Kadarka


title: 7_FP

description: other (small RNA fracture)

value: Kunsag

value: Generosa (new variety)


title: xylose rep1

value: xylose


title: 6_MP

description: other (small RNA fracture)

value: Szekszard

value: Merlot


title: arabinose, rep2

source_name: Mycelium sample, arabinose

value: arabinose


title: cellobiose rep2

value: cellobiose


title: 5_CS

description: other (small RNA fracture)

value: Balaton

value: Csabagyongye - Pearl of Csaba


title: arabinose, rep1


title: xylose, rep2


title: 4_PP

description: other (small RNA fracture)

value: Villany

value: Cabernet Sauvignon


title: cellobiose, rep1

value: wild type


title: 2_PH

description: other (small RNA fracture)

value: Pannonhalma

value: Olaszrizling - Welschriesling


title: 3_HT

description: other (small RNA fracture)

value: Neszmely

value: Chardonnay


title: glucose, rep1

source_name: Mycelium sample, glucose

value: mycelium

value: glucose

value: 5 days


title: glucose, rep2


title: DGM-11463_M0_lae-bc

status: Public on Apr 04 2018

city: New York

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

data_processing:
HiSeq Control Software (Illumina) was used to perform image analysis, base calling and sequence analysis on HiSeq generated sequence images resulting in fastq files.
Expression analysis was performed using the human reference genome build GRCh37/hg19, STAR (2.3.1z13_r470) for aligning reads, RefSeq gene definitions (2014-06-02) and Cufflinks (v2.2, http://cufflinks.cbcb.umd.edu)
To correct for transcript length and depth of coverage raw paired-end sequenced reads were converted into fragments per kilobase of exon per million fragments sequenced (FPKM).
This process was carried out independently for each sample lane. Before running Cufflinks, Samtools (v0.1.18.0, http://samtools.sourceforge.net) was used to merge each sample's independent STAR results into one file. This file contains all the aligned reads for each read pair. Finally Cufflinks was run on the merged STAR output to produce a file with FPKM values for each sample
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: FPKM text files include the UniqueID (GeneID_location), GeneID and the FPKM values for all samples

source_name: large airway basal cells

growth_protocol: Pure populations of nonsmoker large and small airway samples and nonsmoker derived large and small airway basal cells (BC) were obtained and characterized using detailed protocols as previously described (PMID:1572528). Primary BC were maintained in Bronchial Epithelial Growth Media (BEGM, Lonza, Walkersville, MD) and passaged by seeding at a cell density of 3000 cells/cm2 in BEGM with fresh media changed every 2 days (PMID:24298994). RNA sequencing of primary (Passage 0) BC was performed on cells once they had reached 70-80% confluence as well as large and small airway samples.

extract_protocol:
Total RNA from nonsmoker epithelium and  harvested nonsmoker basal cells was extracted with TRIzol with subsequent RNA clean-up using the RNeasy MinElute RNA purification kit to remove residual DNA
The TruSeq RNA Sample Prep Kit (Illumina, San Diego, CA) was utilized as per protocol to generate cDNA that was then purified with QIA-quick PCR purification kit (Qiagen, Valencia, CA)
Samples were loaded onto an Illumina flowcell for paired-end 125 x 2 sequencing reactions using the Illumina HiSeq 2500.  HiSeq Control Software (Illumina) was used to perform image analysis, base calling and sequence analysis on HiSeq generated sequence images.

tag: smoking status

value: COPD smoker

tag: cell type

value: large airway basal cells cultured from airway epithelium


title: DGM-12446_lae-bc


title: DGM-11261_M6_lae-bc


title: K562_MYC-AID_DMSO_rep-2

extract_protocol:
Total RNA was extracted using a commercial column purification kit and treated with iodoacetamide for alkylation of 4-thiouridine.
3'UTR sequencing libraries were generated from 500ng of alkylated total RNA using a commercial kit (QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina, Lexogen).

tag: cell line

tag: genetic modification

value: MYC-AID / SFFV-OsTir1-T2A-BlastR


title: DGM-11001_M6_lae-bc


title: DGM-10984_M6_lae-bc


title: 10_EH

description: other (small RNA fracture)

value: Tokaj, Erdobenye

value: Furmint


title: DGM-10794_M3_lae-bc


title: DGM-00692_lae-bc


title: DGM-10262_M6_lae-bc


title: cellobiose, rep2

value: cellobiose


title: DGM-02164_M3_lae-bc


title: DGM-12005_lae-bc

value: smoker


title: 1_TK

description: other (small RNA fracture)

value: Sopron

value: Kekfrankos - Blaufrankisch, Lemberger


title: DGM-00061_M28_lae-bc


title: DGM-10406_M12_lae-bc


title: DGM-12088_lae-bc


title: DGM-11156_lae-bc


title: DGM-11529_lae-bc


title: 12_DF

description: other (small RNA fracture)


title: DGM-02019_lae-bc


title: DGM-10201_M12_lae-bc


title: DGM-12163_lae-bc


title: DGM-11270_M0_lae-bc


title: DGM-12833_140320_sae-bc

source_name: small airway basal cells

value: nonsmoker

value: small airway basal cells cultured from airway epithelium


title: DGM-11007_M6_lae-bc


title: DGM-12833_131003_sae-bc


title: DGM-12857_sae-bc


title: DGM-10707_M0_sm

source_name: small airway epithelial cells

value: small airway epithelial cells


title: DGM-10568_M0_sm


title: DGM-10565_M12_sm


title: DGM-11280_lae-bc


title: DGM-10383_M12_sm


title: DGM-10380_M12_sm


title: DGM-10698_M12_lae-bc


title: DGM-10500_M6_sm


title: DGM-10254_M12_sm


title: DGM-10343_M12_sm


title: DGM-00342_M12_sm


title: DGM-10161_M12_sm


title: DGM-01774_M3_sm


title: DGM-10123_M12_sm


title: DGM-10284_M12_sm


title: DGM-12748_lae-bc


title: DGM-10159_M12_sm


title: DGM-12825_lae-bc


title: DGM-12489_lae-bc


title: DGM-12535_lae-bc


title: DGM-10475_M3_sm


title: DGM-12251_lae-bc


title: DGM-10270_M12_sm


title: DGM-10503_M12_sm


title: DGM-10288_M12_sm


title: DGM-10194_M12_sm


title: DGM-12023_lae-bc


title: DGM-12027_lae-bc


title: DGM-12044_lae-bc


title: DGM-10261_M0_sm


title: DGM-11963_lae-bc


title: DGM-11956_lae-bc


title: DGM-12203_lae-bc


title: DGM-11921_lae-bc


title: DGM-11213_lae-bc


title: DGM-10500_M12_lae-bc


title: DGM-10447_M0_lae-bc


title: DGM-01624_lae-bc


title: DGM-01578_lae-bc


title: DGM-12334_lae-bc


title: sc_5

city: Vancouver

first: Mark

middle: Steven

last: Cembrowski

state: BC

address: 2350 Health Sciences Mall

department: Cellular and Physiological Sciences

institute: University of British Columbia

description:
processed data file:
scQuant.txt

data_processing:
As described in methods of manuscript
Genome_build: mm9
Supplementary_files_format_and_content: Tab delimited files containing FPKM values and pairwise DE calls for population-level RNA-seq, as well as tab delimited files for single-cell quanitification

source_name: subiculum single cell

extract_protocol:
Manual sorting to purify for fluorescent neurons from microdissected slices was performed according to previous methods (Hempel et al., 2007).
As described in methods of manuscript.

tag: location

value: Subiculum

value: Subiculum pyramidal cell

tag: sample type

value: single cell


title: sc_7

description:
processed data file:
scQuant.txt


title: sc_6

description:
processed data file:
scQuant.txt


title: sc_4

description:
processed data file:
scQuant.txt


title: sc_3

description:
processed data file:
scQuant.txt


title: sc_8

description:
processed data file:
scQuant.txt


title: NKG2C plus

city: Jerusalem

first: Moriya

last: Gamliel

address: Ein Kerem

department: Immunology

country: Israel

institute: Hebrew University

description: Sample 2 plus

data_processing:
The NextSeq basecalls files were converted to fastq files with the bcl2fastq (v2.15.0.4) program and default parameters.
According to the FastQC report, reads were then quality-trimmed at both ends, using in-house perl scripts, with a quality threshold of 32. Following quality-trimming, adapter sequences were removed by Trim Galore using the command “trim_galore -a $adseq –length 15” where $adseq is the appropriate adapter sequence.
The remaining reads were further filtered to remove very low quality reads, using the fastq_quality_filter program of the FASTX package (version 0.0.14, http://hannonlab.cshl.edu/fastx_toolkit/), with a quality threshold of 20 at 90 percent or more of the read's positions.
The cleaned fastq files were mapped to the human transcriptome and genome using TopHat (v2.0.13). The genome version was GRCh38, with annotations from Ensembl release 78. Mapping allowed up to 5 mismatches per read, a maximum gap of 5 bases, and a total edit distance of 10
Quantification, normalization and differential expression were done with the Cufflinks package (v2.2.1).
Counts and FPKM distributions were used for comparing global expression between the two samples and estimating background expression level. Differential expression was calculated with cuffdiff, using a count threshold (-c parameter) of at least 3 for statistical significance testing.
Samples were assigned a condition, “minus” for the NKG2C negative and “plus” for the NKG2C positive (-L parameter), and expression in the “plus” condition was compared to that in the “minus” condition. Gene-level cuffdiff output was combined with gene details (such as symbol, Entrez accession, etc.) taken from the results of a BioMart query (Ensembl, release 78).
Significantly differentially expressed genes were defined as ones with at least 0.2 FPKM level of expression in at least one of the conditions and a q-value less than 0.1. Differential expression results were visualized in R with in-house scripts based on the cummeRbund code.
Genome_build: GRCh38, with annotations from Ensembl release 78
Supplementary_files_format_and_content: Excel file reports gene-level abundance measurements.

source_name: NKG2CBright dNK cells from multigravida decidua samples

extract_protocol:
Total RNA extract was purified form each population by Quick-RNA™ MiniPrep (ZYMO).
The libraries were constructed using TrueSeq RNA V2 kit of Illumina

treatment_protocol: Lymphocytes samples from five different decidua samples (pooled together to obtain sufficient number of cells). dNK were purified by EasySep™ Human NK Cell Enrichment Kit (STEMCELLS).Subset purity was routinely checked to be higher than 95%.

value: Decidua

tag: individual

value: Multigravida women

value: NKG2C bright dNK cells


title: DGM-10123_lae-bc

value: large airway basal cells cultured from airway epithelium


title: sc_2

description:
processed data file:
scQuant.txt


title: NKG2C minus

description: Sample 1 minus

source_name: NKG2CNeg dNK cells from multigravida decidua samples

value: NKG2C neg dNK cells


title: sc_1

description:
processed data file:
scQuant.txt


title: vhn_3

description:
processed data file:
gene_exp.diff
genes.read_group_tracking
genes.fpkm_tracking

source_name: subPCs projecting to VHN

value: bulk


title: vhn_2


title: rsc_3

source_name: subPCs projecting to RSC


title: rsc_2


title: rsc_1


title: pfc_1

source_name: subPCs projecting to PFC


title: pfc_2


title: na_3

source_name: subPCs projecting to NA


title: na_1


title: DGM-02007_lae-bc


title: delta lvrA/B I

city: New Haven

first: Sameet

last: Mehta

state: CT

address: 300 Cedar St.

institute: Yale University

data_processing:
Base calling was done using CASAVA pipeline on the Illumina HiSeq2500 sequencer.
The obtained reads were trimmed at both ends to remove the "N" added by the sequencer, and were further filtered to keep only the bases with high-quality base calls ( Q30 <), and with read length of at least 45 bases
The reads were aligned to
the Leptospira_interrogans_serovar_Manilae_L495 genome
using TopHat (version 2.0.12) with default parameters.
htseq-count was used on aligned files to generate raw-counts.
The raw counts were processed in DESeq2 with rle normalization to generate normalized abundance values, and were further proccessed in R.
Genome_build: L. interrogans serovar Manilae L495 - chromosome LMAN
http://www.genoscope.cns.fr/agc/microscope/home/index.php
http://www.genoscope.cns.fr/agc/microscope/mage/viewer.php?O_id=1351&submit=LOAD+INTO+GENOME+BROWSER
Supplementary_files_format_and_content: HTSeq-count

organism: Leptospira interrogans serovar Manilae

source_name: Transposon Mutant_ΔlvrA/B

growth_protocol: Leptospira WT and mutant strains ΔlvrA/B, and ΔlvrB were cultured till late-log phase.

extract_protocol:
RNA was extracted using the TRIzol (Invitrogen) method.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cultures were harvested via centrifugation at 3,200 g.

value: delta lvrA/B

tag: growth phase

value: late-log phase


title: delta lvrB II

source_name: Transposon Mutant_ΔlvrB

value: delta lvrB


title: delta lvrA/B II


title: delta lvrB I


title: WTManilaeI

description: WTManilaeI

source_name: Wild type cells without modificaiton

value: WT


title: vhn_1


title: WTManilaeII

description: WTManilaeII


title: F1N_hippo_Nes-cKO_rep1

city: LOS ANGELES

first: Chia-ho

last: Lin

address: 6577 MRL. 675 CHARLES E YOUNG DR. SOUTH

institute: UCLA

data_processing:
illumina Casava software used for basecalling
Gene expression values, FPKM were calculated using a cufflinks program
Exon inclusion ratios were calculated using a splicetrap program
Genome_build: mm9
Supplementary_files_format_and_content: F1N-hippocampus_splicetrap_psi_over10percent_with_pvalues.xls: exon inclusion level
Supplementary_files_format_and_content: F1N-hippocampus_cuffdiff.xls: fpkm for genes

source_name: 2-3mo hippocampus

growth_protocol: 2-3 month old male mice

extract_protocol:
Total RNA was extracted using Trizol (Invitrogen) according to the manufacturer's instructions, then DNAse treatment and acid-phenol and isopropanol precipitation
Illumina TruSeq stranded mRNA kit, 6-plex
50bp paired-end RNA sequencing (Illumina Hi-Seq 2000 platform)
Strand specific

value: adult mouse hippocampus


title: F1N_hippo_Nes-cKO_rep3


title: F1N_hippo_wildtype_rep3


title: SP8_Mouse302_SeqID_73451

city: Ann Arbor

first: Tomonori

last: Hosoya

state: MI

address: 109 Zina Pitcher Place

department: CDB

institute: University of Michigan

data_processing:
In order to account for sequencing depth differences between each library, we down-sampled reads (keeping read pairs intact) to the median depth of all libraries after the pruning steps. This ensures that sequencing depth does not confound this analysis.
After this step, we combined all replicates from each stage into a single BAM file to increase sequencing depth (ranging from 120 to 134 million reads per stage) and called peaks using macs2 with options --nomodel --shift -50 --extsize 100  -B --keep-dup all.
macs2 analyses. Files with .fdr0.05.noBlackList.bed extension are the coordinates of the peak calls for each sample. Additionally, we removed peaks with FDR < 0.05 and in non-mappable regions (blacklisted) to generate a more stringent peak set.
We used CENTIPEDE to generate the posterior probability of each motif instance being bound. We subsequently selected motifs that had a posterior >= 0.99 and fully intersected an ATAC-seq peak in their sample of origin to be considered as bound motifs (footprints).
Genome_build: mm10
Supplementary_files_format_and_content: bigwig, bed

source_name: CD8 SP thymocytes

extract_protocol: Libraries were prepared following  Buenrostro et al, 2013 Nat Methods 10:1213-1218.

treatment_protocol: Single-cell suspension isolated from thymus were stained for cell surface marker, and then each stage of thymoctytes were isolated by flow cytometer

value: CD8 SP thymocytes

tag: strain

tag: age

value: 9 weeks old

tag: genotype

value: wild type


title: F1N_hippo_Nes-cKO_rep2

tag: tissue


title: F1N_hippo_wildtype_rep2


title: F1N_hippo_wildtype_rep1


title: pfc_3

value: Subiculum


title: DN_Mouse4220_SeqID_73442

source_name: DN thymocytes

value: DN thymocytes