title: NP1131_WF_2B

description:
NP1131_WF_1B
Samples run across two lanes and pooled

data_processing:
Multiplexing barcode: CACTCA
Cut and adapt the barcodes and remove poly A and T. Using Galaxy: Cutadapt: Removes sequences of 10 As or Ts along with barcodes.  Max error rate=.11, Matchtimes=1, Min Overlap length=9, Min length =36, Max length = 0,
Run Tophat2. Using Galaxy: Tophat2: Full parameter list: Max realign edit dist=1000, max edit dist =2, library type = FR Unstranded, Final read mismatches = 2, Use bowtie-n-mode = no, Anchor length = 8, max number mismatches in anchor region = 0, min length intron =70, max intron length = 500000, allow indel search = no, max number of alignments = 1, min intron length found during split-segment = 50, Max intron length found during split-segment = 500000, number of mismatches allowed in each segment alignment for reads mapped independently=2, Min length read segements= 25, Use own junctions = yes, Use Gene annotation model = Yes, Use raw junctions = no, Only look for supplied junctions = yes, Use coverage search= No, Use Microexon search = no, Do Fusion search = no, Set Bowtie2 settings = no, Specify read group = No
Run HTseqCounts. Using Galaxy: htseq-counts: Mode: Intersection Strict, Feature type: exon, ID Attribute: gene_id
DESEQ2. Using R: Deseq2 Version 1.4
Genome_build: ensembl_dmel_bdgp5.25; Drosophila_melanogaster.BDGP5.74.gtf
Supplementary_files_format_and_content: Htseq counts reported in .txt file.
Supplementary_files_format_and_content: A total of 4 files linked as supplementary files to the Series record:  One is an overall target file describing each sample in the combined data files and whether that sample was removed due to quality issues.  2nd file is the combined raw counts (HTseq-Count) for each sample we sequenced and set up so the rows are the genes and columns are the sample names.  3rd file is a file converting all gene counts to counts per million mapped reads (CPM). This file was used for z-scoring and removing genes with less than 2 CPM.  4th File is combined data normalized using DESeq2 and regularized log transformed, this file removed 5 samples (ab KC technicals, Brain samples and one G386 sample).  All genes for each cell type with <2CPM in half samples were replaced with zeros.


title: NP1131_WF_4

status: Public on May 05 2016

type: SRA

city: Middlebury College

first: Amanda

last: Crocker

state: Vermont

address: 276 Bicentennial Way

department: Neuroscience

country: USA

institute: Middlebury College

description:
NP1131_WF_2B
Samples run across two lanes and pooled

library_source: transcriptomic

data_processing:
Multiplexing barcode: CTCAGA
Cut and adapt the barcodes and remove poly A and T. Using Galaxy: Cutadapt: Removes sequences of 10 As or Ts along with barcodes.  Max error rate=.11, Matchtimes=1, Min Overlap length=9, Min length =36, Max length = 0,
Run Tophat2. Using Galaxy: Tophat2: Full parameter list: Max realign edit dist=1000, max edit dist =2, library type = FR Unstranded, Final read mismatches = 2, Use bowtie-n-mode = no, Anchor length = 8, max number mismatches in anchor region = 0, min length intron =70, max intron length = 500000, allow indel search = no, max number of alignments = 1, min intron length found during split-segment = 50, Max intron length found during split-segment = 500000, number of mismatches allowed in each segment alignment for reads mapped independently=2, Min length read segements= 25, Use own junctions = yes, Use Gene annotation model = Yes, Use raw junctions = no, Only look for supplied junctions = yes, Use coverage search= No, Use Microexon search = no, Do Fusion search = no, Set Bowtie2 settings = no, Specify read group = No
Run HTseqCounts. Using Galaxy: htseq-counts: Mode: Intersection Strict, Feature type: exon, ID Attribute: gene_id
DESEQ2. Using R: Deseq2 Version 1.4
Genome_build: ensembl_dmel_bdgp5.25; Drosophila_melanogaster.BDGP5.74.gtf
Supplementary_files_format_and_content: Htseq counts reported in .txt file.
Supplementary_files_format_and_content: A total of 4 files linked as supplementary files to the Series record:  One is an overall target file describing each sample in the combined data files and whether that sample was removed due to quality issues.  2nd file is the combined raw counts (HTseq-Count) for each sample we sequenced and set up so the rows are the genes and columns are the sample names.  3rd file is a file converting all gene counts to counts per million mapped reads (CPM). This file was used for z-scoring and removing genes with less than 2 CPM.  4th File is combined data normalized using DESeq2 and regularized log transformed, this file removed 5 samples (ab KC technicals, Brain samples and one G386 sample).  All genes for each cell type with <2CPM in half samples were replaced with zeros.

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: Whole Fly

growth_protocol: Flies were raised at 25C.  Parents consisted of 5 females of the UAS-eGFP;UAS-eGFP;+ and 4 males of corresponding GAL4 line.  Parents were placed in a new vial every 4 days for 2 weeks to minimize overcrowding and keep the larval density relatively constant.  All flies were kept in a 12:12 Light Dark cycle.

extract_protocol:
Neurons were identified through anatomical location and GFP expression and then harvested into a patch pipet on an electrophysiology rig from alive flies.  Cells were harvested into .5ul Nuclease Free water to cause the cells to lyse.
cDNA was made and amplified using the Clontech SMARTer Ultra low RNA kit (version 2 HV). 15 rounds of amplification was perfromed on the samples.   This was then sheared to 200bp and put into an IXI Chip-seq protocol  (automated system) and barcoded following another 12 rounds of amplification. 12 samples were run in a lane and each sample was run across two lanes.

treatment_protocol: Animals undergoing memory formation were subjected to 8 spaced trainings of an odor (either 3-Octanol or 4-Methylcyclohexanol) with a 12 cycle 5 second 60V shock for 1 minute.

tag: cell class

value: NP1131-GAL4/UAS-GFP Background

tag: number cells

value: Millions

tag: training

value: Control

tag: quality

value: more than >4 million mapped reads-across 2 lanes


title: T0.Control_9

city: Boston

first: Raivo

last: Kolde

state: MASSACHUSETTS

address: 185 Cambridge St.

department: Center for Computational and Integrative Biology

institute: Massachusetts General Hospital

description:
Agencourt AMPURE XP Purified Total RNA
12.5% lysate, 1ng NexteraXT

data_processing:
demultiplexing: The gene expression sequencing returns paired-end reads. Read 1 contains the plate-index, well-tag and RNA unique molecular identifier (UMI). Read 2 contains a fragment from the 3′ end of the transcript. The demultiplexing was done with a custom script that required perfect plate index and allowed one mismatch for the well tag.
mapping: The reads in read 2 were mapped to the refseq mouse mm10 gene using BWA with default parameters.
quantification: To quantify the expression genes we calculated the number of reads with unique UMI for each gene. The UMI information is embedded to the raw files as last 10 characters for every read description.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data file contains counts of unique RNA molecules for every gene.

molecule: total RNA

organism: Mus musculus

source_name: BMDM

growth_protocol: BMDM cultured from WT  bones shipped o/n on wet ice from Luke O'Neil lab by Annie Curtis in Dublin Ireland, gown in 30% FBS DMEM +P/S and 20% CMG, replaced fresh 30% Serum Media and 20% CMG on Day2 and Day4 when transducing in 10cm dishes with 10x 58-TF-seq virus. Cells grown in 10 cm petri dishes until day 9 when they were scraped and counted on the hemocytometer and replated in 96-well format at a density of 125K cells per well.

extract_protocol:
RLT lysis, SPRI purification, Turbo DNase, MaximaRT, Random hexamer 2nd strand cDNA 50% of total first strand cDNA, 1ng of ds_cDNA per 96-well plate, 12 minutes and run for 16 cycles PCR according to Nextera manufactures protocol
Modified SCRB-Seq, Soumillon, M., Cacchiarelli, D., Semrau, S., Oudenaarden, A. van & Mikkelsen, T. S. Characterization of directed differentiation by high-throughput single-cell RNA-Seq. bioRxiv 003236 (2014). doi:10.1101/003236; Modified Nextera protocol to PCR enrich only  the 3' end of mRNA transcripts and create digital gene expression libraries for Illumina sequencing.

treatment_protocol: 4 hour dose curve on Halofuginone with and without LPS treatment

tag: tissue

value: bone marrow

tag: cell type

value: macrophages

tag: gender

value: male

tag: strain

tag: age

value: 12 weeks old

tag: time

tag: dose (nm)

tag: treatment

tag: replicate


title: T1.39nM_Halofuginone_2mM_Proline_1


title: T0.Control_11


title: T0.Control_8


title: T1.10000nM_Halofuginone_2

value: Halofuginone


title: NP1131_WF_1

description:
NP1131_WF_1A
Samples run across two lanes and pooled

data_processing:
Multiplexing barcode: CACGAT
Cut and adapt the barcodes and remove poly A and T. Using Galaxy: Cutadapt: Removes sequences of 10 As or Ts along with barcodes.  Max error rate=.11, Matchtimes=1, Min Overlap length=9, Min length =36, Max length = 0,
Run Tophat2. Using Galaxy: Tophat2: Full parameter list: Max realign edit dist=1000, max edit dist =2, library type = FR Unstranded, Final read mismatches = 2, Use bowtie-n-mode = no, Anchor length = 8, max number mismatches in anchor region = 0, min length intron =70, max intron length = 500000, allow indel search = no, max number of alignments = 1, min intron length found during split-segment = 50, Max intron length found during split-segment = 500000, number of mismatches allowed in each segment alignment for reads mapped independently=2, Min length read segements= 25, Use own junctions = yes, Use Gene annotation model = Yes, Use raw junctions = no, Only look for supplied junctions = yes, Use coverage search= No, Use Microexon search = no, Do Fusion search = no, Set Bowtie2 settings = no, Specify read group = No
Run HTseqCounts. Using Galaxy: htseq-counts: Mode: Intersection Strict, Feature type: exon, ID Attribute: gene_id
DESEQ2. Using R: Deseq2 Version 1.4
Genome_build: ensembl_dmel_bdgp5.25; Drosophila_melanogaster.BDGP5.74.gtf
Supplementary_files_format_and_content: Htseq counts reported in .txt file.
Supplementary_files_format_and_content: A total of 4 files linked as supplementary files to the Series record:  One is an overall target file describing each sample in the combined data files and whether that sample was removed due to quality issues.  2nd file is the combined raw counts (HTseq-Count) for each sample we sequenced and set up so the rows are the genes and columns are the sample names.  3rd file is a file converting all gene counts to counts per million mapped reads (CPM). This file was used for z-scoring and removing genes with less than 2 CPM.  4th File is combined data normalized using DESeq2 and regularized log transformed, this file removed 5 samples (ab KC technicals, Brain samples and one G386 sample).  All genes for each cell type with <2CPM in half samples were replaced with zeros.


title: T0.Control_6


title: T0.Control_5


title: R71D08_WF_3

description:
R71D08_WF_3
Samples run across two lanes and pooled

data_processing:
Multiplexing barcode: AGTTCC
Cut and adapt the barcodes and remove poly A and T. Using Galaxy: Cutadapt: Removes sequences of 10 As or Ts along with barcodes.  Max error rate=.11, Matchtimes=1, Min Overlap length=9, Min length =36, Max length = 0,
Run Tophat2. Using Galaxy: Tophat2: Full parameter list: Max realign edit dist=1000, max edit dist =2, library type = FR Unstranded, Final read mismatches = 2, Use bowtie-n-mode = no, Anchor length = 8, max number mismatches in anchor region = 0, min length intron =70, max intron length = 500000, allow indel search = no, max number of alignments = 1, min intron length found during split-segment = 50, Max intron length found during split-segment = 500000, number of mismatches allowed in each segment alignment for reads mapped independently=2, Min length read segements= 25, Use own junctions = yes, Use Gene annotation model = Yes, Use raw junctions = no, Only look for supplied junctions = yes, Use coverage search= No, Use Microexon search = no, Do Fusion search = no, Set Bowtie2 settings = no, Specify read group = No
Run HTseqCounts. Using Galaxy: htseq-counts: Mode: Intersection Strict, Feature type: exon, ID Attribute: gene_id
DESEQ2. Using R: Deseq2 Version 1.4
Genome_build: ensembl_dmel_bdgp5.25; Drosophila_melanogaster.BDGP5.74.gtf
Supplementary_files_format_and_content: Htseq counts reported in .txt file.
Supplementary_files_format_and_content: A total of 4 files linked as supplementary files to the Series record:  One is an overall target file describing each sample in the combined data files and whether that sample was removed due to quality issues.  2nd file is the combined raw counts (HTseq-Count) for each sample we sequenced and set up so the rows are the genes and columns are the sample names.  3rd file is a file converting all gene counts to counts per million mapped reads (CPM). This file was used for z-scoring and removing genes with less than 2 CPM.  4th File is combined data normalized using DESeq2 and regularized log transformed, this file removed 5 samples (ab KC technicals, Brain samples and one G386 sample).  All genes for each cell type with <2CPM in half samples were replaced with zeros.

value: R71D08-GAL4/UAS-GFP Background


title: T0.Control_10


title: T0.Control_12


title: T0.Control_4


title: T0.Control_3


title: R71D08_WF_3B


title: R71D08_WF_2

description:
R71D08_WF_2
Samples run across two lanes and pooled

data_processing:
Multiplexing barcode: AGTCAA
Cut and adapt the barcodes and remove poly A and T. Using Galaxy: Cutadapt: Removes sequences of 10 As or Ts along with barcodes.  Max error rate=.11, Matchtimes=1, Min Overlap length=9, Min length =36, Max length = 0,
Run Tophat2. Using Galaxy: Tophat2: Full parameter list: Max realign edit dist=1000, max edit dist =2, library type = FR Unstranded, Final read mismatches = 2, Use bowtie-n-mode = no, Anchor length = 8, max number mismatches in anchor region = 0, min length intron =70, max intron length = 500000, allow indel search = no, max number of alignments = 1, min intron length found during split-segment = 50, Max intron length found during split-segment = 500000, number of mismatches allowed in each segment alignment for reads mapped independently=2, Min length read segements= 25, Use own junctions = yes, Use Gene annotation model = Yes, Use raw junctions = no, Only look for supplied junctions = yes, Use coverage search= No, Use Microexon search = no, Do Fusion search = no, Set Bowtie2 settings = no, Specify read group = No
Run HTseqCounts. Using Galaxy: htseq-counts: Mode: Intersection Strict, Feature type: exon, ID Attribute: gene_id
DESEQ2. Using R: Deseq2 Version 1.4
Genome_build: ensembl_dmel_bdgp5.25; Drosophila_melanogaster.BDGP5.74.gtf
Supplementary_files_format_and_content: Htseq counts reported in .txt file.
Supplementary_files_format_and_content: A total of 4 files linked as supplementary files to the Series record:  One is an overall target file describing each sample in the combined data files and whether that sample was removed due to quality issues.  2nd file is the combined raw counts (HTseq-Count) for each sample we sequenced and set up so the rows are the genes and columns are the sample names.  3rd file is a file converting all gene counts to counts per million mapped reads (CPM). This file was used for z-scoring and removing genes with less than 2 CPM.  4th File is combined data normalized using DESeq2 and regularized log transformed, this file removed 5 samples (ab KC technicals, Brain samples and one G386 sample).  All genes for each cell type with <2CPM in half samples were replaced with zeros.


title: R71D08_WF_2B


title: R71D08_WF_1B

description:
R71D08_WF_1
Samples run across two lanes and pooled

data_processing:
Multiplexing barcode: GGCTAC
Cut and adapt the barcodes and remove poly A and T. Using Galaxy: Cutadapt: Removes sequences of 10 As or Ts along with barcodes.  Max error rate=.11, Matchtimes=1, Min Overlap length=9, Min length =36, Max length = 0,
Run Tophat2. Using Galaxy: Tophat2: Full parameter list: Max realign edit dist=1000, max edit dist =2, library type = FR Unstranded, Final read mismatches = 2, Use bowtie-n-mode = no, Anchor length = 8, max number mismatches in anchor region = 0, min length intron =70, max intron length = 500000, allow indel search = no, max number of alignments = 1, min intron length found during split-segment = 50, Max intron length found during split-segment = 500000, number of mismatches allowed in each segment alignment for reads mapped independently=2, Min length read segements= 25, Use own junctions = yes, Use Gene annotation model = Yes, Use raw junctions = no, Only look for supplied junctions = yes, Use coverage search= No, Use Microexon search = no, Do Fusion search = no, Set Bowtie2 settings = no, Specify read group = No
Run HTseqCounts. Using Galaxy: htseq-counts: Mode: Intersection Strict, Feature type: exon, ID Attribute: gene_id
DESEQ2. Using R: Deseq2 Version 1.4
Genome_build: ensembl_dmel_bdgp5.25; Drosophila_melanogaster.BDGP5.74.gtf
Supplementary_files_format_and_content: Htseq counts reported in .txt file.
Supplementary_files_format_and_content: A total of 4 files linked as supplementary files to the Series record:  One is an overall target file describing each sample in the combined data files and whether that sample was removed due to quality issues.  2nd file is the combined raw counts (HTseq-Count) for each sample we sequenced and set up so the rows are the genes and columns are the sample names.  3rd file is a file converting all gene counts to counts per million mapped reads (CPM). This file was used for z-scoring and removing genes with less than 2 CPM.  4th File is combined data normalized using DESeq2 and regularized log transformed, this file removed 5 samples (ab KC technicals, Brain samples and one G386 sample).  All genes for each cell type with <2CPM in half samples were replaced with zeros.


title: R71D08_WF_1


title: NP1131_WF_2


title: T0.Control_1


title: T0.Control_2


title: R27G01_WF_3B

description:
R27G01_WF_3
Samples run across two lanes and pooled

data_processing:
Multiplexing barcode: TACAGC
Cut and adapt the barcodes and remove poly A and T. Using Galaxy: Cutadapt: Removes sequences of 10 As or Ts along with barcodes.  Max error rate=.11, Matchtimes=1, Min Overlap length=9, Min length =36, Max length = 0,
Run Tophat2. Using Galaxy: Tophat2: Full parameter list: Max realign edit dist=1000, max edit dist =2, library type = FR Unstranded, Final read mismatches = 2, Use bowtie-n-mode = no, Anchor length = 8, max number mismatches in anchor region = 0, min length intron =70, max intron length = 500000, allow indel search = no, max number of alignments = 1, min intron length found during split-segment = 50, Max intron length found during split-segment = 500000, number of mismatches allowed in each segment alignment for reads mapped independently=2, Min length read segements= 25, Use own junctions = yes, Use Gene annotation model = Yes, Use raw junctions = no, Only look for supplied junctions = yes, Use coverage search= No, Use Microexon search = no, Do Fusion search = no, Set Bowtie2 settings = no, Specify read group = No
Run HTseqCounts. Using Galaxy: htseq-counts: Mode: Intersection Strict, Feature type: exon, ID Attribute: gene_id
DESEQ2. Using R: Deseq2 Version 1.4
Genome_build: ensembl_dmel_bdgp5.25; Drosophila_melanogaster.BDGP5.74.gtf
Supplementary_files_format_and_content: Htseq counts reported in .txt file.
Supplementary_files_format_and_content: A total of 4 files linked as supplementary files to the Series record:  One is an overall target file describing each sample in the combined data files and whether that sample was removed due to quality issues.  2nd file is the combined raw counts (HTseq-Count) for each sample we sequenced and set up so the rows are the genes and columns are the sample names.  3rd file is a file converting all gene counts to counts per million mapped reads (CPM). This file was used for z-scoring and removing genes with less than 2 CPM.  4th File is combined data normalized using DESeq2 and regularized log transformed, this file removed 5 samples (ab KC technicals, Brain samples and one G386 sample).  All genes for each cell type with <2CPM in half samples were replaced with zeros.

value: R27G01-GAL4/UAS-GFP Background


title: R27G01_WF_4B

description:
R27G01_WF_4
Samples run across two lanes and pooled

data_processing:
Multiplexing barcode: TCGAAG
Cut and adapt the barcodes and remove poly A and T. Using Galaxy: Cutadapt: Removes sequences of 10 As or Ts along with barcodes.  Max error rate=.11, Matchtimes=1, Min Overlap length=9, Min length =36, Max length = 0,
Run Tophat2. Using Galaxy: Tophat2: Full parameter list: Max realign edit dist=1000, max edit dist =2, library type = FR Unstranded, Final read mismatches = 2, Use bowtie-n-mode = no, Anchor length = 8, max number mismatches in anchor region = 0, min length intron =70, max intron length = 500000, allow indel search = no, max number of alignments = 1, min intron length found during split-segment = 50, Max intron length found during split-segment = 500000, number of mismatches allowed in each segment alignment for reads mapped independently=2, Min length read segements= 25, Use own junctions = yes, Use Gene annotation model = Yes, Use raw junctions = no, Only look for supplied junctions = yes, Use coverage search= No, Use Microexon search = no, Do Fusion search = no, Set Bowtie2 settings = no, Specify read group = No
Run HTseqCounts. Using Galaxy: htseq-counts: Mode: Intersection Strict, Feature type: exon, ID Attribute: gene_id
DESEQ2. Using R: Deseq2 Version 1.4
Genome_build: ensembl_dmel_bdgp5.25; Drosophila_melanogaster.BDGP5.74.gtf
Supplementary_files_format_and_content: Htseq counts reported in .txt file.
Supplementary_files_format_and_content: A total of 4 files linked as supplementary files to the Series record:  One is an overall target file describing each sample in the combined data files and whether that sample was removed due to quality issues.  2nd file is the combined raw counts (HTseq-Count) for each sample we sequenced and set up so the rows are the genes and columns are the sample names.  3rd file is a file converting all gene counts to counts per million mapped reads (CPM). This file was used for z-scoring and removing genes with less than 2 CPM.  4th File is combined data normalized using DESeq2 and regularized log transformed, this file removed 5 samples (ab KC technicals, Brain samples and one G386 sample).  All genes for each cell type with <2CPM in half samples were replaced with zeros.


title: NP1131_WF_3

description:
NP1131_WF_2A
Samples run across two lanes and pooled

data_processing:
Multiplexing barcode: CTAGCT
Cut and adapt the barcodes and remove poly A and T. Using Galaxy: Cutadapt: Removes sequences of 10 As or Ts along with barcodes.  Max error rate=.11, Matchtimes=1, Min Overlap length=9, Min length =36, Max length = 0,
Run Tophat2. Using Galaxy: Tophat2: Full parameter list: Max realign edit dist=1000, max edit dist =2, library type = FR Unstranded, Final read mismatches = 2, Use bowtie-n-mode = no, Anchor length = 8, max number mismatches in anchor region = 0, min length intron =70, max intron length = 500000, allow indel search = no, max number of alignments = 1, min intron length found during split-segment = 50, Max intron length found during split-segment = 500000, number of mismatches allowed in each segment alignment for reads mapped independently=2, Min length read segements= 25, Use own junctions = yes, Use Gene annotation model = Yes, Use raw junctions = no, Only look for supplied junctions = yes, Use coverage search= No, Use Microexon search = no, Do Fusion search = no, Set Bowtie2 settings = no, Specify read group = No
Run HTseqCounts. Using Galaxy: htseq-counts: Mode: Intersection Strict, Feature type: exon, ID Attribute: gene_id
DESEQ2. Using R: Deseq2 Version 1.4
Genome_build: ensembl_dmel_bdgp5.25; Drosophila_melanogaster.BDGP5.74.gtf
Supplementary_files_format_and_content: Htseq counts reported in .txt file.
Supplementary_files_format_and_content: A total of 4 files linked as supplementary files to the Series record:  One is an overall target file describing each sample in the combined data files and whether that sample was removed due to quality issues.  2nd file is the combined raw counts (HTseq-Count) for each sample we sequenced and set up so the rows are the genes and columns are the sample names.  3rd file is a file converting all gene counts to counts per million mapped reads (CPM). This file was used for z-scoring and removing genes with less than 2 CPM.  4th File is combined data normalized using DESeq2 and regularized log transformed, this file removed 5 samples (ab KC technicals, Brain samples and one G386 sample).  All genes for each cell type with <2CPM in half samples were replaced with zeros.


title: T0.2.4nM_Halofuginone_2


title: T0.2.4nM_Halofuginone_2mM_Proline_2


title: R27G01_WF_2B

description:
R27G01_WF_2
Samples run across two lanes and pooled

data_processing:
Multiplexing barcode: GCGCTA
Cut and adapt the barcodes and remove poly A and T. Using Galaxy: Cutadapt: Removes sequences of 10 As or Ts along with barcodes.  Max error rate=.11, Matchtimes=1, Min Overlap length=9, Min length =36, Max length = 0,
Run Tophat2. Using Galaxy: Tophat2: Full parameter list: Max realign edit dist=1000, max edit dist =2, library type = FR Unstranded, Final read mismatches = 2, Use bowtie-n-mode = no, Anchor length = 8, max number mismatches in anchor region = 0, min length intron =70, max intron length = 500000, allow indel search = no, max number of alignments = 1, min intron length found during split-segment = 50, Max intron length found during split-segment = 500000, number of mismatches allowed in each segment alignment for reads mapped independently=2, Min length read segements= 25, Use own junctions = yes, Use Gene annotation model = Yes, Use raw junctions = no, Only look for supplied junctions = yes, Use coverage search= No, Use Microexon search = no, Do Fusion search = no, Set Bowtie2 settings = no, Specify read group = No
Run HTseqCounts. Using Galaxy: htseq-counts: Mode: Intersection Strict, Feature type: exon, ID Attribute: gene_id
DESEQ2. Using R: Deseq2 Version 1.4
Genome_build: ensembl_dmel_bdgp5.25; Drosophila_melanogaster.BDGP5.74.gtf
Supplementary_files_format_and_content: Htseq counts reported in .txt file.
Supplementary_files_format_and_content: A total of 4 files linked as supplementary files to the Series record:  One is an overall target file describing each sample in the combined data files and whether that sample was removed due to quality issues.  2nd file is the combined raw counts (HTseq-Count) for each sample we sequenced and set up so the rows are the genes and columns are the sample names.  3rd file is a file converting all gene counts to counts per million mapped reads (CPM). This file was used for z-scoring and removing genes with less than 2 CPM.  4th File is combined data normalized using DESeq2 and regularized log transformed, this file removed 5 samples (ab KC technicals, Brain samples and one G386 sample).  All genes for each cell type with <2CPM in half samples were replaced with zeros.


title: R27G01_WF_4


title: T0.2.4nM_Halofuginone_1


title: T0.9.7nM_Halofuginone_2mM_Proline_2


title: T0.9.7nM_Halofuginone_2


title: T0.Control_7


title: T0.9.7nM_Halofuginone_2mM_Proline_1


title: R27G01_WF_3


title: T4.625nM_Halofuginone_1


title: T0.39nM_Halofuginone_2mM_Proline_2


title: T0.9.7nM_Halofuginone_1


title: R27G01_WF_2


title: T0.39nM_Halofuginone_2


title: T0.39nM_Halofuginone_1


title: T0.39nM_Halofuginone_2mM_Proline_1


title: GFP_WF_3

description:
GFP_WF_3
Samples run across two lanes and pooled

data_processing:
Multiplexing barcode: TCGGCA
Cut and adapt the barcodes and remove poly A and T. Using Galaxy: Cutadapt: Removes sequences of 10 As or Ts along with barcodes.  Max error rate=.11, Matchtimes=1, Min Overlap length=9, Min length =36, Max length = 0,
Run Tophat2. Using Galaxy: Tophat2: Full parameter list: Max realign edit dist=1000, max edit dist =2, library type = FR Unstranded, Final read mismatches = 2, Use bowtie-n-mode = no, Anchor length = 8, max number mismatches in anchor region = 0, min length intron =70, max intron length = 500000, allow indel search = no, max number of alignments = 1, min intron length found during split-segment = 50, Max intron length found during split-segment = 500000, number of mismatches allowed in each segment alignment for reads mapped independently=2, Min length read segements= 25, Use own junctions = yes, Use Gene annotation model = Yes, Use raw junctions = no, Only look for supplied junctions = yes, Use coverage search= No, Use Microexon search = no, Do Fusion search = no, Set Bowtie2 settings = no, Specify read group = No
Run HTseqCounts. Using Galaxy: htseq-counts: Mode: Intersection Strict, Feature type: exon, ID Attribute: gene_id
DESEQ2. Using R: Deseq2 Version 1.4
Genome_build: ensembl_dmel_bdgp5.25; Drosophila_melanogaster.BDGP5.74.gtf
Supplementary_files_format_and_content: Htseq counts reported in .txt file.
Supplementary_files_format_and_content: A total of 4 files linked as supplementary files to the Series record:  One is an overall target file describing each sample in the combined data files and whether that sample was removed due to quality issues.  2nd file is the combined raw counts (HTseq-Count) for each sample we sequenced and set up so the rows are the genes and columns are the sample names.  3rd file is a file converting all gene counts to counts per million mapped reads (CPM). This file was used for z-scoring and removing genes with less than 2 CPM.  4th File is combined data normalized using DESeq2 and regularized log transformed, this file removed 5 samples (ab KC technicals, Brain samples and one G386 sample).  All genes for each cell type with <2CPM in half samples were replaced with zeros.

value: UAS-GFP Background


title: GFP_WF_2


title: DAL_WF_2B

description:
DAL_WF_2
Samples run across two lanes and pooled

data_processing:
Multiplexing barcode: GGTAGC
Cut and adapt the barcodes and remove poly A and T. Using Galaxy: Cutadapt: Removes sequences of 10 As or Ts along with barcodes.  Max error rate=.11, Matchtimes=1, Min Overlap length=9, Min length =36, Max length = 0,
Run Tophat2. Using Galaxy: Tophat2: Full parameter list: Max realign edit dist=1000, max edit dist =2, library type = FR Unstranded, Final read mismatches = 2, Use bowtie-n-mode = no, Anchor length = 8, max number mismatches in anchor region = 0, min length intron =70, max intron length = 500000, allow indel search = no, max number of alignments = 1, min intron length found during split-segment = 50, Max intron length found during split-segment = 500000, number of mismatches allowed in each segment alignment for reads mapped independently=2, Min length read segements= 25, Use own junctions = yes, Use Gene annotation model = Yes, Use raw junctions = no, Only look for supplied junctions = yes, Use coverage search= No, Use Microexon search = no, Do Fusion search = no, Set Bowtie2 settings = no, Specify read group = No
Run HTseqCounts. Using Galaxy: htseq-counts: Mode: Intersection Strict, Feature type: exon, ID Attribute: gene_id
DESEQ2. Using R: Deseq2 Version 1.4
Genome_build: ensembl_dmel_bdgp5.25; Drosophila_melanogaster.BDGP5.74.gtf
Supplementary_files_format_and_content: Htseq counts reported in .txt file.
Supplementary_files_format_and_content: A total of 4 files linked as supplementary files to the Series record:  One is an overall target file describing each sample in the combined data files and whether that sample was removed due to quality issues.  2nd file is the combined raw counts (HTseq-Count) for each sample we sequenced and set up so the rows are the genes and columns are the sample names.  3rd file is a file converting all gene counts to counts per million mapped reads (CPM). This file was used for z-scoring and removing genes with less than 2 CPM.  4th File is combined data normalized using DESeq2 and regularized log transformed, this file removed 5 samples (ab KC technicals, Brain samples and one G386 sample).  All genes for each cell type with <2CPM in half samples were replaced with zeros.

value: DAL-GAL4/UAS-GFP Background


title: DAL_WF_3B

description:
DAL_WF_3
Samples run across two lanes and pooled

data_processing:
Multiplexing barcode: ACTGAT
Cut and adapt the barcodes and remove poly A and T. Using Galaxy: Cutadapt: Removes sequences of 10 As or Ts along with barcodes.  Max error rate=.11, Matchtimes=1, Min Overlap length=9, Min length =36, Max length = 0,
Run Tophat2. Using Galaxy: Tophat2: Full parameter list: Max realign edit dist=1000, max edit dist =2, library type = FR Unstranded, Final read mismatches = 2, Use bowtie-n-mode = no, Anchor length = 8, max number mismatches in anchor region = 0, min length intron =70, max intron length = 500000, allow indel search = no, max number of alignments = 1, min intron length found during split-segment = 50, Max intron length found during split-segment = 500000, number of mismatches allowed in each segment alignment for reads mapped independently=2, Min length read segements= 25, Use own junctions = yes, Use Gene annotation model = Yes, Use raw junctions = no, Only look for supplied junctions = yes, Use coverage search= No, Use Microexon search = no, Do Fusion search = no, Set Bowtie2 settings = no, Specify read group = No
Run HTseqCounts. Using Galaxy: htseq-counts: Mode: Intersection Strict, Feature type: exon, ID Attribute: gene_id
DESEQ2. Using R: Deseq2 Version 1.4
Genome_build: ensembl_dmel_bdgp5.25; Drosophila_melanogaster.BDGP5.74.gtf
Supplementary_files_format_and_content: Htseq counts reported in .txt file.
Supplementary_files_format_and_content: A total of 4 files linked as supplementary files to the Series record:  One is an overall target file describing each sample in the combined data files and whether that sample was removed due to quality issues.  2nd file is the combined raw counts (HTseq-Count) for each sample we sequenced and set up so the rows are the genes and columns are the sample names.  3rd file is a file converting all gene counts to counts per million mapped reads (CPM). This file was used for z-scoring and removing genes with less than 2 CPM.  4th File is combined data normalized using DESeq2 and regularized log transformed, this file removed 5 samples (ab KC technicals, Brain samples and one G386 sample).  All genes for each cell type with <2CPM in half samples were replaced with zeros.


title: T0.156nM_Halofuginone_2mM_Proline_1


title: T0.156nM_Halofuginone_2


title: GFP_WF_3B


title: GFP_WF_1

data_processing:
Multiplexing barcode: TAGCTT
Cut and adapt the barcodes and remove poly A and T. Using Galaxy: Cutadapt: Removes sequences of 10 As or Ts along with barcodes.  Max error rate=.11, Matchtimes=1, Min Overlap length=9, Min length =36, Max length = 0,
Run Tophat2. Using Galaxy: Tophat2: Full parameter list: Max realign edit dist=1000, max edit dist =2, library type = FR Unstranded, Final read mismatches = 2, Use bowtie-n-mode = no, Anchor length = 8, max number mismatches in anchor region = 0, min length intron =70, max intron length = 500000, allow indel search = no, max number of alignments = 1, min intron length found during split-segment = 50, Max intron length found during split-segment = 500000, number of mismatches allowed in each segment alignment for reads mapped independently=2, Min length read segements= 25, Use own junctions = yes, Use Gene annotation model = Yes, Use raw junctions = no, Only look for supplied junctions = yes, Use coverage search= No, Use Microexon search = no, Do Fusion search = no, Set Bowtie2 settings = no, Specify read group = No
Run HTseqCounts. Using Galaxy: htseq-counts: Mode: Intersection Strict, Feature type: exon, ID Attribute: gene_id
DESEQ2. Using R: Deseq2 Version 1.4
Genome_build: ensembl_dmel_bdgp5.25; Drosophila_melanogaster.BDGP5.74.gtf
Supplementary_files_format_and_content: Htseq counts reported in .txt file.
Supplementary_files_format_and_content: A total of 4 files linked as supplementary files to the Series record:  One is an overall target file describing each sample in the combined data files and whether that sample was removed due to quality issues.  2nd file is the combined raw counts (HTseq-Count) for each sample we sequenced and set up so the rows are the genes and columns are the sample names.  3rd file is a file converting all gene counts to counts per million mapped reads (CPM). This file was used for z-scoring and removing genes with less than 2 CPM.  4th File is combined data normalized using DESeq2 and regularized log transformed, this file removed 5 samples (ab KC technicals, Brain samples and one G386 sample).  All genes for each cell type with <2CPM in half samples were replaced with zeros.


title: T0.2.4nM_Halofuginone_2mM_Proline_1


title: T0.156nM_Halofuginone_1


title: T0.625nM_Halofuginone_2mM_Proline_2


title: T0.156nM_Halofuginone_2mM_Proline_2


title: DAL_WF_1B

description:
DAL_WF_1
Samples run across two lanes and pooled

data_processing:
Multiplexing barcode: GAGTGG
Cut and adapt the barcodes and remove poly A and T. Using Galaxy: Cutadapt: Removes sequences of 10 As or Ts along with barcodes.  Max error rate=.11, Matchtimes=1, Min Overlap length=9, Min length =36, Max length = 0,
Run Tophat2. Using Galaxy: Tophat2: Full parameter list: Max realign edit dist=1000, max edit dist =2, library type = FR Unstranded, Final read mismatches = 2, Use bowtie-n-mode = no, Anchor length = 8, max number mismatches in anchor region = 0, min length intron =70, max intron length = 500000, allow indel search = no, max number of alignments = 1, min intron length found during split-segment = 50, Max intron length found during split-segment = 500000, number of mismatches allowed in each segment alignment for reads mapped independently=2, Min length read segements= 25, Use own junctions = yes, Use Gene annotation model = Yes, Use raw junctions = no, Only look for supplied junctions = yes, Use coverage search= No, Use Microexon search = no, Do Fusion search = no, Set Bowtie2 settings = no, Specify read group = No
Run HTseqCounts. Using Galaxy: htseq-counts: Mode: Intersection Strict, Feature type: exon, ID Attribute: gene_id
DESEQ2. Using R: Deseq2 Version 1.4
Genome_build: ensembl_dmel_bdgp5.25; Drosophila_melanogaster.BDGP5.74.gtf
Supplementary_files_format_and_content: Htseq counts reported in .txt file.
Supplementary_files_format_and_content: A total of 4 files linked as supplementary files to the Series record:  One is an overall target file describing each sample in the combined data files and whether that sample was removed due to quality issues.  2nd file is the combined raw counts (HTseq-Count) for each sample we sequenced and set up so the rows are the genes and columns are the sample names.  3rd file is a file converting all gene counts to counts per million mapped reads (CPM). This file was used for z-scoring and removing genes with less than 2 CPM.  4th File is combined data normalized using DESeq2 and regularized log transformed, this file removed 5 samples (ab KC technicals, Brain samples and one G386 sample).  All genes for each cell type with <2CPM in half samples were replaced with zeros.


title: DAL_WF_4

description:
DAL_WF_4
Samples run across two lanes and pooled

data_processing:
Multiplexing barcode: ATGAGC
Cut and adapt the barcodes and remove poly A and T. Using Galaxy: Cutadapt: Removes sequences of 10 As or Ts along with barcodes.  Max error rate=.11, Matchtimes=1, Min Overlap length=9, Min length =36, Max length = 0,
Run Tophat2. Using Galaxy: Tophat2: Full parameter list: Max realign edit dist=1000, max edit dist =2, library type = FR Unstranded, Final read mismatches = 2, Use bowtie-n-mode = no, Anchor length = 8, max number mismatches in anchor region = 0, min length intron =70, max intron length = 500000, allow indel search = no, max number of alignments = 1, min intron length found during split-segment = 50, Max intron length found during split-segment = 500000, number of mismatches allowed in each segment alignment for reads mapped independently=2, Min length read segements= 25, Use own junctions = yes, Use Gene annotation model = Yes, Use raw junctions = no, Only look for supplied junctions = yes, Use coverage search= No, Use Microexon search = no, Do Fusion search = no, Set Bowtie2 settings = no, Specify read group = No
Run HTseqCounts. Using Galaxy: htseq-counts: Mode: Intersection Strict, Feature type: exon, ID Attribute: gene_id
DESEQ2. Using R: Deseq2 Version 1.4
Genome_build: ensembl_dmel_bdgp5.25; Drosophila_melanogaster.BDGP5.74.gtf
Supplementary_files_format_and_content: Htseq counts reported in .txt file.
Supplementary_files_format_and_content: A total of 4 files linked as supplementary files to the Series record:  One is an overall target file describing each sample in the combined data files and whether that sample was removed due to quality issues.  2nd file is the combined raw counts (HTseq-Count) for each sample we sequenced and set up so the rows are the genes and columns are the sample names.  3rd file is a file converting all gene counts to counts per million mapped reads (CPM). This file was used for z-scoring and removing genes with less than 2 CPM.  4th File is combined data normalized using DESeq2 and regularized log transformed, this file removed 5 samples (ab KC technicals, Brain samples and one G386 sample).  All genes for each cell type with <2CPM in half samples were replaced with zeros.


title: DAL_WF_3


title: DAL_WF_4B


title: DAL_WF_2


title: DAL_WF_1


title: T0.625nM_Halofuginone_2mM_Proline_1


title: R27G01_1T_02B

description:
R27G01_1T_02
Samples run across two lanes and pooled

data_processing:
Multiplexing barcode: CGTACG
Cut and adapt the barcodes and remove poly A and T. Using Galaxy: Cutadapt: Removes sequences of 10 As or Ts along with barcodes.  Max error rate=.11, Matchtimes=1, Min Overlap length=9, Min length =36, Max length = 0,
Run Tophat2. Using Galaxy: Tophat2: Full parameter list: Max realign edit dist=1000, max edit dist =2, library type = FR Unstranded, Final read mismatches = 2, Use bowtie-n-mode = no, Anchor length = 8, max number mismatches in anchor region = 0, min length intron =70, max intron length = 500000, allow indel search = no, max number of alignments = 1, min intron length found during split-segment = 50, Max intron length found during split-segment = 500000, number of mismatches allowed in each segment alignment for reads mapped independently=2, Min length read segements= 25, Use own junctions = yes, Use Gene annotation model = Yes, Use raw junctions = no, Only look for supplied junctions = yes, Use coverage search= No, Use Microexon search = no, Do Fusion search = no, Set Bowtie2 settings = no, Specify read group = No
Run HTseqCounts. Using Galaxy: htseq-counts: Mode: Intersection Strict, Feature type: exon, ID Attribute: gene_id
DESEQ2. Using R: Deseq2 Version 1.4
Genome_build: ensembl_dmel_bdgp5.25; Drosophila_melanogaster.BDGP5.74.gtf
Supplementary_files_format_and_content: Htseq counts reported in .txt file.
Supplementary_files_format_and_content: A total of 4 files linked as supplementary files to the Series record:  One is an overall target file describing each sample in the combined data files and whether that sample was removed due to quality issues.  2nd file is the combined raw counts (HTseq-Count) for each sample we sequenced and set up so the rows are the genes and columns are the sample names.  3rd file is a file converting all gene counts to counts per million mapped reads (CPM). This file was used for z-scoring and removing genes with less than 2 CPM.  4th File is combined data normalized using DESeq2 and regularized log transformed, this file removed 5 samples (ab KC technicals, Brain samples and one G386 sample).  All genes for each cell type with <2CPM in half samples were replaced with zeros.

source_name: Neuron

value: Trained


title: T0.625nM_Halofuginone_2


title: R27G01_10T_02B

description:
R27G01_10T_02
Samples run across two lanes and pooled

data_processing:
Multiplexing barcode: GTGGCC
Cut and adapt the barcodes and remove poly A and T. Using Galaxy: Cutadapt: Removes sequences of 10 As or Ts along with barcodes.  Max error rate=.11, Matchtimes=1, Min Overlap length=9, Min length =36, Max length = 0,
Run Tophat2. Using Galaxy: Tophat2: Full parameter list: Max realign edit dist=1000, max edit dist =2, library type = FR Unstranded, Final read mismatches = 2, Use bowtie-n-mode = no, Anchor length = 8, max number mismatches in anchor region = 0, min length intron =70, max intron length = 500000, allow indel search = no, max number of alignments = 1, min intron length found during split-segment = 50, Max intron length found during split-segment = 500000, number of mismatches allowed in each segment alignment for reads mapped independently=2, Min length read segements= 25, Use own junctions = yes, Use Gene annotation model = Yes, Use raw junctions = no, Only look for supplied junctions = yes, Use coverage search= No, Use Microexon search = no, Do Fusion search = no, Set Bowtie2 settings = no, Specify read group = No
Run HTseqCounts. Using Galaxy: htseq-counts: Mode: Intersection Strict, Feature type: exon, ID Attribute: gene_id
DESEQ2. Using R: Deseq2 Version 1.4
Genome_build: ensembl_dmel_bdgp5.25; Drosophila_melanogaster.BDGP5.74.gtf
Supplementary_files_format_and_content: Htseq counts reported in .txt file.
Supplementary_files_format_and_content: A total of 4 files linked as supplementary files to the Series record:  One is an overall target file describing each sample in the combined data files and whether that sample was removed due to quality issues.  2nd file is the combined raw counts (HTseq-Count) for each sample we sequenced and set up so the rows are the genes and columns are the sample names.  3rd file is a file converting all gene counts to counts per million mapped reads (CPM). This file was used for z-scoring and removing genes with less than 2 CPM.  4th File is combined data normalized using DESeq2 and regularized log transformed, this file removed 5 samples (ab KC technicals, Brain samples and one G386 sample).  All genes for each cell type with <2CPM in half samples were replaced with zeros.


title: T0.2500nM_Halofuginone_2mM_Proline_2

data_processing:
demultiplexing: The gene expression sequencing returns paired-end reads. Read 1 contains the plate-index, well-tag and RNA unique molecular identifier (UMI). Read 2 contains a fragment from the 3′ end of the transcript. The demultiplexing was done with a custom script that required perfect plate index and allowed one mismatch for the well tag.
mapping: The reads in read 2 were mapped to the refseq mouse mm10 gene using BWA with default parameters.
quantification: To quantify the expression genes we calculated the number of reads with unique UMI for each gene. The UMI information is embedded to the raw files as last 10 characters for every read description.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data file contains counts of unique RNA molecules for every gene.


title: T0.625nM_Halofuginone_1


title: R27G01_8C_04B

description:
R27G01_8C_04
Samples run across two lanes and pooled


title: T0.2500nM_Halofuginone_2

description:
Agencourt AMPURE XP Purified Total RNA
12.5% lysate, 1ng NexteraXT


title: R27G01_4T_02B

description:
R27G01_4T_02
Samples run across two lanes and pooled

data_processing:
Multiplexing barcode: CACTCA
Cut and adapt the barcodes and remove poly A and T. Using Galaxy: Cutadapt: Removes sequences of 10 As or Ts along with barcodes.  Max error rate=.11, Matchtimes=1, Min Overlap length=9, Min length =36, Max length = 0,
Run Tophat2. Using Galaxy: Tophat2: Full parameter list: Max realign edit dist=1000, max edit dist =2, library type = FR Unstranded, Final read mismatches = 2, Use bowtie-n-mode = no, Anchor length = 8, max number mismatches in anchor region = 0, min length intron =70, max intron length = 500000, allow indel search = no, max number of alignments = 1, min intron length found during split-segment = 50, Max intron length found during split-segment = 500000, number of mismatches allowed in each segment alignment for reads mapped independently=2, Min length read segements= 25, Use own junctions = yes, Use Gene annotation model = Yes, Use raw junctions = no, Only look for supplied junctions = yes, Use coverage search= No, Use Microexon search = no, Do Fusion search = no, Set Bowtie2 settings = no, Specify read group = No
Run HTseqCounts. Using Galaxy: htseq-counts: Mode: Intersection Strict, Feature type: exon, ID Attribute: gene_id
DESEQ2. Using R: Deseq2 Version 1.4
Genome_build: ensembl_dmel_bdgp5.25; Drosophila_melanogaster.BDGP5.74.gtf
Supplementary_files_format_and_content: Htseq counts reported in .txt file.
Supplementary_files_format_and_content: A total of 4 files linked as supplementary files to the Series record:  One is an overall target file describing each sample in the combined data files and whether that sample was removed due to quality issues.  2nd file is the combined raw counts (HTseq-Count) for each sample we sequenced and set up so the rows are the genes and columns are the sample names.  3rd file is a file converting all gene counts to counts per million mapped reads (CPM). This file was used for z-scoring and removing genes with less than 2 CPM.  4th File is combined data normalized using DESeq2 and regularized log transformed, this file removed 5 samples (ab KC technicals, Brain samples and one G386 sample).  All genes for each cell type with <2CPM in half samples were replaced with zeros.


title: T0.2500nM_Halofuginone_1


title: T0.10000nM_Halofuginone_2mM_Proline_2


title: T0.2500nM_Halofuginone_2mM_Proline_1


title: R27G01_10C_02B

description:
R27G01_10C_02
Samples run across two lanes and pooled

data_processing:
Multiplexing barcode: GTAGAG
Cut and adapt the barcodes and remove poly A and T. Using Galaxy: Cutadapt: Removes sequences of 10 As or Ts along with barcodes.  Max error rate=.11, Matchtimes=1, Min Overlap length=9, Min length =36, Max length = 0,
Run Tophat2. Using Galaxy: Tophat2: Full parameter list: Max realign edit dist=1000, max edit dist =2, library type = FR Unstranded, Final read mismatches = 2, Use bowtie-n-mode = no, Anchor length = 8, max number mismatches in anchor region = 0, min length intron =70, max intron length = 500000, allow indel search = no, max number of alignments = 1, min intron length found during split-segment = 50, Max intron length found during split-segment = 500000, number of mismatches allowed in each segment alignment for reads mapped independently=2, Min length read segements= 25, Use own junctions = yes, Use Gene annotation model = Yes, Use raw junctions = no, Only look for supplied junctions = yes, Use coverage search= No, Use Microexon search = no, Do Fusion search = no, Set Bowtie2 settings = no, Specify read group = No
Run HTseqCounts. Using Galaxy: htseq-counts: Mode: Intersection Strict, Feature type: exon, ID Attribute: gene_id
DESEQ2. Using R: Deseq2 Version 1.4
Genome_build: ensembl_dmel_bdgp5.25; Drosophila_melanogaster.BDGP5.74.gtf
Supplementary_files_format_and_content: Htseq counts reported in .txt file.
Supplementary_files_format_and_content: A total of 4 files linked as supplementary files to the Series record:  One is an overall target file describing each sample in the combined data files and whether that sample was removed due to quality issues.  2nd file is the combined raw counts (HTseq-Count) for each sample we sequenced and set up so the rows are the genes and columns are the sample names.  3rd file is a file converting all gene counts to counts per million mapped reads (CPM). This file was used for z-scoring and removing genes with less than 2 CPM.  4th File is combined data normalized using DESeq2 and regularized log transformed, this file removed 5 samples (ab KC technicals, Brain samples and one G386 sample).  All genes for each cell type with <2CPM in half samples were replaced with zeros.


title: R27G01_1C_02B

description:
R27G01_1C_02
Samples run across two lanes and pooled

data_processing:
Multiplexing barcode: ATGTCA
Cut and adapt the barcodes and remove poly A and T. Using Galaxy: Cutadapt: Removes sequences of 10 As or Ts along with barcodes.  Max error rate=.11, Matchtimes=1, Min Overlap length=9, Min length =36, Max length = 0,
Run Tophat2. Using Galaxy: Tophat2: Full parameter list: Max realign edit dist=1000, max edit dist =2, library type = FR Unstranded, Final read mismatches = 2, Use bowtie-n-mode = no, Anchor length = 8, max number mismatches in anchor region = 0, min length intron =70, max intron length = 500000, allow indel search = no, max number of alignments = 1, min intron length found during split-segment = 50, Max intron length found during split-segment = 500000, number of mismatches allowed in each segment alignment for reads mapped independently=2, Min length read segements= 25, Use own junctions = yes, Use Gene annotation model = Yes, Use raw junctions = no, Only look for supplied junctions = yes, Use coverage search= No, Use Microexon search = no, Do Fusion search = no, Set Bowtie2 settings = no, Specify read group = No
Run HTseqCounts. Using Galaxy: htseq-counts: Mode: Intersection Strict, Feature type: exon, ID Attribute: gene_id
DESEQ2. Using R: Deseq2 Version 1.4
Genome_build: ensembl_dmel_bdgp5.25; Drosophila_melanogaster.BDGP5.74.gtf
Supplementary_files_format_and_content: Htseq counts reported in .txt file.
Supplementary_files_format_and_content: A total of 4 files linked as supplementary files to the Series record:  One is an overall target file describing each sample in the combined data files and whether that sample was removed due to quality issues.  2nd file is the combined raw counts (HTseq-Count) for each sample we sequenced and set up so the rows are the genes and columns are the sample names.  3rd file is a file converting all gene counts to counts per million mapped reads (CPM). This file was used for z-scoring and removing genes with less than 2 CPM.  4th File is combined data normalized using DESeq2 and regularized log transformed, this file removed 5 samples (ab KC technicals, Brain samples and one G386 sample).  All genes for each cell type with <2CPM in half samples were replaced with zeros.


title: R27G01_5C_02B

description:
R27G01_5C_02
Samples run across two lanes and pooled


title: R27G01_3T_02B

description:
R27G01_3T_02
Samples run across two lanes and pooled

data_processing:
Multiplexing barcode: CTCAGA
Cut and adapt the barcodes and remove poly A and T. Using Galaxy: Cutadapt: Removes sequences of 10 As or Ts along with barcodes.  Max error rate=.11, Matchtimes=1, Min Overlap length=9, Min length =36, Max length = 0,
Run Tophat2. Using Galaxy: Tophat2: Full parameter list: Max realign edit dist=1000, max edit dist =2, library type = FR Unstranded, Final read mismatches = 2, Use bowtie-n-mode = no, Anchor length = 8, max number mismatches in anchor region = 0, min length intron =70, max intron length = 500000, allow indel search = no, max number of alignments = 1, min intron length found during split-segment = 50, Max intron length found during split-segment = 500000, number of mismatches allowed in each segment alignment for reads mapped independently=2, Min length read segements= 25, Use own junctions = yes, Use Gene annotation model = Yes, Use raw junctions = no, Only look for supplied junctions = yes, Use coverage search= No, Use Microexon search = no, Do Fusion search = no, Set Bowtie2 settings = no, Specify read group = No
Run HTseqCounts. Using Galaxy: htseq-counts: Mode: Intersection Strict, Feature type: exon, ID Attribute: gene_id
DESEQ2. Using R: Deseq2 Version 1.4
Genome_build: ensembl_dmel_bdgp5.25; Drosophila_melanogaster.BDGP5.74.gtf
Supplementary_files_format_and_content: Htseq counts reported in .txt file.
Supplementary_files_format_and_content: A total of 4 files linked as supplementary files to the Series record:  One is an overall target file describing each sample in the combined data files and whether that sample was removed due to quality issues.  2nd file is the combined raw counts (HTseq-Count) for each sample we sequenced and set up so the rows are the genes and columns are the sample names.  3rd file is a file converting all gene counts to counts per million mapped reads (CPM). This file was used for z-scoring and removing genes with less than 2 CPM.  4th File is combined data normalized using DESeq2 and regularized log transformed, this file removed 5 samples (ab KC technicals, Brain samples and one G386 sample).  All genes for each cell type with <2CPM in half samples were replaced with zeros.


title: R27G01_10T_02


title: R27G01_10C_02


title: T0.10000nM_Halofuginone_2mM_Proline_1


title: R27G01_1T_02


title: T0.10000nM_Halofuginone_1


title: T0.10000nM_Halofuginone_2


title: R27G01_8C_04


title: R27G01_1C_02


title: 2 month organoid 2

city: La Jolla

first: Tariq

last: Rana

state: CA

address: 9500 Gilman Dr.

department: Pediatrics

institute: University of California, San Diego

description:
Group 3
6_S6_R1_001.sorted

data_processing:
BWA alignment to hg19
mRNA quantification and annotatino Ensembl in Partek Genomic Suite 6.6
Filtering RPKM for all samples <=0.5, data transformation (log2+1), normalization (quantile normalization)
Differential expression analysis (ANOVA) abs>=2, FDR adjusted P-value<=0.05
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample, fold change, p-value, etc

organism: Homo sapiens

source_name: 2 month organoid

growth_protocol: H9 human embryonic stem cell(hESCs) (WA09) from WiCell was cultured on a feeder layer of irradiated mouse embryonic fibroblasts following previously established protocols. H9 hESCs were detached from their feeder layer using 1mg/ml collagenase for 15-20 minutes and 0.5mg/ml dispase for an additional 15 minutes. Wells were washed with media to collect floating undifferentiated hESCs and colonies were dissociated using Accumax at 37°C for 10 minutes to generate a single cell suspension.  At day 0, embryoid bodies were formed using the hanging drop method with 4500 cells/drop in DMEM/F12 media supplemented with 20% knockout serum replacement, 4ng/ml bFGF, NEAA and glutamine. After 2 days of hanging drop culture, embryoid bodies were transferred to sterile petri dishes with refreshed media. After 6 days in culture, embryoid bodies were transferred to new petri dishes containing neural induction media consisting of DMEM/F12, 1:100 N2 supplement, NEAA, glutamine and 1ug/ml heparin until day 11. At day 11, organoids were transferred to Matrigel droplets and cultured in 1:1 mixture of DMEM/F12 and Neurobasal medium supplemented with 1:100 B27 without vitamin A, 1:200 N2, NEAA, insulin, beta-mercaptoethanol and glutamine. Organoids were then transferred to stir flask bioreactors for long term growth on day 15 in the same differentiation media except with the addition of retinoic acid and vitamin A. Media was changed every 3 days.

extract_protocol:
Total RNAs were collected using Qiagen RNeasy MiniKit following manufacturer's instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

value: hESC-derived cerebral organoids

value: 2 months old


title: R27G01_5C_02


title: 2 month organoid 1

description:
Group 3
5_S5_R1_001.sorted


title: R27G01_3T_02


title: R27G01_4T_02


title: H9 hESC 1

description:
Group 1
1_S1_R1_001.sorted

source_name: H9 hESC

tag: cell line

value: human embryonic stem cells (hESCs)


title: 1 month organoid 2

description:
Group 2
3_S3_R1_001.sorted

source_name: 1 month organoid

value: 1 month old


title: H9 hESC 2

description:
Group 1
2_S2_R1_001.sorted


title: G386_11C_04B

description:
G386_11C_04
Samples run across two lanes and pooled


title: G386_12T_05B

description:
G386_12T_05
Samples run across two lanes and pooled


title: G386_2C_0502B

description:
G386_2C_0502
Samples run across two lanes and pooled


title: G386_2C_0528B

description:
G386_2C_0528
Samples run across two lanes and pooled


title: gtaG–_development 24h : replicate 2

city: Houston

first: Gad

last: Shaulsky

state: TX

address: One Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

data_processing:
After demultiplexing, the data was mapped to the D. discoideum genome with bowtie version 0.12.7. Read qualities were used. Other parameters: seed length = 28, allowed mismatches = 2, allowed up to 1 alignment per read, with bowtie options -a, --strata, --best. Unmapped reads were trimmed from 3' by 2 nucleotides, which was repeated 5 times.
Raw expression values were computed as the number of reads that were uniquely mapped to gene exons.
Normalized expression were scaled with mappable exon lengths. This normalization is similar to the RPKM normalization (Reads Per Kilobase of exon per Megabase of library size), but instead of dividing by exon lengths we used the uniquely mappable parts of the exon. To obtain uniquely mappable parts, all possible subsequences of the reference genome (of the same length as reads in raw data) are mapped back to the reference genome, obtaining the number of uniquely mapped sequences to the exons (Exon_mappable). As a library size we used the total number of all uniquely mapped reads from the experiment, excluding the non-polyadenylated genes (N_unique). Normalized expressions were computed as follows: Exp = 10^9*raw/(N_unique * Exon_mappable).
Genome_build: D. discoideum Chromosomal DNA: 1,2,3,4,5,6,M, and floating contigs (created: 05-13-2009 13:53) from the DictyBase (chromosomes 1,2,3,4,5,6 and mitochondrial DNA are the same as on NCBI assembly "dicty_2.7"). Regions [3016085, 3768655] from chr2, [64985, 72996] from chrBF and [42801, 78150] from chrR were masked.
Supplementary_files_format_and_content: Processed data files are tab-separated files with two columns: the first containing gene names and the second its expression. Files ending with "_expr_raw.txt" contain raw expression values while files ending with "_expr_nor.txt" contain normalized expression values.

organism: Dictyostelium discoideum

source_name: gtaG–

growth_protocol: Wild-type and gtaG– strains were cultured axenically in HL5.

extract_protocol:
At each time point, we harvested the cells directly into 1 mL of Trizol® (life technologies, CA, USA) and extracted total RNA according to the manufacturer’s recommended protocol. We performed two rounds of poly-A selection and fragmented 100 ng of the resulting mRNA into approximately 200 bases fragments. We prepared cDNA and the second strand.
We prepared Illumina multiplexed libraries. We prepared 14 individual libraries separately (one from each sample) and added a unique barcode to each library at the final step of PCR amplification. We pooled equal amounts of DNA from each library and sequenced one pool per lane of a flow cell on Illumina Genome Analyzer II using the manufacturer's recommended pipeline (versions 1.2 and 1.3, read length = 50 bases)

treatment_protocol: cells were washed with PDF and plated on nitrocellulse filter on filter paper saturated in PDF at 1.8x106 cells/cm2.

value: gtaG-

tag: genotype

tag: developmental time

value: 24 hr


title: gtaG–_development 24h : replicate 1


title: gtaG–_development 20h : replicate 1

value: 20 hr


title: gtaG–_development 20h : replicate 2


title: WT_development 24h : replicate 1

value: WT


title: G386_13C_05B

description:
G386_13C_05
Samples run across two lanes and pooled

value: Control

value: more than >4 million mapped reads-across 2 lanes


title: 1 month organoid 1

description:
Group 2
4_S4_R1_001.sorted


title: G386_6C_06B

description:
G386_6C_06
Samples run across two lanes and pooled

data_processing:
Multiplexing barcode: CACGAT
Cut and adapt the barcodes and remove poly A and T. Using Galaxy: Cutadapt: Removes sequences of 10 As or Ts along with barcodes.  Max error rate=.11, Matchtimes=1, Min Overlap length=9, Min length =36, Max length = 0,
Run Tophat2. Using Galaxy: Tophat2: Full parameter list: Max realign edit dist=1000, max edit dist =2, library type = FR Unstranded, Final read mismatches = 2, Use bowtie-n-mode = no, Anchor length = 8, max number mismatches in anchor region = 0, min length intron =70, max intron length = 500000, allow indel search = no, max number of alignments = 1, min intron length found during split-segment = 50, Max intron length found during split-segment = 500000, number of mismatches allowed in each segment alignment for reads mapped independently=2, Min length read segements= 25, Use own junctions = yes, Use Gene annotation model = Yes, Use raw junctions = no, Only look for supplied junctions = yes, Use coverage search= No, Use Microexon search = no, Do Fusion search = no, Set Bowtie2 settings = no, Specify read group = No
Run HTseqCounts. Using Galaxy: htseq-counts: Mode: Intersection Strict, Feature type: exon, ID Attribute: gene_id
DESEQ2. Using R: Deseq2 Version 1.4
Genome_build: ensembl_dmel_bdgp5.25; Drosophila_melanogaster.BDGP5.74.gtf
Supplementary_files_format_and_content: Htseq counts reported in .txt file.
Supplementary_files_format_and_content: A total of 4 files linked as supplementary files to the Series record:  One is an overall target file describing each sample in the combined data files and whether that sample was removed due to quality issues.  2nd file is the combined raw counts (HTseq-Count) for each sample we sequenced and set up so the rows are the genes and columns are the sample names.  3rd file is a file converting all gene counts to counts per million mapped reads (CPM). This file was used for z-scoring and removing genes with less than 2 CPM.  4th File is combined data normalized using DESeq2 and regularized log transformed, this file removed 5 samples (ab KC technicals, Brain samples and one G386 sample).  All genes for each cell type with <2CPM in half samples were replaced with zeros.


title: WT_development 20h : replicate 2


title: WT_development 20h : replicate 1


title: gtaG–_development 16h : replicate 2

value: 16 hr


title: G386_1T_06B

description:
G386_1T_06
Samples run across two lanes and pooled


title: WT_development 16h : replicate 2


title: gtaG–_development 16h : replicate 1


title: gtaG–_development 12h : replicate 2

value: 12 hr


title: G386_1T_04B

description:
G386_1T_04
Samples run across two lanes and pooled


title: gtaG–_development 12h : replicate 1


title: G386_2C_04B

description:
G386_2C_04
Samples run across two lanes and pooled


title: WT_development 12h : replicate 2


title: 56 hr RNA-seq Rep 3

city: Ann Arbor

first: Indika

last: Rajapakse

state: MI

address: 1600 Huron Parkway, NCRC Building 520, Rm. 3392

department: Department of Computational Medicine & Bioinformatics

institute: University of Michigan

description: S33733_S39889_Rich_fib_Counts.csv, S33733_S39889_Rich_fib_Fpkms.xlsx

data_processing:
Reads aligned to HG19 with Tophat 2.0.9 and Bowtie 2.1.0.0 with optional parameters “–b2-very-sensitive”,  “–no- coverage-search” and “–no-novel-juncs”.
Cufflinks and Cuffdiff were used for expression quantification with UCSC hg19.fa/.gtf as the reference genome and transcriptome with additional parameter settings “–multi-read-correct”, “–compatible-hits-norm” and “–upper-quartile- norm”.
Homer was used for Hi-C tabulation with “makeTagDirectory” with the “–tbp 1” setting, and with “analyzeHiC” with the “-raw” and “-res 1000000” settings to produce the raw contact matrix at 1MB resolution.
Genome_build: hg19
Supplementary_files_format_and_content: Each text file includes one of the time points 100 kb matrices. The csv contains the raw count  RNA-seq data while the xls file contains the  normalized (FPKM) RNA-seq values.

source_name: fibroblast

growth_protocol: Fibroblasts (CRL-2522) were grown in MEM, 10% FBS, X non-essential amino acids, and 1X antibiotic/antimycotic. Cells were dissociated with 0.25% trypsin then plated in 150mm plates for Hi-C, and 6-well plates for RNA-seq.

extract_protocol:
For Hi-C, 25 X 106 cells were cross linked with 1% formaldehyde in situ. Cross linked cells were harvested and flash frozen in liquid nitrogen. For RNA-seq, We used TRIzolr Reagent to extract RNA from cells grown in 6-well plates. Full details in PMC4491792.
All extracted RNA was treated with RNAse-free DNaseI, then submitted to the University of Michigan Bioinformaics Core lab for library construction andRNA-seq on the Illumina Hiseq-2000 platform. Single-end 50-base sequence reads were generated at a multiplex of 4 per sequencing lane. We adopted the methods for Hi- C library construction from Belton et al. (Methods 58:268, 2012). Full details in PMC4491792.

treatment_protocol: Cell cycle synchronization was performed by serum-starvation for 48 hours. After 48th hours, we added dexamethasone to 100nM or ethanol to the control group. 1 hr later baseline samples were taken and time 0 was set. Thereafter, time series sampling of cells treated with dexamethasone was performed at 8-hour intervals for a total of 56 hours. Full details in PMC4491792

value: ATCC CRL-2522

tag: passages


title: G386_12T_05

tag: cell class


title: G386_1T_04

tag: number cells


title: WT_development 24h : replicate 2


title: gtaG–_development 8h : replicate 2

value: 8 hr


title: 56 hr RNA-seq Rep 1


title: G386_11C_04

tag: training


title: G386_1T_05B

description:
G386_1T_05
Samples run across two lanes and pooled

tag: quality


title: gtaG–_development 8h : replicate 1


title: WT_development 8h : replicate 2


title: WT_development 8h : replicate 1


title: 48 hr RNA-seq Rep 2


title: G386_13C_05


title: gtaG–_development 4h : replicate 2

value: 4 hr


title: 48 hr RNA-seq Rep 1


title: 56 hr RNA-seq Rep 2


title: G386_2C_0502


title: WT_development 16h : replicate 1


title: WT_development 4h : replicate 2


title: G386_2C_0528


title: 40 hr RNA-seq Rep 3


title: 40 hr RNA-seq Rep 2


title: G386_6C_06


title: gtaG–_development 0h : replicate 1

value: 0 hr


title: WT_development 12h : replicate 1


title: WT_development 0h : replicate 2


title: WT_development 4h : replicate 1


title: gtaG–_development 0h : replicate 2


title: G386_1T_05

value: Trained


title: WT_development 0h : replicate 1


title: w3031a strain input

city: New York

first: zhiguo

last: zhang

state: NY

address: 1130 St. Nicholas Avenue

department: Pediatric and Genetics and Development

institute: Columbia University

library_source: genomic

data_processing:
ChIP-Seq and MNase-seq reads were aligned to the yeast genome (sacCer3) using the Bowtie2 (Langmead et al. 2009) software. RNA-seq reads were aligned to the yeast genome and to gene annotations from Refseq gene using TopHat (Trapnell et al. 2009).
The coverage of each base pair was computed across the genome and rendered in the Integrative Genomics Viewer. For the RNA-seq, the coverage was cacluated for the Watson and Crick strands, respectively.
spt16 peaks detection indentified by MACS (Feng et al. 2012), we used P-value < 1 × 10-5. The dynamic nucleosome were called by DANPOS (Chen et al. 2013).
Genome_build: sacCer3
Supplementary_files_format_and_content: bigwig files were generated, scores represent the normalization reads density.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: whole cell

growth_protocol: Wild type (WT) ,spt16(G132D) , rpb1-1 and spt16(G132D) rpb1-1 mutant cells were arrested in G1 phase using α-factor at 25 °C. These cells were either kept at 25 °C or shifted to the non-permissive temperature (37 °C) for 45 min.

extract_protocol:
For MNase-seq, Cells were cross-linked by 0.1% Para formaldehyde for 15 min and then treated with 0.125 M glycine. The pellets were subjected to MNase digestion as previously reported (Kaplan et al. 2008). The DNA with the size of mononucleosomes was used to construct libraries. For RNA-seq, Total RNAs were extracted as previously described with phenol/freeze method (Schmitt et al. 1990). RNA qualities were checked with the Fragment Analyzer (AATI).
The DNA from Mmase and ChIP was used to construct libraries according to manufacture’s guide (Illumina). The library was sequenced using the Illumina 1G Genome Analyzer and Highseq-2000. For RNA-seq, The extracted RNAs were further processed to RNA fragmentation and construct library for Illumina sequencing with the TruSeq Stranded mRNA Sample Prep Kit - Illumina.

tag: media

value: YPD

tag: cell cycle stage

value: G1 phase

tag: chip antibody

value: no


title: G386_1T_06


title: w3031a strain Spt16 ChIP-seq

value: TAP


title: gtaG–_development 4h : replicate 1

tag: strain

value: gtaG-


title: 32 hr RNA-seq Rep 3


title: G386_2C_04


title: 48 hr RNA-seq Rep 3


title: 32 hr RNA-seq Rep 1


title: Spt16 TAP tagged input


title: rpb1-1 T0 MNase-seq

tag: genotype/variation


title: Spt16(G132D)rpb1-1 T45 MNase-seq


title: Spt16(G132D)rpb1-1 T0 MNase-seq


title: V3_15T_09B

description:
V3_15T_09
Samples run across two lanes and pooled


title: 24 hr RNA-seq Rep 3


title: Spt16(G132D) T45 MNase-seq _3


title: 40 hr RNA-seq Rep 1


title: 32 hr RNA-seq Rep 2


title: 24 hr RNA-seq Rep 2


title: V3_14T_11B

description:
V3_14T_11
Samples run across two lanes and pooled


title: Spt16(G132D) T45 MNase-seq _1


title: Spt16(G132D) T45 MNase-seq _2


title: V3_4C_11B

description:
V3_4C_11
Samples run across two lanes and pooled


title: Spt16(G132D) T0 MNase-seq _3


title: V3_16C_09

description:
V3_16C_09
Samples run across two lanes and pooled


title: 24 hr RNA-seq Rep 1


title: Spt16(G132D) T0 MNase-seq _2


title: Spt16(G132D) T0 MNase-seq _1


title: 16 hr RNA-seq Rep 3


title: Spt16 TAP tagged ChIP-seq


title: rpb1-1 T45 MNase-seq


title: V3_16C_09B


title: 16 hr RNA-seq Rep 2


title: WT T45 MNase-seq_2

value: wild type


title: WT T45 MNase-seq_1


title: V3_14T_11


title: 16 hr RNA-seq Rep 1


title: 8 hr RNA-seq Rep 3


title: WT T0 MNase-seq_2


title: V3_4C_11


title: 8 hr RNA-seq Rep 2


title: WT T0 MNase-seq_1


title: V3_13C_09

data_processing:
Multiplexing barcode: CTAGCT
Cut and adapt the barcodes and remove poly A and T. Using Galaxy: Cutadapt: Removes sequences of 10 As or Ts along with barcodes.  Max error rate=.11, Matchtimes=1, Min Overlap length=9, Min length =36, Max length = 0,
Run Tophat2. Using Galaxy: Tophat2: Full parameter list: Max realign edit dist=1000, max edit dist =2, library type = FR Unstranded, Final read mismatches = 2, Use bowtie-n-mode = no, Anchor length = 8, max number mismatches in anchor region = 0, min length intron =70, max intron length = 500000, allow indel search = no, max number of alignments = 1, min intron length found during split-segment = 50, Max intron length found during split-segment = 500000, number of mismatches allowed in each segment alignment for reads mapped independently=2, Min length read segements= 25, Use own junctions = yes, Use Gene annotation model = Yes, Use raw junctions = no, Only look for supplied junctions = yes, Use coverage search= No, Use Microexon search = no, Do Fusion search = no, Set Bowtie2 settings = no, Specify read group = No
Run HTseqCounts. Using Galaxy: htseq-counts: Mode: Intersection Strict, Feature type: exon, ID Attribute: gene_id
DESEQ2. Using R: Deseq2 Version 1.4
Genome_build: ensembl_dmel_bdgp5.25; Drosophila_melanogaster.BDGP5.74.gtf
Supplementary_files_format_and_content: Htseq counts reported in .txt file.
Supplementary_files_format_and_content: A total of 4 files linked as supplementary files to the Series record:  One is an overall target file describing each sample in the combined data files and whether that sample was removed due to quality issues.  2nd file is the combined raw counts (HTseq-Count) for each sample we sequenced and set up so the rows are the genes and columns are the sample names.  3rd file is a file converting all gene counts to counts per million mapped reads (CPM). This file was used for z-scoring and removing genes with less than 2 CPM.  4th File is combined data normalized using DESeq2 and regularized log transformed, this file removed 5 samples (ab KC technicals, Brain samples and one G386 sample).  All genes for each cell type with <2CPM in half samples were replaced with zeros.

value: more than >4 million mapped reads-single lane


title: V3_2C__09

data_processing:
Multiplexing barcode: GCGCTA
Cut and adapt the barcodes and remove poly A and T. Using Galaxy: Cutadapt: Removes sequences of 10 As or Ts along with barcodes.  Max error rate=.11, Matchtimes=1, Min Overlap length=9, Min length =36, Max length = 0,
Run Tophat2. Using Galaxy: Tophat2: Full parameter list: Max realign edit dist=1000, max edit dist =2, library type = FR Unstranded, Final read mismatches = 2, Use bowtie-n-mode = no, Anchor length = 8, max number mismatches in anchor region = 0, min length intron =70, max intron length = 500000, allow indel search = no, max number of alignments = 1, min intron length found during split-segment = 50, Max intron length found during split-segment = 500000, number of mismatches allowed in each segment alignment for reads mapped independently=2, Min length read segements= 25, Use own junctions = yes, Use Gene annotation model = Yes, Use raw junctions = no, Only look for supplied junctions = yes, Use coverage search= No, Use Microexon search = no, Do Fusion search = no, Set Bowtie2 settings = no, Specify read group = No
Run HTseqCounts. Using Galaxy: htseq-counts: Mode: Intersection Strict, Feature type: exon, ID Attribute: gene_id
DESEQ2. Using R: Deseq2 Version 1.4
Genome_build: ensembl_dmel_bdgp5.25; Drosophila_melanogaster.BDGP5.74.gtf
Supplementary_files_format_and_content: Htseq counts reported in .txt file.
Supplementary_files_format_and_content: A total of 4 files linked as supplementary files to the Series record:  One is an overall target file describing each sample in the combined data files and whether that sample was removed due to quality issues.  2nd file is the combined raw counts (HTseq-Count) for each sample we sequenced and set up so the rows are the genes and columns are the sample names.  3rd file is a file converting all gene counts to counts per million mapped reads (CPM). This file was used for z-scoring and removing genes with less than 2 CPM.  4th File is combined data normalized using DESeq2 and regularized log transformed, this file removed 5 samples (ab KC technicals, Brain samples and one G386 sample).  All genes for each cell type with <2CPM in half samples were replaced with zeros.


title: 8 hr RNA-seq Rep 1


title: 0D RNA-seq Rep 3


title: V3_16T_09

data_processing:
Multiplexing barcode: TACAGC
Cut and adapt the barcodes and remove poly A and T. Using Galaxy: Cutadapt: Removes sequences of 10 As or Ts along with barcodes.  Max error rate=.11, Matchtimes=1, Min Overlap length=9, Min length =36, Max length = 0,
Run Tophat2. Using Galaxy: Tophat2: Full parameter list: Max realign edit dist=1000, max edit dist =2, library type = FR Unstranded, Final read mismatches = 2, Use bowtie-n-mode = no, Anchor length = 8, max number mismatches in anchor region = 0, min length intron =70, max intron length = 500000, allow indel search = no, max number of alignments = 1, min intron length found during split-segment = 50, Max intron length found during split-segment = 500000, number of mismatches allowed in each segment alignment for reads mapped independently=2, Min length read segements= 25, Use own junctions = yes, Use Gene annotation model = Yes, Use raw junctions = no, Only look for supplied junctions = yes, Use coverage search= No, Use Microexon search = no, Do Fusion search = no, Set Bowtie2 settings = no, Specify read group = No
Run HTseqCounts. Using Galaxy: htseq-counts: Mode: Intersection Strict, Feature type: exon, ID Attribute: gene_id
DESEQ2. Using R: Deseq2 Version 1.4
Genome_build: ensembl_dmel_bdgp5.25; Drosophila_melanogaster.BDGP5.74.gtf
Supplementary_files_format_and_content: Htseq counts reported in .txt file.
Supplementary_files_format_and_content: A total of 4 files linked as supplementary files to the Series record:  One is an overall target file describing each sample in the combined data files and whether that sample was removed due to quality issues.  2nd file is the combined raw counts (HTseq-Count) for each sample we sequenced and set up so the rows are the genes and columns are the sample names.  3rd file is a file converting all gene counts to counts per million mapped reads (CPM). This file was used for z-scoring and removing genes with less than 2 CPM.  4th File is combined data normalized using DESeq2 and regularized log transformed, this file removed 5 samples (ab KC technicals, Brain samples and one G386 sample).  All genes for each cell type with <2CPM in half samples were replaced with zeros.


title: V3_13T_09

data_processing:
Multiplexing barcode: TCGGCA
Cut and adapt the barcodes and remove poly A and T. Using Galaxy: Cutadapt: Removes sequences of 10 As or Ts along with barcodes.  Max error rate=.11, Matchtimes=1, Min Overlap length=9, Min length =36, Max length = 0,
Run Tophat2. Using Galaxy: Tophat2: Full parameter list: Max realign edit dist=1000, max edit dist =2, library type = FR Unstranded, Final read mismatches = 2, Use bowtie-n-mode = no, Anchor length = 8, max number mismatches in anchor region = 0, min length intron =70, max intron length = 500000, allow indel search = no, max number of alignments = 1, min intron length found during split-segment = 50, Max intron length found during split-segment = 500000, number of mismatches allowed in each segment alignment for reads mapped independently=2, Min length read segements= 25, Use own junctions = yes, Use Gene annotation model = Yes, Use raw junctions = no, Only look for supplied junctions = yes, Use coverage search= No, Use Microexon search = no, Do Fusion search = no, Set Bowtie2 settings = no, Specify read group = No
Run HTseqCounts. Using Galaxy: htseq-counts: Mode: Intersection Strict, Feature type: exon, ID Attribute: gene_id
DESEQ2. Using R: Deseq2 Version 1.4
Genome_build: ensembl_dmel_bdgp5.25; Drosophila_melanogaster.BDGP5.74.gtf
Supplementary_files_format_and_content: Htseq counts reported in .txt file.
Supplementary_files_format_and_content: A total of 4 files linked as supplementary files to the Series record:  One is an overall target file describing each sample in the combined data files and whether that sample was removed due to quality issues.  2nd file is the combined raw counts (HTseq-Count) for each sample we sequenced and set up so the rows are the genes and columns are the sample names.  3rd file is a file converting all gene counts to counts per million mapped reads (CPM). This file was used for z-scoring and removing genes with less than 2 CPM.  4th File is combined data normalized using DESeq2 and regularized log transformed, this file removed 5 samples (ab KC technicals, Brain samples and one G386 sample).  All genes for each cell type with <2CPM in half samples were replaced with zeros.


title: WT T45 MNase-seq_3


title: 0D RNA-seq Rep 1


title: V3_6C_09


title: V3_15T_09


title: sample 77_RNA_LU_Th2_Nippo_rpt1

city: Bethesda

first: Yuka

last: Kanno

state: MD

address: 10 Center Drive, Rm13C120

department: NIAMS

institute: NIH

description: 150730_0381 and 150806_0382 (merged)_S21

data_processing:
alignment, ATAC-seq: ATAC-seq reads from two biological replicates for each sample were mapped to the mouse genome (mm9 assembly) using Bowtie 0.12.8.
peak-calling, ATAC-seq: Redundant reads were removed using fastquniq (Xu et al., 2012). Only one mapped read to each unique regions of the genome that was less than 175 base pairs was kept and used for peak calling with MACS (version 1.4.2)(Zhang et al., 2008) using a P-value threshold of 1 x 10-5. Peaks called from replicates of the same cell type were merged using the mergePeaks module in HOMER. Only peaks called in both replicates were used to generate a bed file for a cell type.
alignment, RNA-seq: Raw sequencing data were processed with CASAVA 1.8.2 to generate FastQ files. Reads of sequentially varying length were mapped to the mouse genome mm9 using TopHat 2.0.
bw file, RNA-seq: Intron-less bigWig files were generated using USCS genome browser’s program bedGraphToBigWig, from bedGraph files made with the BEDtools package (Quinlan and Hall, Bioinformatics:26(6):841-2, 2010).
alignment, ChIP-seq: Reads of 50 bases were aligned to the mouse genome build mm9 with Bowtie 0.12.8, allowing two mismatches. Uniquely mapped and non-redundant reads were retained and used for peak calling.
peaks, ChIP-seq: Peak detection was performed with SICER (Zang et al, 2009 Bioinformatics, 25:1952-1958 for histone mark K27Ac. Peak detection was performed with MACS1.4.2 with the default parameters and a p value <1.0E-05 fortransscription factors p300 and Tbet.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files for ATAC-seq, RNA-seq and transcription factor ChIP-seq (p300, Tbet); bedgraph for histone modification ChIP-seq (K27Ac). bed file for common ATAC-seq peaks of replicates (linked as supplementary files on Series record).

source_name: Effector CD4 T cells

growth_protocol:
cell isolation protocol: Cells from bone marrow, liver, and spleen were obtained by mechanical disruption. Cells from lung were isolated after incubating lungfragments with 0.5 mg/ml Liberase TL for 1h followed by purification with 40% Percoll (GE Healthcare) (Meylan et al., 2013). Cells from siLP were isolated after incubating fine-cut intestine in HBSS solution with 0.5 mg/ml DNase I (Roche) and 0.25 mg/ml  Liberase TL (Roche) followed by filtering with 100 μm cell strainer and purification with 40% Percoll (Sciumé et al., 2012). NK cells were isolated from spleen and liver; ILC1s were isolated from liver; Treg, IL17GFP+Th17, ILC2s, CD4+ILC3 and NCR+ILC3 were isolated from siLP; HSC, CLP, NKp, immature NK, and ILC2p were isolated from bone marrow; Nippo-infected ILC2 and Th2 cells were isolated from lung. Isolated cells were further sorted as based on their surface markers.
in vitro culture protocol: All cells were stimulated in RPMI medium with 10% (vol/vol) FCS (Invitrogen), 2 mM glutamine (Invitrogen), 100 IU/ml penicillin (Invitrogen), 0.1 mg/ml streptomycin (Invitrogen), and 20 mM HEPES buffer, pH 7.2–7.5 (Invitrogen), and 2 mM β-mercaptoethanol (Sigma-Aldrich). NK cells were treated with 1000 U/ml IL-2 and 10 ng/ml IL-12 (R&D) for 6 hours; ILC2 cells were treated with 50 ng/ml IL-25 (BioLegend) and 50 ng/ml IL-33 (Biolegend) for 4 hours; NCR+ILC3 were treated with 50ug/ml of IL-23 (R&D Systems) for 6 hours.
Nippostrongylus brasiliensis infection protocol: Mice of at least 8 weeks of age were infected with 500 infective third-stage N. brasiliensis by subcutaneous injection. Cells from lungs were isolated after 10 days of infection.

extract_protocol:
RNA-seq was performed as described previously with slight modification (Hirahara et al., Immunity 2015). Total RNA was prepared from approximately 30-50,000 cells by using TRIzol following manufacture’s protocol (Life Technologies).
RNA-seq: Total RNA was subsequently processed to mRNA-seq library using TruSeq SR mRNA sample prep kit (FC-122-1001, Illumina).
ChIP-seq: Cells were chemically cross linked by 1% formaldehyde. Cell lysates were made by appropriate sonication and protein-DNA complexes were isolated with antibody.
ATAC-seq was performed according to published protocol (Buenrostro et al., 2013) with minor modification. 50,000 cells were pelleted and washed with 50ul 1xPBS, followed by treatment with 50ul lysis buffer (10mM Tris-HCl, pH7.4, 10mM NaCl, 3mM MgCl2, 0.1% of IGEPAL CA-630). After pelleting the nuclei by centrifuging at 500x g for 10min, the pellets were re-suspended in 40ul transposition reaction with 2ul Tn5  transposase (Illumina Cat# FC-121-1030) to tag and fragmentalize accessible chromatin. The reaction was incubated at 37ºC with shaking at 300rpm for 30min. The fragmentalized DNAs were then purified using Qiagen MinElute Kit and amplified with 10-11 cycles of PCR based on the amplification curve. Once the libraries are purified using Qiagen PCR Cleanup Kit, they were further sequenced for 50 cycles (paired-end reads) on HiSeq2500.
RNA-Seq: The purified libraries were multiplexed and captured on an Illumina flow cell for cluster generation. Libraries were sequenced for 50 single read cycles on HiSeq 2000 or 2500 following the manufacturer's protocols.
ChIP-seq: Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired and the blunt-ended, then phosphorylated ends were treated with Taq polymerase and dATP to yield a protruding 3- 'A' base for ligation of NEBNext adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation, DNA was PCR amplified with NEBNext index primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel, and quantitated by Qubit (Invitrogen).
ChIP-Seq (size fractionation). The purified libraries were multiplexed and captured on an Illumina flow cell for cluster generation. Libraries were sequenced for 50 single read cycles on GAII, HiSeq 2000 or 2500 following the manufacturer's protocols.

tag: tissue

value: Lung

tag: surface marker

tag: culture condition

value: ex vivo, infected w/ Nippo for 10 days

tag: cell type

value: Effector CD4 T cells


title: sample 76_RNA_LU_ILC2_Nippo_rpt2

description: 150730_0381 and 150806_0382 (merged)_S27

source_name: Group 2 innate lymphoid cells

value: Group 2 innate lymphoid cells


title: sample 78_RNA_LU_Th2_Nippo_rpt2

description: 150730_0381 and 150806_0382 (merged)_S33


title: V3_11T_09

data_processing:
Multiplexing barcode: TCGAAG
Cut and adapt the barcodes and remove poly A and T. Using Galaxy: Cutadapt: Removes sequences of 10 As or Ts along with barcodes.  Max error rate=.11, Matchtimes=1, Min Overlap length=9, Min length =36, Max length = 0,
Run Tophat2. Using Galaxy: Tophat2: Full parameter list: Max realign edit dist=1000, max edit dist =2, library type = FR Unstranded, Final read mismatches = 2, Use bowtie-n-mode = no, Anchor length = 8, max number mismatches in anchor region = 0, min length intron =70, max intron length = 500000, allow indel search = no, max number of alignments = 1, min intron length found during split-segment = 50, Max intron length found during split-segment = 500000, number of mismatches allowed in each segment alignment for reads mapped independently=2, Min length read segements= 25, Use own junctions = yes, Use Gene annotation model = Yes, Use raw junctions = no, Only look for supplied junctions = yes, Use coverage search= No, Use Microexon search = no, Do Fusion search = no, Set Bowtie2 settings = no, Specify read group = No
Run HTseqCounts. Using Galaxy: htseq-counts: Mode: Intersection Strict, Feature type: exon, ID Attribute: gene_id
DESEQ2. Using R: Deseq2 Version 1.4
Genome_build: ensembl_dmel_bdgp5.25; Drosophila_melanogaster.BDGP5.74.gtf
Supplementary_files_format_and_content: Htseq counts reported in .txt file.
Supplementary_files_format_and_content: A total of 4 files linked as supplementary files to the Series record:  One is an overall target file describing each sample in the combined data files and whether that sample was removed due to quality issues.  2nd file is the combined raw counts (HTseq-Count) for each sample we sequenced and set up so the rows are the genes and columns are the sample names.  3rd file is a file converting all gene counts to counts per million mapped reads (CPM). This file was used for z-scoring and removing genes with less than 2 CPM.  4th File is combined data normalized using DESeq2 and regularized log transformed, this file removed 5 samples (ab KC technicals, Brain samples and one G386 sample).  All genes for each cell type with <2CPM in half samples were replaced with zeros.


title: 0E RNA-seq Rep 3

tag: cell line


title: WT T0 MNase-seq_3


title: sample 74_RNA_BM_CLP_rpt2

source_name: Common lymphoid progenitor cells

value: Bone marrow

value: ex vivo

value: Common lymphoid progenitor cells


title: R71D08_6C_09B

description:
R71D08_6C_09
Samples run across two lanes and pooled

data_processing:
Multiplexing barcode: GGTAGC
Cut and adapt the barcodes and remove poly A and T. Using Galaxy: Cutadapt: Removes sequences of 10 As or Ts along with barcodes.  Max error rate=.11, Matchtimes=1, Min Overlap length=9, Min length =36, Max length = 0,
Run Tophat2. Using Galaxy: Tophat2: Full parameter list: Max realign edit dist=1000, max edit dist =2, library type = FR Unstranded, Final read mismatches = 2, Use bowtie-n-mode = no, Anchor length = 8, max number mismatches in anchor region = 0, min length intron =70, max intron length = 500000, allow indel search = no, max number of alignments = 1, min intron length found during split-segment = 50, Max intron length found during split-segment = 500000, number of mismatches allowed in each segment alignment for reads mapped independently=2, Min length read segements= 25, Use own junctions = yes, Use Gene annotation model = Yes, Use raw junctions = no, Only look for supplied junctions = yes, Use coverage search= No, Use Microexon search = no, Do Fusion search = no, Set Bowtie2 settings = no, Specify read group = No
Run HTseqCounts. Using Galaxy: htseq-counts: Mode: Intersection Strict, Feature type: exon, ID Attribute: gene_id
DESEQ2. Using R: Deseq2 Version 1.4
Genome_build: ensembl_dmel_bdgp5.25; Drosophila_melanogaster.BDGP5.74.gtf
Supplementary_files_format_and_content: Htseq counts reported in .txt file.
Supplementary_files_format_and_content: A total of 4 files linked as supplementary files to the Series record:  One is an overall target file describing each sample in the combined data files and whether that sample was removed due to quality issues.  2nd file is the combined raw counts (HTseq-Count) for each sample we sequenced and set up so the rows are the genes and columns are the sample names.  3rd file is a file converting all gene counts to counts per million mapped reads (CPM). This file was used for z-scoring and removing genes with less than 2 CPM.  4th File is combined data normalized using DESeq2 and regularized log transformed, this file removed 5 samples (ab KC technicals, Brain samples and one G386 sample).  All genes for each cell type with <2CPM in half samples were replaced with zeros.

value: Control

value: more than >4 million mapped reads-across 2 lanes


title: sample 71_RNA_BM_MPP_rpt1

source_name: Multipotent progenitor cells

value: Multipotent progenitor cells


title: sample 73_RNA_BM_CLP_rpt1


title: sample 70_RNA_BM_HSC_rpt2

source_name: Hematopoietic stem cells

value: Hematopoietic stem cells


title: 0E RNA-seq Rep 2

value: ATCC CRL-2522


title: sample 72_RNA_BM_MPP_rpt2


title: sample 69_RNA_BM_HSC_rpt1


title: 0D RNA-seq Rep 2


title: sample 68_RNA_BM_iNK_rpt2

source_name: Immature NK cells

value: Immature NK cells


title: sample 67_RNA_BM_iNK_rpt1


title: 0E RNA-seq Rep 1


title: 56 hr Hi-C


title: R71D08_2T_0821B

description:
R71D08_2T_0821
Samples run across two lanes and pooled

value: Trained


title: sample 75_RNA_LU_ILC2_Nippo_rpt1

description: 150730_0381 and 150806_0382 (merged)_S15


title: R71D08_1C_09B

description:
R71D08_1C_09
Samples run across two lanes and pooled

data_processing:
Multiplexing barcode: TAGCTT
Cut and adapt the barcodes and remove poly A and T. Using Galaxy: Cutadapt: Removes sequences of 10 As or Ts along with barcodes.  Max error rate=.11, Matchtimes=1, Min Overlap length=9, Min length =36, Max length = 0,
Run Tophat2. Using Galaxy: Tophat2: Full parameter list: Max realign edit dist=1000, max edit dist =2, library type = FR Unstranded, Final read mismatches = 2, Use bowtie-n-mode = no, Anchor length = 8, max number mismatches in anchor region = 0, min length intron =70, max intron length = 500000, allow indel search = no, max number of alignments = 1, min intron length found during split-segment = 50, Max intron length found during split-segment = 500000, number of mismatches allowed in each segment alignment for reads mapped independently=2, Min length read segements= 25, Use own junctions = yes, Use Gene annotation model = Yes, Use raw junctions = no, Only look for supplied junctions = yes, Use coverage search= No, Use Microexon search = no, Do Fusion search = no, Set Bowtie2 settings = no, Specify read group = No
Run HTseqCounts. Using Galaxy: htseq-counts: Mode: Intersection Strict, Feature type: exon, ID Attribute: gene_id
DESEQ2. Using R: Deseq2 Version 1.4
Genome_build: ensembl_dmel_bdgp5.25; Drosophila_melanogaster.BDGP5.74.gtf
Supplementary_files_format_and_content: Htseq counts reported in .txt file.
Supplementary_files_format_and_content: A total of 4 files linked as supplementary files to the Series record:  One is an overall target file describing each sample in the combined data files and whether that sample was removed due to quality issues.  2nd file is the combined raw counts (HTseq-Count) for each sample we sequenced and set up so the rows are the genes and columns are the sample names.  3rd file is a file converting all gene counts to counts per million mapped reads (CPM). This file was used for z-scoring and removing genes with less than 2 CPM.  4th File is combined data normalized using DESeq2 and regularized log transformed, this file removed 5 samples (ab KC technicals, Brain samples and one G386 sample).  All genes for each cell type with <2CPM in half samples were replaced with zeros.


title: sample 65_RNA_BM_NKp_rpt1

source_name: NK precursor cells

value: NK precursor cells


title: 48 hr Hi-C


title: sample 64_RNA_BM_ILC2p_rpt2

source_name: ILC2 precursor  cells

value: ILC2 precursor  cells


title: 40 hr Hi-C