title: PF061-34

city: New Delhi

first: Shashank

last: Jatav

state: Delhi

address: 212, C/o Brijendar Pawar, Near Dalip Singh Chowk, Shahpur Jat

country: India

institute: Elucidata

description:
Matched RNAseq, untargeted metabolomics, and O-link (from supernatants)
processed data file:
Experiment10_DrugTreatment.csv
Processed data file column headers with technical replicate IDs:
10A03_S11_L001_R1_001.fastq.gz
10A03_S11_L002_R1_001.fastq.gz
10A03_S11_L003_R1_001.fastq.gz
10A03_S11_L004_R1_001.fastq.gz

data_processing:
Transcriptional data was aligned using STAR (https://github.com/alexdobin/STAR) aligner.
Gene counts from resulting bam files were generated using featurecounts using GTF file from UCSC (http://bioinf.wehi.edu.au/featureCounts/).
Genome_build: hg38
Supplementary_files_format_and_content: comma separated text files include raw counts for each Sample, the first column contains the geneid, the raw counts start from column 7, the format followed is same featurecounts' output

source_name: Human T cells

growth_protocol: Blood was collected from healthy human patients in accordance with IRB standards. CD4+ T cells were purified using RosetteSep isolation kit (StemCell) as per manufacturer’s protocol. Cells were cultured in RPMI supplemented with 10% heat inactivated FBS, HEPES, penicillin/streptomycin, non-essential amino acids, glutamax, and sodium pyruvate. Cells were initially activated for 72 hours on plate-bound CD3 (200 ng/mL; OKT3; BioXCell) and CD28 (200 ng/mL; 9.3; BioXCell) on goat-anti-mouse (10 µg/mL; Jackson Immuno Research Labs) pre-coated high- binding plates (Corning Costar). After 72 hours, cells were removed from plate activation and were expanded until Day 8-12, maintained at ~1X106 cells/mL by supplementing with fresh media as required. Cells were then washed with PBS and either rested or re-activated at 0.5-1x106 cells/mL in fresh media with plate-bound CD3/CD28 (100 ng/mL each) or with soluble CD3/CD28 Immunocult (1:100 dilution; StemCell).

extract_protocol:
5x10^6 cells were collected at the indicated time-points, lysed with RNeasy (Qiagen) kit, and purified according to manufacturer?s protocol. RNA quantity was assessed using the QIAxpert and RNA quality was assessed using the Agilent 4200 TapeStation.
Each sample is represented by 4 technical replicates. Technical replicates were produced by sequencing the same library in 4 separate flowcell lanes.
RNA library preparation was performed using Illumina Stranded mRNA library preparation kit and sequencing was performed using NextSeq High Output Run with single end read 1x75bp.

value: Primary human CD4+ T cells

tag: re-activation

value: Plate bound CD3/CD28 (100ng)

tag: reactivation hours

tag: knockdown

tag: drug

tag: donor

tag: plate # (submitted to seqmatic)

tag: seqmatic run

tag: date of seqmatic run

tag: sample name (randomized)

tag: experiment number


title: lc/fas_6dpi_R1

status: Public on Apr 16 2019

type: SRA

city: Athens

first: Esther

last: van der Knaap

state: GA

address: 111 Riverbend Rd

department: Horticulture

country: USA

institute: University of Georgia

library_source: transcriptomic

data_processing:
Reads were filtered using fqtrim program with QC score< 20 as well as poly-A tail contaminations
Clean reads mapped to ITAG2.4 Released Tomato Genome through Rsubread 3.4
The significance of differentially expressed genes (DEGs) was determined by linear factorial modeling in DEseq2, of which likelihood ratio test was applied.
Genome_build: ITAG2.4 Released Tomato Genome
Supplementary_files_format_and_content: csv text files include read counts per gene for each sample

molecule: total RNA

organism: Solanum pimpinellifolium

source_name: 6dpi floral buds

growth_protocol: Seeds were sown small pots and allowed to germinate under natural light supplemented with artificial light (16/8 hr light/dark cycle) in the greenhouse in Columbus, OH, USA, 2016. Approximately 300 first and second inflorescences with only 3-4 visible floral buds were collected from 5 to 7-week old plants that were sown over a six-week window.

extract_protocol:
During the collection, all inflorescences were immediately immersed in ice-cold RNAlater (QIAGEN) solution at five times the volume of the sample in order to prevent RNA degradation. After sample collection, vacuum infiltration was applied until tissues sunk to the bottom of RNAlater solution. The tissues were then stored in RNAlater at -80℃.  For the dissection, meristems and buds of different developmental stages were isolated by forceps under a dissection microscope and immediately put into a 1.5 ml eppendorf tube in 1 ml of fresh RNAlater that was kept on ice. The samples were stored at -80 ℃ prior to the RNA extraction. RNA extraction was conducted using Trizol® (Invitrogen Inc. USA) following manufacture’s recommendation.
3'Tag RNA-seq libraries of approximately 300 bp fragments were prepared following the 3’-Tagseq protocol of Meyer et al., (2011)

tag: tissue

value: 6dpi floral buds

tag: genotype

value: lc and fas double mutants in LA1589 background

tag: cultivar


title: genomic DNA from cord blood 16

type: genomic

city: Chicago

first: Yinan

last: Zheng

state: Illinois

address: 680 N Lake Shore Drive, Suite 1400

department: Department of Preventive Medicine

institute: Northwestern University

description: cord blood sample

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450K Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using Illumina iScan using standard recommended Illumina scanner setting

data_processing: Raw Illumina IDAT data were imported and preprocessed using the R package methylumi

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: cord blood 16

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted and purified from neonatal cord blood using an Autopure LS Automated DNA Purification System with Autopure reagents (Autogen, Inc., Holliston, MA).

tag: gender

value: female

tag: leptin

tag: birth weight

tag: fat mass

tag: percent fat


title: PF061-33

description:
Matched RNAseq, untargeted metabolomics, and O-link (from supernatants)
processed data file:
Experiment10_DrugTreatment.csv
Processed data file column headers with technical replicate IDs:
10A02_S10_L001_R1_001.fastq.gz
10A02_S10_L002_R1_001.fastq.gz
10A02_S10_L003_R1_001.fastq.gz
10A02_S10_L004_R1_001.fastq.gz

molecule: polyA RNA

tag: cell type

tag: re-activation

tag: reactivation hours


title: genomic DNA from cord blood 6

description: cord blood sample

source_name: cord blood 6

value: male


title: lc/fas_4dip_R1

source_name: 4dpi floral buds

value: 4dpi floral buds


title: genomic DNA from cord blood 12

description: cord blood sample

source_name: cord blood 12


title: PF061-32

description:
Matched RNAseq, untargeted metabolomics, and O-link (from supernatants)
processed data file:
Experiment10_DrugTreatment.csv
Processed data file column headers with technical replicate IDs:
10D01_S9_L001_R1_001.fastq.gz
10D01_S9_L002_R1_001.fastq.gz
10D01_S9_L003_R1_001.fastq.gz
10D01_S9_L004_R1_001.fastq.gz

tag: knockdown

tag: drug

value: CsA

tag: donor


title: genomic DNA from cord blood 10

description: cord blood sample

source_name: cord blood 10


title: lc/fas_F&IM_R1

source_name: floral and inflorescence meristems (F&IM)


title: genomic DNA from cord blood 2

description: cord blood sample

source_name: cord blood 2


title: lc/fas_4dip_R2


title: lc/fas_2dpi_R1

source_name: 2dpi floral buds

value: 2dpi floral buds


title: ID132 GMP

city: Zurich

first: Slavica

last: Dimitrieva Janeva

state: Zurich

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich

country: Switzerland

institute: ETH Zürich / University of Zurich

data_processing:
Generation of fastq files was done using bcl2fastq software version 2.19.0
Reads were trimmed with Trimmomatic version 0.33 (4 and 3 bases were hard-trimmed from the start and end respectively; adapter trimming was done at the end).
Trimmed reads were aligned to the Ensembl GRCh38 human reference genome and transcriptome with STAR version 2.5.1b.
Read quantification was done using the R/Bioconductor package Rsubread version 1.26.0.
Genome_build: Ensembl Human reference GRCh38 release 86
Supplementary_files_format_and_content: tab-delimited text file showing raw read counts for each sample (columns) and each gene (rows)

source_name: Blood

growth_protocol: Fresh human hematopoietic stem/progenitor cells were obtained from 5 healthy donors aged between 28 and 57 years old (average: 39.8); 4 males, 1 female; with informed consent and approval of the local ethics committee (KEK-ZH-Nr: 2015-0564, Clinical Hematology, University Hospital Zurich, Zurich Switzerland).

extract_protocol:
After mobilization with granulocyte-colony stimulating factor (G-CSF), stem-cell enriched mononuclear leukocytes were obtained via plasmapheresis from peripheral blood of donors for clinical stem cell transplantation (Clinical Hematology, University Hospital Zurich, Zurich Switzerland). Left-over material after clinical transplantation was enrichted for CD34+ stem/progenitor cells using immunomagnetic beads according to manufacturer instructions (CD34 MicroBead Kit; Miltenyi Biotec). Fluorescence-activated cell sorting and antibodies specific for CD2, CD3, CD4, CD7, CD8, CD14, CD19, CD56, CD10, CD11b, CD20, CD235a, CD34, CD38, CD123, CD45RA were used to isolate the various cell types (HSC, CMP, GMP, MEP). 10'000 cells of each subpopulations were sorted into RNeasy lysis buffer containing beta-mercaptoethanol. Total RNA was purified according to manufacturer instructions using the RNeasy Plus Micro Kit (Qiagen). The samples were of high enough quality for a poly-A tail based approach for RNA sequencing. RNA sequencing was performed as described in Picelli S. et al. Nature Protocols 2014 using the Illumina HiSeq 4000 sequencing platform.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Stem-cell enriched mononuclear leukocytes were mobilized from the bone marrow using granulocyte-colony stimulating factor (G-CSF) (twice daily administrations over 4 days).

value: granulocyte-macrophage progenitors

tag: donor age

value: 28 years

tag: donor sex


title: fas_6dpi_R3

value: fas mutant in LA1589 background


title: genomic DNA from cord blood 1

description: cord blood sample

source_name: cord blood 1


title: ID132 CMP

value: common myeloid progenitors


title: fas_4dip_R3


title: genomic DNA from cord blood 9

description: cord blood sample

source_name: cord blood 9


title: lc/fas_SYM_R1

source_name: sympodial shoot apical meristem (SYM)

value: sympodial shoot apical meristem (SYM)


title: PF061-23

description:
Matched RNAseq, untargeted metabolomics, and O-link (from supernatants)
processed data file:
Experiment10_DrugTreatment.csv
Processed data file column headers with technical replicate IDs:
10F02_S12_L001_R1_001.fastq.gz
10F02_S12_L002_R1_001.fastq.gz
10F02_S12_L003_R1_001.fastq.gz
10F02_S12_L004_R1_001.fastq.gz

value: CsA+Rapa

tag: plate # (submitted to seqmatic)

tag: seqmatic run

tag: date of seqmatic run

tag: sample name (randomized)

tag: experiment number


title: fas_2dpi_R3

tag: tissue

tag: genotype

tag: cultivar


title: genomic DNA from cord blood 7

description: cord blood sample

source_name: cord blood 7

tag: gender

tag: leptin

tag: birth weight

tag: fat mass

tag: percent fat


title: WT-Fed-Rep4-RNA-seq

first: Grant

middle: D.

last: Barish

state: IL

address: 303 E Superior Street

department: Medicine

description: male wild type ad lib fed liver total RNA

data_processing:
Alignment:  Sequenced reads were aligned to the mm10 reference mouse genome using STAR
Quantification of gene expression: gene expression at exons was quantified as integer counts using HOMER
Differenial expression analysis: differentially expressed exonic RNAs were identified using DESeq2 (FDR-adjusted p-value <0.05 and |LFC| > 1).
Genome_build: mm10
Supplementary_files_format_and_content: Excel file with differential expression and individual replicate normalized rlog values

organism: Mus musculus

source_name: liver

extract_protocol:
Total RNA was isolated from mouse liver tissue using RLT Buffer (Qiagen) and RNeasy columns (Qiagen).  RNA quality was assessed using a Bioanalyzer (Agilent).
Stranded RNA-seq Kit with RiboErase (HMR) (Kapa)

tag: strain

value: liver

value: Bcl6 fl/fl


title: fas_F&IM_R3

value: floral and inflorescence meristems (F&IM)


title: PF061-22

description:
Matched RNAseq, untargeted metabolomics, and O-link (from supernatants)
processed data file:
Experiment10_DrugTreatment.csv
Processed data file column headers with technical replicate IDs:
10D03_S11_L001_R1_001.fastq.gz
10D03_S11_L002_R1_001.fastq.gz
10D03_S11_L003_R1_001.fastq.gz
10D03_S11_L004_R1_001.fastq.gz

tag: cell type

value: Primary human CD4+ T cells

tag: re-activation

value: Plate bound CD3/CD28 (100ng)

tag: reactivation hours

tag: knockdown

tag: drug

tag: donor


title: genomic DNA from cord blood 8

description: cord blood sample

source_name: cord blood 8


title: fas_SYM_R3


title: PF061-21

description:
Matched RNAseq, untargeted metabolomics, and O-link (from supernatants)
processed data file:
Experiment10_DrugTreatment.csv
Processed data file column headers with technical replicate IDs:
10E01_S10_L001_R1_001.fastq.gz
10E01_S10_L002_R1_001.fastq.gz
10E01_S10_L003_R1_001.fastq.gz
10E01_S10_L004_R1_001.fastq.gz

source_name: Human T cells

value: Rapa

tag: plate # (submitted to seqmatic)

tag: seqmatic run

tag: date of seqmatic run

tag: sample name (randomized)


title: ID185 MEP

value: megakaryocyte-erythrocyte progenitors

tag: donor age

value: 51 years

tag: donor sex


title: fas_2dpi_R2

tag: tissue

tag: genotype

tag: cultivar


title: PF061-20

description:
Matched RNAseq, untargeted metabolomics, and O-link (from supernatants)
processed data file:
Experiment10_DrugTreatment.csv
Processed data file column headers with technical replicate IDs:
10F03_S9_L001_R1_001.fastq.gz
10F03_S9_L002_R1_001.fastq.gz
10F03_S9_L003_R1_001.fastq.gz
10F03_S9_L004_R1_001.fastq.gz

tag: experiment number


title: fas_F&IM_R2


title: PF061-19

description:
Matched RNAseq, untargeted metabolomics, and O-link (from supernatants)
processed data file:
Experiment10_DrugTreatment.csv
Processed data file column headers with technical replicate IDs:
10B03_S8_L001_R1_001.fastq.gz
10B03_S8_L002_R1_001.fastq.gz
10B03_S8_L003_R1_001.fastq.gz
10B03_S8_L004_R1_001.fastq.gz

value: DMSO


title: PF061-30

description:
Matched RNAseq, untargeted metabolomics, and O-link (from supernatants)
processed data file:
Experiment10_DrugTreatment.csv
Processed data file column headers with technical replicate IDs:
10D02_S7_L001_R1_001.fastq.gz
10D02_S7_L002_R1_001.fastq.gz
10D02_S7_L003_R1_001.fastq.gz
10D02_S7_L004_R1_001.fastq.gz

value: CsA


title: ID185 CMP

value: male


title: PF061-17

description:
Matched RNAseq, untargeted metabolomics, and O-link (from supernatants)
processed data file:
Experiment10_DrugTreatment.csv
Processed data file column headers with technical replicate IDs:
10B01_S6_L001_R1_001.fastq.gz
10B01_S6_L002_R1_001.fastq.gz
10B01_S6_L003_R1_001.fastq.gz
10B01_S6_L004_R1_001.fastq.gz


title: ID234 MEP

value: 34 years


title: fas_2dpi_R1

value: 2dpi floral buds


title: PF061-14

description:
Matched RNAseq, untargeted metabolomics, and O-link (from supernatants)
processed data file:
Experiment10_DrugTreatment.csv
Processed data file column headers with technical replicate IDs:
10A01_S3_L001_R1_001.fastq.gz
10A01_S3_L002_R1_001.fastq.gz
10A01_S3_L003_R1_001.fastq.gz
10A01_S3_L004_R1_001.fastq.gz


title: fas_SYM_R1

value: fas mutant in LA1589 background


title: fas_6dpi_R2

source_name: 6dpi floral buds

value: 6dpi floral buds


title: ID234 GMP

value: granulocyte-macrophage progenitors


title: fas_6dpi_R1


title: fas_F&IM_R1


title: ID185 GMP


title: lc_4dip_R3

value: 4dpi floral buds

value: lc mutant in LA1589 background


title: PF061-10

description:
Matched RNAseq, untargeted metabolomics, and O-link (from supernatants)
processed data file:
Experiment10_DrugTreatment.csv
Processed data file column headers with technical replicate IDs:
10B02_S11_L001_R1_001.fastq.gz
10B02_S11_L002_R1_001.fastq.gz
10B02_S11_L003_R1_001.fastq.gz
10B02_S11_L004_R1_001.fastq.gz


title: PF061-08

description:
Matched RNAseq, untargeted metabolomics, and O-link (from supernatants)
processed data file:
Experiment10_DrugTreatment.csv
Processed data file column headers with technical replicate IDs:
10E03_S9_L001_R1_001.fastq.gz
10E03_S9_L002_R1_001.fastq.gz
10E03_S9_L003_R1_001.fastq.gz
10E03_S9_L004_R1_001.fastq.gz


title: lc_SYM_R3

value: sympodial shoot apical meristem (SYM)


title: PF061-02

description:
Matched RNAseq, untargeted metabolomics, and O-link (from supernatants)
processed data file:
Experiment10_DrugTreatment.csv
Processed data file column headers with technical replicate IDs:
10E02_S3_L001_R1_001.fastq.gz
10E02_S3_L002_R1_001.fastq.gz
10E02_S3_L003_R1_001.fastq.gz
10E02_S3_L004_R1_001.fastq.gz


title: fas_4dip_R2


title: lc_6dpi_R2


title: fas_SYM_R2


title: lc_4dip_R2


title: fas_4dip_R1


title: lc_2dpi_R2


title: lc_6dpi_R3


title: PF061-01

description:
Matched RNAseq, untargeted metabolomics, and O-link (from supernatants)
processed data file:
Experiment10_DrugTreatment.csv
Processed data file column headers with technical replicate IDs:
10F01_S2_L001_R1_001.fastq.gz
10F01_S2_L002_R1_001.fastq.gz
10F01_S2_L003_R1_001.fastq.gz
10F01_S2_L004_R1_001.fastq.gz

value: CsA+Rapa


title: PF061-35

description:
Matched RNAseq, untargeted metabolomics, and O-link (from supernatants)
processed data file:
Experiment9_CRISPR_Counts.csv
Processed data file column headers with technical replicate IDs:
9C03_S12_L001_R1_001.fastq.gz
9C03_S12_L002_R1_001.fastq.gz
9C03_S12_L003_R1_001.fastq.gz
9C03_S12_L004_R1_001.fastq.gz

value: Primary human CD4+ T cells

value: crmTOR


title: ID236 GMP

value: 57 years

value: female


title: ID234 CMP

value: common myeloid progenitors


title: lc_SYM_R2


title: lc_4dip_R1


title: lc_2dpi_R1


title: ID236 HSC

value: hematopoietic stem cells


title: lc_6dpi_R1


title: lc_F&IM_R1

value: floral and inflorescence meristems (F&IM)


title: PF061-28

description:
Matched RNAseq, untargeted metabolomics, and O-link (from supernatants)
processed data file:
Experiment9_CRISPR_Counts.csv
Processed data file column headers with technical replicate IDs:
9C06_S5_L001_R1_001.fastq.gz
9C06_S5_L002_R1_001.fastq.gz
9C06_S5_L003_R1_001.fastq.gz
9C06_S5_L004_R1_001.fastq.gz

value: Plate bound CD3/CD28 (100ng)


title: lc_SYM_R1


title: ID235 MEP

value: megakaryocyte-erythrocyte progenitors

value: 29 years

value: male


title: PF061-31

description:
Matched RNAseq, untargeted metabolomics, and O-link (from supernatants)
processed data file:
Experiment9_CRISPR_Counts.csv
Processed data file column headers with technical replicate IDs:
9A04_S8_L001_R1_001.fastq.gz
9A04_S8_L002_R1_001.fastq.gz
9A04_S8_L003_R1_001.fastq.gz
9A04_S8_L004_R1_001.fastq.gz

value: crNT CTL


title: ID235 GMP

value: granulocyte-macrophage progenitors


title: PF061-27

description:
Matched RNAseq, untargeted metabolomics, and O-link (from supernatants)
processed data file:
Experiment9_CRISPR_Counts.csv
Processed data file column headers with technical replicate IDs:
9A02_S4_L001_R1_001.fastq.gz
9A02_S4_L002_R1_001.fastq.gz
9A02_S4_L003_R1_001.fastq.gz
9A02_S4_L004_R1_001.fastq.gz


title: genomic DNA from cord blood 3

description: cord blood sample

source_name: cord blood 3

tag: gender

tag: leptin

tag: birth weight

tag: fat mass

tag: percent fat


title: WT_6dpi_R3

value: 6dpi floral buds

value: Wild type (LA1589)


title: WT_4dip_R3

value: 4dpi floral buds


title: PF061-26

description:
Matched RNAseq, untargeted metabolomics, and O-link (from supernatants)
processed data file:
Experiment9_CRISPR_Counts.csv
Processed data file column headers with technical replicate IDs:
9A01_S3_L001_R1_001.fastq.gz
9A01_S3_L002_R1_001.fastq.gz
9A01_S3_L003_R1_001.fastq.gz
9A01_S3_L004_R1_001.fastq.gz

tag: cell type

tag: re-activation

tag: reactivation hours

tag: knockdown

tag: drug


title: WT_2dpi_R3

value: 2dpi floral buds


title: ID235 CMP


title: lc_F&IM_R2

value: lc mutant in LA1589 background


title: ID236 CMP


title: WT_F&IM_R3


title: ID132 MEP

value: 28 years


title: WT_SYM_R3

value: sympodial shoot apical meristem (SYM)


title: PF061-25

description:
Matched RNAseq, untargeted metabolomics, and O-link (from supernatants)
processed data file:
Experiment9_CRISPR_Counts.csv
Processed data file column headers with technical replicate IDs:
9B04_S2_L001_R1_001.fastq.gz
9B04_S2_L002_R1_001.fastq.gz
9B04_S2_L003_R1_001.fastq.gz
9B04_S2_L004_R1_001.fastq.gz

value: Primary human CD4+ T cells

tag: donor

tag: plate # (submitted to seqmatic)

tag: seqmatic run

tag: date of seqmatic run

tag: sample name (randomized)


title: WT_6dpi_R2

tag: tissue

tag: genotype

tag: cultivar


title: PF061-24

description:
Matched RNAseq, untargeted metabolomics, and O-link (from supernatants)
processed data file:
Experiment9_CRISPR_Counts.csv
Processed data file column headers with technical replicate IDs:
9C01_S13_L001_R1_001.fastq.gz
9C01_S13_L002_R1_001.fastq.gz
9C01_S13_L003_R1_001.fastq.gz
9C01_S13_L004_R1_001.fastq.gz

value: crmTOR

tag: experiment number


title: WT_4dip_R2


title: PF061-18

description:
Matched RNAseq, untargeted metabolomics, and O-link (from supernatants)
processed data file:
Experiment9_CRISPR_Counts.csv
Processed data file column headers with technical replicate IDs:
9B06_S7_L001_R1_001.fastq.gz
9B06_S7_L002_R1_001.fastq.gz
9B06_S7_L003_R1_001.fastq.gz
9B06_S7_L004_R1_001.fastq.gz


title: WT_F&IM_R2


title: WT_SYM_R2


title: WT_6dpi_R1


title: WT_4dip_R1


title: PF061-16

description:
Matched RNAseq, untargeted metabolomics, and O-link (from supernatants)
processed data file:
Experiment9_CRISPR_Counts.csv
Processed data file column headers with technical replicate IDs:
9A03_S5_L001_R1_001.fastq.gz
9A03_S5_L002_R1_001.fastq.gz
9A03_S5_L003_R1_001.fastq.gz
9A03_S5_L004_R1_001.fastq.gz


title: C_3

city: Changchun

first: zi

last: wang

address: Xincheng Street No.#2888

country: China

institute: Jilin Agricultural University

description: miRNA-seq; control.txt

data_processing:
Subsequently, unique sequences with length in 18~26 nucleotide were mapped to bovine in miRBase 21.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to bovine mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of bovine hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3pderived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 21.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The unmapped sequences were BLASTed against the specific genomes, and the hairpin RNA structures containing sequences were predicated from the flank 80 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤20). (6) number of nucleotides in one bulge in mature region (≤8) (7) number of biased errors in one bulge in mature region (≤4) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤7) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Genome_build: miRBase 21.0
Supplementary_files_format_and_content: text files, normalize expressions of miRNAs

organism: Bos taurus

source_name: Peripheral Blood

growth_protocol: The cells were grown in 24-well dishes at a density of 1 × 106 cells per well in RPMI 1640 medium supplemented with 10% FCS, 1% non-essential amino acids and gentamicin.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
Approximately 5 µg of total RNA were used to prepare six small RNA libraries (MAP_1, MAP_2, MAP_3, C_1, C_2, C_3) according to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA). And then the libraries were sequenced by Illumina Hiseq 2500 at the LC-BIO following the vendor’s recommended protocol. Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.

value: monocyte derived macrophages

value: Peripheral Blood


title: C_1

description: miRNA-seq; control.txt


title: WT_F&IM_R1

value: floral and inflorescence meristems (F&IM)


title: WT_2dpi_R1


title: WT_2dpi_R2


title: MAP_3

description: miRNA-seq; MAP.txt


title: PF061-15

description:
Matched RNAseq, untargeted metabolomics, and O-link (from supernatants)
processed data file:
Experiment9_CRISPR_Counts.csv
Processed data file column headers with technical replicate IDs:
9B03_S4_L001_R1_001.fastq.gz
9B03_S4_L002_R1_001.fastq.gz
9B03_S4_L003_R1_001.fastq.gz
9B03_S4_L004_R1_001.fastq.gz

value: Plate bound CD3/CD28 (100ng)


title: PF061-13

description:
Matched RNAseq, untargeted metabolomics, and O-link (from supernatants)
processed data file:
Experiment9_CRISPR_Counts.csv
Processed data file column headers with technical replicate IDs:
9B02_S2_L001_R1_001.fastq.gz
9B02_S2_L002_R1_001.fastq.gz
9B02_S2_L003_R1_001.fastq.gz
9B02_S2_L004_R1_001.fastq.gz


title: WT_SYM_R1


title: MAP_2

description: miRNA-seq; MAP.txt


title: HiChIP_Pax3_6day_shLdb1_rep2

city: Minneapolis

first: Alessandro

last: Magli

state: MN

address: 2231 6th St SE

institute: University of Minnesota

description:
processed data file:  6day_shLdb1.allValidPairs.hic
Pax3_HiChIP_6day_dox_iPax3_shLdb1_02

library_source: genomic

data_processing:
library strategy: HiChIP
ChIP-seq analysis. Each sample’s reads were aligned to the mouse (mm10) genome using Bowtie2 followed by removal of PCR duplicates using Samtools. Peak calling was performed using MACS with the following parameters: --bw 300 -p 1e-3. Similar results were obtained by performing peak calling using QESEQ with the following parameters: -s 100 -c 15 -p 0.01. Peak analysis was performed using bedtools. For triplicate experiments, peaks called in 2 of the 3 replicates were further considered. For duplicate experiments, common peaks between the 2 replicates were further considered. In addition, the peak lists were filtered (intersect –v option) for sites overlapping to peaks detected in the uninduced control ChIP-seq and in the mouse ChIP-seq black-list. Density maps were generated with SeqMiner using the enrichment file enr.sgr produced by QESEQ. Bigwig files for visualization on IGV were generated by converting the wig files obtained from MACS  using the Kent tool Wig-to-BigWig.
HiChIP analysis. Paired-end samples were processed using the HiC-Pro pipeline. Contact matrices were generated for 10Kb bin pairs using default parameters in HiC-Pro to map the reads to the mm10 genome, remove duplicate reads, assign reads to Mbol restriction fragments, and acquire valid interactions. Statistically significant bin pairs and number of contacts were determined using the Fit-Hi-C contact caller using default settings and interaction distance less than 2 Mb.   Generation of Contact Matrix Heat Maps. Raw contact matrices from the HiC-Pro pipeline were normalized by read depth. The resulting normalized matrices were used to generate heat maps. The matrix acquired for the condition with no addition of doxycycline (non-induced) was subtracted from the matrices for 1-day and 6-day in doxycycline conditions. This enhanced the visualization of the heat maps for contacts specific to the manipulated condition. Similarly, the matrix for the Ldb1 knockdown sample was subtracted from the shSCR matrix to emphasize loss of contacts with the knockdown of Ldb1. R Bioconductor package “HiTC” was used to assist the generation of the contact heat maps.
Genome_build: mm10
Supplementary_files_format_and_content: ChIP-seq: processed files represent author-curated list of peaks obtained by removing Encode blacklist and peaks detected in non-induced samples or input
Supplementary_files_format_and_content: HiChIP: processed files represent .hic matrix

growth_protocol: Mouse ES cell differentiation was achieved by diluting 40000 cells/ml in EB differentiation medium and incubation in an orbital shaker at 80 RPM. EB differentiation medium: IMDM supplemented with 15% FBS , 1% Penicillin/Streptomycin, 2mM Glutamax, 50 μg/ml Ascorbic acid, 4.5 mM Monothioglycerol. Trangene induction was achieved by adding doxycycline (Sigma-Aldrich) to day 3 EBs cultures (final concentration 1µg/ml), and then maintained throughout the differentiation protocol by replacing the media (including dox) every two days. At day 5, EBs were disgregated and single cells were incubated for 20 minutes with PDGFRα-PE and FLK1-APC conjugated antibodies. PDGFRα+FLK1- cells were sorted using FACSAriaII (BD biosciences) and replated on gelatin coated dishes using serum- or serum-free EB differentiation media supplemented with 1µg/ml doxycycline and 10ng/ml mouse basic-FGF.

extract_protocol:
ChIP-seq: D4 EBs (1-day induced and control Pax3 mouse cells) were trypsin-treated at 37°C for 1 minute with gentle shacking and reaction was inhibited by adding 10%FBS/PBS. 1-day induced Pax3 NIH3T3 cells and 6-day induced Pax3 mouse cells growing in monolayer were harvested by incubation with trypsin for 1-2 minutes. Single cells were washed once with PBS, resuspended in 10%FBS/PBS and supplemented with formaldehyde (final concentration 1%) for crosslinking of protein-DNA complexes (10 minutes at RT) followed by quenching with glycine and staining with PDGFRα-PE antibody. PDGFRα+ cells were sorted using FACSAriaII, snap-frozen in liquid nitrogen and stored at -80°C if not processed immediately. Cell pellets were incubated in lysis buffer LB1 supplemented with protease inhibitors (50mM HEPES KOH pH7.5, 140mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP40, 0.25% Triton X-100 + Complete-mini - Roche) for 10 minutes at +4°C followed by incubation in buffer LB2 supplemented with protease inhibitors (10mM TRIS HCl pH 8, 200mM NaCl, 1mM EDTA, 0.5mM EGTA + Complete-mini - Roche) for 10 minutes at +4°C. Cell pellet was then resuspended in LB3 supplemented with protease inhibitors (10mM TRIS HCl pH 8, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Sodium Deoxycholate, 0.5% N-lauroylsarcosine + Complete-mini - Roche) and then sonicated. Cells were sonicated with a Branson sonicator at 18% power for 1 minute with intervals of 10 sec ON-10 sec OFF to achieve an average chromatin size of 300bp. After shearing, samples were centrifuged for 10 minutes at 16000g and snap frozen in liquid nitrogen if not processed immediately. 10-15µg (histone mark) or 25-40µg (Ldb1, Smc1, Ctcf) of chromatin were diluted to 250µl and 500µl, respectivley, and then precleared for 4h at 4°C with 20µl of BSA-blocked Protein A (or Protein G)-conjugated sepharose beads (GE healthcare). Samples were supplemented with 1/10 volume of 10% Triton X-100 and incubated overnight with the indicated antibody. Immune complexes were recovered by incubation with 20µl of BSA-blocked Protein G-conjugated sepharose beads for 4h at 4°C and then washed 5 times with RIPA wash buffer (50mM HEPES KOH pH7.5, 500mM LiCl, 1mM EDTA, 1% NP40, 0.25% Triton X-100, 0.7% Sodium Deoxycholate) and one time with TEN buffer (10mM TRIS HCl pH 8, 1mM EDTA, 50mM NaCl). Immunoprecipitated chromatin was recovered by incubating beads with 200µl of Elution buffer (50mM TRIS HCl pH 8, 10mM EDTA, 1% Sodium Dodecyl Sulfate) for 20 minutes at 65°C. Chromatin from IP and Input (equivalent to 1% of starting material) was reverse crosslinked overnight at 65°C, then diluted 1:1 with TE (10mM TRIS HCl pH 8, 1mM EDTA) supplemented with 4µl of RNaseA 20mg/ml and incubated for 2 hours at 37°C followed by Proteinase K treatment (4µl of 20mg/ml stock for each sample) for 30 minutes at 55°C. DNA was purified by Phenol-chloroform-isoamyl alcol extraction (twice) followed by chloroform extraction, then supplemented with 1/10 of volume of 3M Sodium Acetate pH 5 and 1.5µl of Glycogen and precipitated with 2 volumes of 100% Ethanol at -80°C for >1 hour. Followed 30 minutes centrifuge at 16000g, pellet were washed with 75% ethanol, air dried and dissolved in 45µl H2O.
ChIP-seq libraries were generated following a gel-free protocol using AMPure XP beads (Beckman Coulter) for all the purification and size selection steps. 10ng or less of DNA were end repaired using End-it DNA end repair (Epicentre), then A-tailed using Klenow Fragment (3'→5' exo-  NEB) followed by adapter-barcode ligation using T4 DNA ligase (Enzymatics). Illumina compatible adapter-barcodes were purchased from BIOO scientific. After ligation, DNAs were negatively size selected using 0.5x Ampure XP beads and unbound DNAs were positively size selected by adding 0.4x Ampure XP beads (this step allows for retention of DNA fragments ranging 200-500bp). Libraries were amplified using Phusion High Fidelity PCR master mix 2x (NEB) with a 16 cycles program. Libraries from Ldb1, histone marks in 6-day induced cells and H3K4me1 in dTAD and dTAD-Ldb1 immunoprecipitations were generated using the NEBNext DNA library prep kit (NEB).
HiChIP libraries. Long range interactions involving Pax3 binding sites were analyzed following the detailed protocol described by the Chang group. Briefly, non-induced, 1-day and 6-day Pax3-induced cells (respectively mesoderm, paraxial mesoderm precursors and myogenic progenitors) and 6-day+shSCR and 6-day+shLdb1 cells were harvested using trypsin for 1-2 min followed by inactivation with PBS/10%FBS, centrifuged 5 min at 400g, washed with PBS twice and then counted. 13 million cells, diluted to 1million/ml in PBS, were crosslinked for 15 min using methanol-free formaldehyde (Pierce – Thermoscientific). In situ contact generation was performed by digesting chromatin with MboI (NEB) followed by blunting with dNTP mix containing biotin-dATP (Thermo Fisher, 19524016) and ligation using T4 DNA ligase (NEB). After centrifugation, nuclei were resuspended in 880μL in Nuclear Lysis Buffer (50 mM Tris-HCl pH 7.5, 10 mM EDTA, 1% SDS, Complete Protease inhibitor - Roche), transferred in a Millitube and sonicated using a Covaris S220 (parameters: fill level = 10, duty cycle = 5, PIP = 140, cycles/burst = 200, time = 4 min). Chromatin was cleared by centrifugation, diluted 1:2 in ChIP Dilution Buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl pH 7.5, 167 mM NaCl), precleared for 4h at +4°C with 75µl of Protein G-conjugated magnetic beads and then incubated with 30µg of anti-Pax3 and anti-Ldb1 antibodies overnight at +4°C. Immune complexes were recovered by incubation with 60µl of BSA-blocked Protein G-conjugated sepharose beads for 5h at +4°C, then washed 5 times with RIPA wash buffer (50mM HEPES KOH pH7.5, 500mM LiCl, 1mM EDTA, 1% NP40, 0.25% Triton X-100, 0.7% Sodium Deoxycholate) and one time with TEN buffer (10mM TRIS HCl pH 8, 1mM EDTA, 50mM NaCl). Due to the sample volume during the Pax3 IP, Protein-G:Pax3-chromatin bound beads were splitted in two 1.5ml tubes during the previous procedure. Immunoprecipitated chromatin was recovered by incubating beads with 200µl/tube of Elution buffer (50mM TRIS HCl pH 8, 10mM EDTA, 1% Sodium Dodecyl Sulfate) for 30 minutes at 65°C. ChIP samples and Input (equivalent to 1% of starting material) were reverse crosslinked overnight at 65°C, then diluted 1:1 with TE (10mM TRIS HCl pH 8, 1mM EDTA) supplemented with 4µl of RNaseA 20mg/ml and incubated for 2 hours at 37°C followed by Proteinase K treatment (4µl of 20mg/ml stock for each sample) for 30 minutes at 55°C. DNA was purified by Phenol-chloroform-isoamyl alcol extraction (twice) followed by chloroform extraction, then supplemented with 1/10 of volume of 3M Sodium Acetate pH 5 and 1.5µl of Glycogen and precipitated with 2 volumes of 100% Ethanol at -80°C for >1 hour. Following 30 minutes centrifuge at 16000g, pellets were washed with 75% ethanol, air dried and the combined DNA pellet were dissolved in 40µl H2O. Before proceeding with the biotin capture and transposase mediated library generation, ChIP samples were analyzed by qPCR to ensure enrichment at Pax3 sites vs control region. Samples were quantified using Pico-green (Invitrogen), resuspended in binding buffer and then incubated with 20µl of Streptavidin T1-conjugated magnetic beads (Invitrogen). After washing, DNA-bound streptavidin beads were incubated with 1.5µl of Tn5 transposase in a final volume of 50µl for 10 minutes at 55°C. This amount of transposase was selected based on the picogreen results of the ChIP, which yielded 25ng of DNA. Following quenching and washing, transposed DNA was incubated 5 minutes at 65°C with activated NEBNext UltraII QS Taq (+Illumina adaptor/barcodes) to allow primer extension and then amplified for 5 cycles (15 seconds 98°C followed by 1.5 minutes at 65°C). Additional cycles for library amplification were determined by qPCR using T5-T7 primer

value: differentiating mES cells

tag: time

value: day4 of differentiation

tag: purification

value: PDGFRα+FLK1- sorted

tag: doxycycline-treatment

tag: antibody


title: PF061-12

description:
Matched RNAseq, untargeted metabolomics, and O-link (from supernatants)
processed data file:
Experiment9_CRISPR_Counts.csv
Processed data file column headers with technical replicate IDs:
9C02_S13_L001_R1_001.fastq.gz
9C02_S13_L002_R1_001.fastq.gz
9C02_S13_L003_R1_001.fastq.gz
9C02_S13_L004_R1_001.fastq.gz

tag: cell type

tag: re-activation


title: MAP_1

description: miRNA-seq; MAP.txt


title: PF061-11

description:
Matched RNAseq, untargeted metabolomics, and O-link (from supernatants)
processed data file:
Experiment9_CRISPR_Counts.csv
Processed data file column headers with technical replicate IDs:
9B01_S12_L001_R1_001.fastq.gz
9B01_S12_L002_R1_001.fastq.gz
9B01_S12_L003_R1_001.fastq.gz
9B01_S12_L004_R1_001.fastq.gz

tag: reactivation hours

tag: knockdown


title: HiChIP_Pax3_6day_shLdb1_rep1

description:
processed data file:  6day_shLdb1.allValidPairs.hic
Pax3_HiChIP_6day_dox_iPax3_shLdb1_01


title: C_2

description: miRNA-seq; control.txt


title: PF061-09

description:
Matched RNAseq, untargeted metabolomics, and O-link (from supernatants)
processed data file:
Experiment9_CRISPR_Counts.csv
Processed data file column headers with technical replicate IDs:
9C05_S10_L001_R1_001.fastq.gz
9C05_S10_L002_R1_001.fastq.gz
9C05_S10_L003_R1_001.fastq.gz
9C05_S10_L004_R1_001.fastq.gz

tag: drug

tag: donor


title: HiChIP_Pax3_6day_shCtrl_rep1

description:
processed data file:  6day_shSCR.allValidPairs.hic
Pax3_HiChIP_6day_dox_iPax3_shCtrl_01


title: HiChIP_Pax3_1day_rep2

description:
processed data file:  1day_plusdox.allValidPairs.hic
Pax3_HiChIP_1day_dox_iPax3_02

value: day9 of differentiation


title: PF061-06

description:
Matched RNAseq, untargeted metabolomics, and O-link (from supernatants)
processed data file:
Experiment9_CRISPR_Counts.csv
Processed data file column headers with technical replicate IDs:
9A05_S7_L001_R1_001.fastq.gz
9A05_S7_L002_R1_001.fastq.gz
9A05_S7_L003_R1_001.fastq.gz
9A05_S7_L004_R1_001.fastq.gz

value: crNT CTL

tag: plate # (submitted to seqmatic)

tag: seqmatic run


title: brown adipocytes_DMSO3D1

city: Shanghai

first: Zhuanghui

last: Feng

address: 320 Yueyang Road

institute: Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences

data_processing:
Basecalls performed using illumina Bcl2fastq version 2.17.1.14
Map to mouse genome mm9 using Tophat(v 2.1.1)
Bam to Bedgraph using genomeCoverageBed
Bedgraph to bigwig using UCSC bedGraphToBigWig
Gene expression level was calculated using Deseq2
Genome_build: mm10
Supplementary_files_format_and_content: counts

source_name: brown adipocytes

extract_protocol:
Total RNA was extracted from brown adipocytes using TRIzol reagent in accordance with the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: brown adipocytes

tag: treatment

value: DMSO

value: 3 days


title: brown adipocytes_ISO1

value: ISO

value: 1 day


title: brown adipocytes_DMSO3D2


title: PF061-05

description:
Matched RNAseq, untargeted metabolomics, and O-link (from supernatants)
processed data file:
Experiment9_CRISPR_Counts.csv
Processed data file column headers with technical replicate IDs:
9C04_S6_L001_R1_001.fastq.gz
9C04_S6_L002_R1_001.fastq.gz
9C04_S6_L003_R1_001.fastq.gz
9C04_S6_L004_R1_001.fastq.gz

tag: date of seqmatic run

tag: sample name (randomized)


title: brown adipocytes_BML3D1


title: brown adipocytes_BML3D2


title: brown adipocytes_DMSO1D2


title: WT-1

city: Strasbourg

first: Irwin

last: Davidson

address: 1 Rue Laurent Fries

country: France

institute: IGBMC

description:
PolyA RNA
processed data: tumours_bptf_brg1_gene_expression_table.xls

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Reads were preprocessed in order to remove adapter and low-quality sequences (Phred quality score below 20) using cutadapt version 1.10.
Reads were mapped to rRNA sequences using bowtie version 2.2.8, and reads mapping to rRNA sequences were removed for further analysis. Reads were mapped to spike sequences using bowtie2 version 2.2.8, and reads mapping to spike sequences were removed for further analysis.
Sequence reads were mapped to reference genome mm9 using Tophat v2.0.10 51 and the bowtie2 v2.1.0 aligner. Only uniquely aligned reads were retained for further analyses.
Gene expression quantification was performed from uniquely aligned reads using htseq-count version v0.6.1 with annotations from Ensembl version 67.
Data normalization and quantification of gene expression was performed using the DESeq2 Bioconductor package. Significantly deregulated genes were selected using a log2 fold change >1 and <1 and adjusted p-value cutoff of 0.05.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: Excel tables (.xls format) containing raw read counts, counts normalized by library size, counts normalized by both library size and gene length as well as log2(foldchange) and p-values computed by DESeq2. The Excel tables contain additional sheets comprising only upregulated and downregulated genes.

source_name: Mouse tumour

extract_protocol:
RNA prepared using Trizol and isopropanol.
RNA-Seq libraries were generated from 500 ng of total RNA using TruSeq Stranded mRNA LT Sample Preparation Kit (Illumina, San Diego, CA), according to manufacturer's instructions. Briefly, following purification with poly-T oligo attached magnetic beads, the mRNA was fragmented using divalent cations at 94oC for 2 minutes. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity was achieved by replacing dTTP with dUTP during second strand cDNA synthesis using DNA Polymerase I and RNase H. Following addition of a single 'A' base and subsequent ligation of the adapter on double stranded cDNA fragments, the products were purified and enriched with PCR (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC) to create the cDNA library. Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.

tag: strain/background

value: In vitro cultured Braf/Pten melanoma cells

tag: 4oht floxed

value: Control


title: WT-2


title: brown adipocytes_DMSO1D1

tag: time


title: Bptf-2

value: Bptf


title: HiChIP_Pax3_6day_shCtrl_rep2

description:
processed data file:  6day_shSCR.allValidPairs.hic
Pax3_HiChIP_6day_dox_iPax3_shCtrl_02

tag: purification

tag: doxycycline-treatment


title: PF061-03

description:
Matched RNAseq, untargeted metabolomics, and O-link (from supernatants)
processed data file:
Experiment9_CRISPR_Counts.csv
Processed data file column headers with technical replicate IDs:
9A06_S4_L001_R1_001.fastq.gz
9A06_S4_L002_R1_001.fastq.gz
9A06_S4_L003_R1_001.fastq.gz
9A06_S4_L004_R1_001.fastq.gz

tag: cell type

value: Primary human CD4+ T cells

tag: experiment number


title: brown adipocytes_BML1D2


title: Bptf-1


title: WT-3


title: brown adipocytes_BML1D1


title: PF055-31

description:
Matched RNAseq, untargeted metabolomics, and O-link (from supernatants)
processed data file:
Experiment8_Immunocult_Counts.csv
Processed data file column headers with technical replicate IDs:
C02_S10_L001_R1_001.fastq.gz
C02_S10_L002_R1_001.fastq.gz
C02_S10_L003_R1_001.fastq.gz
C02_S10_L004_R1_001.fastq.gz

tag: re-activation

value: Immunocult CD3/CD28 (1:100)

tag: reactivation hours


title: Smarca4-3


title: Smarca4-2


title: Bptf-3


title: PF061-04

description:
Matched RNAseq, untargeted metabolomics, and O-link (from supernatants)
processed data file:
Experiment9_CRISPR_Counts.csv
Processed data file column headers with technical replicate IDs:
9B05_S5_L001_R1_001.fastq.gz
9B05_S5_L002_R1_001.fastq.gz
9B05_S5_L003_R1_001.fastq.gz
9B05_S5_L004_R1_001.fastq.gz

tag: knockdown

tag: drug


title: PF055-30

description:
Matched RNAseq, untargeted metabolomics, and O-link (from supernatants)
processed data file:
Experiment8_Immunocult_Counts.csv
Processed data file column headers with technical replicate IDs:
A03_S9_L001_R1_001.fastq.gz
A03_S9_L002_R1_001.fastq.gz
A03_S9_L003_R1_001.fastq.gz
A03_S9_L004_R1_001.fastq.gz

value: Untransduced

tag: donor

tag: plate # (submitted to seqmatic)


title: Smarca4-1


title: DMSO_exp3_st10p_polyA-RNA_rep1

city: London

first: George

middle: E.

last: Gentsch

state: Greater London

address: 1 Midland Road

department: Developmental Biology Laboratory

country: United Kingdom

institute: The Francis Crick Institute

description: control (uninjected, DMSO), stage 10+ (early gastrula), experiment 3, poly(A)+ RNA, biological replicate 1

data_processing:
Bases were called using Casava version 1.8.2
ChIP-Seq: Single reads of maximal 50 bases were processed using trim_galore v0.4.2 to trim off low-quality bases and adapter contamination from the 3’ end. Processed reads were aligned to the X. tropicalis genome assembly v7.1 (and v9.1 for some ChIP-Seq) running Bowtie2 v2.2.9 with default settings. Alignments were converted to HOMER’s tag density format with redundant reads being removed (makeTagDirectory -single -tbp 1 -unique -mapq 10 -fragLength 175 -totalReads all). For all genomic regions except for the mir427 gene cluster, only uniquely aligned reads (i.e. MAPQ ≥10) were processed. The highly repetitive mir427 locus was profiled with all reads only best aligning up to 80 times (-k 80) to this region. In this case the mass of each read was normalised to the number of alignments. We pooled all input alignments from various developmental stages. This created a comprehensive mappability profile that covered ~400 million unique base pair positions. All chromatin profiles were position-adjusted and normalised to the effective total of 1 million aligned reads including multimappers (counts per million aligned reads, CPM). Transcription factor binding sites were identified using the following or otherwise default parameters of HOMER’s calling of ChIP-mediated read enrichments (hereafter called peaks): findpeaks -style factor -minDist 175 -fragLength 175 -inputFragLength 175 -fdr 0.001 -gsize 1.435e9 -F 3 -L 1 -C 0.97. This means that both ChIP and input alignments were extended 3’ to 175 bp for the detection of significant (0.1% FDR) peaks being separated by ≥175 bp. The effective size of the X. tropicalis genome assembly v7.1 was set to 1.435 billion bp, an estimate obtained from the mappability profile. These peaks showed equal or higher tag density than the surrounding 10 kb, ≥3-fold more tags than the input and ≥0.97 unique tag positions relative to the expected number of tags. To detect focal RNAPII recruitment to putative cis-regulatory elements and avoid calling peaks within broad regions of RNAPII elongation, the threshold of focal ratio and local enrichment within 10 kb was elevated to 0.6 and 3 (-L 3), respectively. To further eliminate any false positive peaks, we removed any peaks with <0.5 (transcription factors including signal mediators) or <1 (RNAPII) CPM and those falling into blacklisted regions showing equivocal mappability due to genome assembly errors, gaps or simple/tandem repeats. Regions of equivocal mappability were identified by a 2-fold lower (poor) or 3-fold higher (excessive) read coverage than the average detected in 400-bp windows sliding at 200-bp intervals through normalised ChIP input and DNase-digested naked genomic DNA. All identified regions ≤800 bp apart were subsequently merged. Gap coordinates were obtained from the Francis Crick UCSC genome browser (http://genomes.crick.ac.uk). Simple repeats were masked with RepeatMasker v4.0.6 using the crossmatch search engine v1.090518 and the following settings: RepeatMasker -species "xenopus silurana tropicalis" -s -xsmall. Tandem repeats were masked with Kent’s trfBig wrapper script of the Tandem Repeat Finder v4.09 using the following settings: weight for match, 2; weight for mismatch, 7; delta, 7; matching probability, 80; indel probability, 10; minimal alignment score, 50; maximum period size, 2,000; and longest tandem repeat array (-l), 2 [million bp].
DNase-Seq: Single and paired-end reads of maximal 50 bases were processed using trim_galore v0.4.2 to trim off low-quality bases and adapter contamination from the 3’ end. Processed reads were aligned to the X. tropicalis genome v7.1 and v9.1 using Bowtie2 v2.2.9 with default settings apart from -X (fragment length), which was reduced to 250 bp for paired-end reads. Alignments were sorted by genomic coordinates and only those with a quality score of ≥10 were retained using samtools v1.3.1. Duplicates were removed using Picard (MarkDuplicates). Paired-end alignments were dissociated using hex flags (-f 0x40 or 0x80) of samtools view. Single alignments were converted to HOMER’s tag density format (makeTagDirectory -single -unique -fragLength 100 -totalReads all). DNase hypersensitive sites (DHSs) were identified using the following or otherwise default parameters of HOMER’s peak calling: findpeaks -style factor -minDist 100 -fragLength 100 -inputFragLength 100 -fdr 0.001 -gsize 1.435e9 -F 3 -L 1 -C 0.97. This means that alignments of DNase-digested chromatin fragments (or naked genomic DNA fragments considered here as ‘input’) were extended 3’ by 100 bp from the DNase cleavage site to detect significant (0.1% FDR) DNase-mediated read enrichments (hereafter called peaks) being separated by ≥100 bp. The effective size of the X. tropicalis genome assembly v7.1 was set to 1.435 billion bp, an estimate obtained from the mappability profile (see ‘ChIP-Seq’ section). These peaks showed equal or higher tag density than the surrounding 10 kb, ≥3-fold more tags than the input and ≥0.97 unique tag positions relative to the expected number of tags. Peaks falling into blacklisted regions (see ‘ChIP-Seq’ section) were removed. DNase-probed chromatin accessibility profiles were position-adjusted and normalised to the effective total of 1 million aligned reads including multimappers.
Next-generation capture-C: Paired-end reads were processed using trim_galore v0.4.2 to trim off low-quality bases and adapter contamination from the 3’ end. Only complete mate pairs were processed further to reconstruct single reads from overlapping paired-end sequences using FLASH v1.2.11 with interleaved output settings for non-extended reads (flash --interleaved-output --max-overlap 150). FLASH reads were split in silico at DpnII restriction sites using a designated perl script (dpnII2E.pl, https://github.com/Hughes-Genome-Group/captureC/releases) before aligning them to the X. tropicalis genome assembly 7.1 using Bowtie2 v2.2.9. The alignment was run with default settings and one thread only to maintain the order of reads. The view function of samtools v1.3.1 was used to retain alignments with a quality score of ≥10. The alignments were analysed further using a suite of perl scripts (https://github.com/Hughes-Genome-Group/captureC/releases) modified to process both chromosome and scaffold coordinates. Viewpoint coordinates included a 1-kb proximity exclusion range. Restriction fragments were classified as capture, proximity-exclusion or reporter. PCR duplicates were removed. The interaction map was based on the number of unique paired-end reads per restriction fragment. Windows of 2 kb incrementing by 200 bp were used to consolidate interactions, which were normalised to 10,000 interactions per viewpoint. Significant chromatin conformation changes were identified using the R package DESeq2 v1.14.1.
RNase-Seq: Paired-end reads were aligned to the X. tropicalis genome assembly v7.1 using STAR v2.5.3a with default settings and a revised version of gene models v7.2 to improve mapping accuracy across splice junctions. The alignments were sorted by read name using the sort function of samtools v1.3.1. Exon and intron counts (-t 'exon;intron') were extracted from unstranded (-s 0) alignment files using VERSE v0.1.5 in featureCounts (default) mode (-z 0). Intron coordinates were adjusted to exclude any overlap with exon annotation. Differential expression analysis was performed with both raw exon and intron counts excluding those belonging to ribosomal and mitochondrial RNA using the R package DESeq2 v1.14.1. In an effort to find genes with consistent fold changes over time, p-values were generated according to a likelihood ratio test reflecting the probability of rejecting the reduced (~ developmental stage) over the full (~ developmental stage + condition) model. Resulting p-values were adjusted to obtain false discovery rates (FDR) according to the Benjamini-H

organism: Xenopus tropicalis

source_name: whole embryo

growth_protocol: Embryos were grown to the indicated developmental stage in 5% MMR at 25ºC.

extract_protocol:
Chromatin immunoprecipitation (ChIP): Briefly, dejellied X. tropicalis embryos were treated with 1% formaldehyde (in 1% Marc’s Modified Ringer’s, MMR) for 15-45 min at room temperature to cross-link chromatin proteins to nearby genomic DNA. Duration of fixation was determined empirically and depended mainly on the developmental stage and antibody epitopes as described in Gentsch and Smith (2017). Efficient Preparation of High-Complexity ChIP-Seq Profiles from Early Xenopus Embryos. Methods in Molecular Biology, 1507, 23-42. Fixation was terminated by rinsing embryos three times with ice-cold 1% MMR. If required, post-fixation embryos were dissected to select specific anatomical regions in ice-cold 1% MMR. Fixed embryos were homogenized in CEWB1 (10 mM Tris pH 8.0, 150 mM NaCl, 1 mM EDTA, 1% Igepal CA-630, 0.25% sodium deoxycholate and 0.1% SDS) supplemented with 0.5 mM DTT, protease inhibitors and, if using phospho-specific antibodies, phosphatase blockers (0.5 mM orthovanadate and 2.5 mM NaF). To solubilise yolk platelets and separate them from the nuclei, the homogenate was left on ice for 5 min and then centrifuged (1000 g) for 5 min at 4ºC. Homogenization and centrifugation was repeated once before resuspending the nuclei containing pellet in 1-3 ml CEWB1. Nuclear chromatin was solubilized and fragmented by isothermal focused or microtip-mediated sonication. The solution of fragmented chromatin was cleared by centrifuging (15,000 g) for 5 min at 4ºC. If required, ~1% of the cleared chromatin extract was set aside for the input sample (negative control for ChIP). ChIP-grade antibodies were used to recognize specific chromatin features and to enrich these by coupling the antibody-chromatin complex to protein G magnetic beads and extensive washing. These steps were carried out at 4ºC. The beads were washed twice in CEWB1, twice in WB2 (10 mM Tris pH 8.0, 500 mM NaCl, 1 mM EDTA, 1% Igepal CA-630, 0.25% sodium deoxycholate and 0.1% SDS), twice in WB3 (10 mM Tris pH 8.0, 250 mM LiCl, 1 mM EDTA, 1% Igepal CA-630 and 1% sodium deoxycholate) and once in TEN (10 mM Tris pH 8.0, 150 mM NaCl and 1 mM EDTA). ChIP was eluted off the beads twice with 100 µl SDS elution buffer (50 mM Tris pH 8.0, 1 mM EDTA and 1% SDS) at 65ºC. ChIP eluates were pooled before reversing DNA-protein cross-links. Input (filled up to 200 µl with SDS elution buffer) and ChIP samples were supplemented with 10 µl 5 M NaCl and incubated for 6-16 h at 65ºC in a hybridization oven. Samples were treated with proteinase K and RNase to remove any proteins and RNA from the co-immunoprecipitated DNA fragments. The DNA was purified with phenol:chloroform:isoamyl alcohol (25:24:1, pH 7.9) using phase-lock gel heavy microcentrifuge tubes for phase separation and precipitated with 1/70 volume of 5 M NaCl, 2 volumes of absolute ethanol and 15 µg blue glycogen (GlycoBlue). After centrifugation, the DNA pellet was air-dried and dissolved in 11 µl elution buffer (10 mM Tris-HCl, pH 8.5). The DNA concentration was determined on a fluorometer using high-sensitivity reagents for double-stranded DNA (10 pg/µl to 100 ng/µl).
DNase-probed chromatin accessibility: The assay to probe chromatin accessibility with DNase was adapted to early X. tropicalis embryos using a novel approach. Ultracentrifugation- or gel electrophoresis-mediated size selection was replaced by two rounds of solid phase reverse immobilization (SPRI) to remove high molecular weight (HMW) DNA from the informative, short DNA fragments. Wide-bore pipette tips were used for the resuspensions and the transfers of biological samples from the second homogenization step until after SPRI to avoid the shearing of HMW DNA. About 250 dejellied mid-blastula embryos (stage 8+) were collected in 2-ml round-bottom microcentrifuge tubes and homogenized in 2 ml ice-cold LB-DNase buffer (15 mM Tris-HCl pH 8.0, 15 mM NaCl, 60 mM KCl, 1 mM EDTA, 0.5 mM EGTA, 0.5 mM and 0.5 mM spermidine) supplemented with 0.05% Igepal CA-630. The homogenate was left on ice for 3 min before centrifuging (1,000 g) for 2 min at 4ºC. The pellet was gently resuspended in 2 ml ice-cold LB-DNase buffer (without Igepal CA-630) before centrifuging (1,000 g) again for 2 min at 4ºC. The pellet was resuspended in 600 µl of room temperature LB-DNase buffer supplemented with 6 mM CaCl2. The sample was distributed equally to two 1.5-ml microcentrifuge tubes. Approximately 0.1 U DNase I was added to one aliquot while leaving the other aliquot untreated (internal control). Both samples were incubated for 8 min at 37ºC before adding 300 µl STOP buffer (50 mM Tris pH8.0, 100 mM NaCl, 100 mM EDTA, 0.1% SDS, 80 µg RNase A, 333 nM spermine and 1 µM spermidine). The samples were incubated for 15 min at 55ºC. Next, they were digested with 200 µg proteinase K for 2 h at 55ºC. The digests were transferred to phase-lock gel heavy microcentrifuge tubes for phenol:chloroform:isoamylalcohol (25:24:1) purification. The DNA was precipitated with 1/20 volume of 3 M sodium acetate (pH 5.2) and 2 volumes of absolute ethanol. The DNA pellets were dissolved in 27 µl elution buffer (10 mM Tris pH8.5). To remove any remaining RNA (i.e. not digested in a first round of RNase treatment), 10 µg RNase A were added to the DNA samples. 5 µl (an equivalent of 20 mid-blastula embryos) from the internal control was digested with 0.3 U DNase I for 5 min at 37ºC to generate a negative control profile (i.e. DNase-treated naked genomic DNA) for chromatin accessibility. The purification and precipitation of negative control DNA was carried out along with the chromatin digest after SPRI-mediated size selection. The DNA sample from the chromatin digest was further processed by two rounds of SPRI. 22.5 µl SPRI beads were added to 25 µl DNA sample without pipetting up and down. After 3 min, by which time HMW DNA caused beads to coalesce, the tubes were clipped into a magnetic stand for microcentrifuge tubes. After 3 min, the supernatant was transferred to a 96-well microplate. 47.5 µl elution buffer and 43 µl SPRI beads were added sequentially and mixed gently by slowly pipetting up and down. After 3 min, the plate was transferred to a magnetic stand for 96-well plates. Once the beads have settled to bottom of the well, the supernatant and the digest of naked genomic DNA (see above) were transferred to separate 1.5-ml phase-lock gel heavy microcentrifuge tubes and purified with phenol:chloroform:isoamylalcohol (25:24:1, pH7.9). The DNA fragments were precipitated with 1/20 volume of 3 M sodium acetate (pH 5.2) and 3 volumes of absolute ethanol. After centrifugation, the DNA pellets were dissolved in 12 µl elution buffer. The DNA concentrations were determined on a fluorometer using high-sensitivity reagents for double-stranded DNA (10 pg/µl to 100 ng/µl).
Chromatin conformation capture (3C): About 500 dejellied mid-blastula embryos (stage 8+) were fixed with 1% formaldehyde (in 1% Marc’s Modified Ringer’s, MMR) for 40 min at room temperature. The fixation reaction was terminated by rinsing the embryos three times with ice-cold 1% MMR. The embryos were aliquoted equally into two 2-ml round-bottom microcentrifuge tubes and homogenized in 2 ml ice-cold CEB-3C (10 mM Tris pH 8.0, 150 mM NaCl, 1 mM EDTA, 1% Igepal CA-630, 0.25% sodium deoxycholate and 0.2% SDS) supplemented with protease inhibitors and 0.05 mM DTT (=CEB-3C*). The homogenates were kept on ice for 5 min before centrifuging (1,000 g) for 2 min at 4ºC. The pellet was resuspended in 0.5 ml ice-cold CEB-3C*. The resuspensions were pooled and then equally divided to two 50-ml conical tubes and each filled up with CEB-3C to 50 ml. The embryonic extracts were incubated at 37ºC for 1 h in a hybridization oven with the tubes rotating inside a hybridization bottle. The tubes were then centrifuged (1,000 g) for 5 min at room temperature. The pellets were resuspended in 50 ml double distilled water. The tubes were centrifuged (1,000 g) agai

treatment_protocol: Injections were carried out into the zygote's animal pole: MyoD-HA mRNA (80 pg); mPouV MO (5 ng Pou5f3.2 MO, 5 ng Pou5f3.3 MO and 5 ng standard control MO); mPouV/Sox3 MOs (5 ng Pou5f3.2 MO, 5 ng Pou5f3.3 MO and 5 ng Sox3 MO); β-catenin MO (5 ng); mVegT MO (10 ng); standard control MO (5-10 ng according to the dose used for the β-catenin or mVegT loss-of-function experiment); and α-amanitin (30 pg). Embryos were treated with 100 µM SB431542 or 10 µM LDN19318 from the 8-cell stage onwards to block Nodal or BMP signaling. Control embryos were treated accordingly with DMSO, the solvent of these antagonists.

tag: strain

value: wild-type (out-bred Nigerian)

tag: developmental stage

value: 10+ (early gastrula)

tag: chip antibody


title: PF055-29

description:
Matched RNAseq, untargeted metabolomics, and O-link (from supernatants)
processed data file:
Experiment8_Immunocult_Counts.csv
Processed data file column headers with technical replicate IDs:
A02_S8_L001_R1_001.fastq.gz
A02_S8_L002_R1_001.fastq.gz
A02_S8_L003_R1_001.fastq.gz
A02_S8_L004_R1_001.fastq.gz

tag: seqmatic run

tag: date of seqmatic run

tag: sample name (randomized)


title: DMSO_exp3_st10p_polyA-RNA_rep3

description: control (uninjected, DMSO), stage 10+ (early gastrula), experiment 3, poly(A)+ RNA, biological replicate 3

tag: treatment


title: siSox10-3

description:
PolyA RNA
processed data: siMITF_siSOX10_gene_expression_table.xls

tag: strain/background

tag: sirna


title: DMSO_exp3_st10p_polyA-RNA_rep2

description: control (uninjected, DMSO), stage 10+ (early gastrula), experiment 3, poly(A)+ RNA, biological replicate 2


title: DMSO_exp3_st9p_polyA-RNA_rep3

description: control (uninjected, DMSO), stage 9+ (late blastula), experiment 3, poly(A)+ RNA, biological replicate 3

value: 9+ (late blastula)


title: PF055-28

description:
Matched RNAseq, untargeted metabolomics, and O-link (from supernatants)
processed data file:
Experiment8_Immunocult_Counts.csv
Processed data file column headers with technical replicate IDs:
C06_S7_L001_R1_001.fastq.gz
C06_S7_L002_R1_001.fastq.gz
C06_S7_L003_R1_001.fastq.gz
C06_S7_L004_R1_001.fastq.gz

tag: cell type


title: PF055-32

description:
Matched RNAseq, untargeted metabolomics, and O-link (from supernatants)
processed data file:
Experiment8_Immunocult_Counts.csv
Processed data file column headers with technical replicate IDs:
D02_S11_L001_R1_001.fastq.gz
D02_S11_L002_R1_001.fastq.gz
D02_S11_L003_R1_001.fastq.gz
D02_S11_L004_R1_001.fastq.gz

value: shmTOR

tag: experiment number


title: PF055-27

description:
Matched RNAseq, untargeted metabolomics, and O-link (from supernatants)
processed data file:
Experiment8_Immunocult_Counts.csv
Processed data file column headers with technical replicate IDs:
B07_S6_L001_R1_001.fastq.gz
B07_S6_L002_R1_001.fastq.gz
B07_S6_L003_R1_001.fastq.gz
B07_S6_L004_R1_001.fastq.gz

tag: re-activation

value: shNT CTL


title: DMSO_exp3_st9p_polyA-RNA_rep1

description: control (uninjected, DMSO), stage 9+ (late blastula), experiment 3, poly(A)+ RNA, biological replicate 1


title: DMSO_exp3_st9p_polyA-RNA_rep2

description: control (uninjected, DMSO), stage 9+ (late blastula), experiment 3, poly(A)+ RNA, biological replicate 2


title: DMSO_exp3_st8p_polyA-RNA_rep3

description: control (uninjected, DMSO), stage 8+ (mid-blastula transition), experiment 3, poly(A)+ RNA, biological replicate 3

value: 8+ (mid-blastula transition)


title: siSox10-2


title: BMP-LOF_exp3_st10p_polyA-RNA_rep3

description: BMP loss-of-function, stage 10+ (early gastrula), experiment 3, poly(A)+ RNA, biological replicate 3

value: treatment with LDN193189 (BMP inhibition)


title: DMSO_exp3_st8p_polyA-RNA_rep2

description: control (uninjected, DMSO), stage 8+ (mid-blastula transition), experiment 3, poly(A)+ RNA, biological replicate 2

value: DMSO


title: BMP-LOF_exp3_st10p_polyA-RNA_rep2

description: BMP loss-of-function, stage 10+ (early gastrula), experiment 3, poly(A)+ RNA, biological replicate 2


title: siSox10-1


title: DMSO_exp3_st8p_polyA-RNA_rep1

description: control (uninjected, DMSO), stage 8+ (mid-blastula transition), experiment 3, poly(A)+ RNA, biological replicate 1


title: siMitf-3

value: Mitf


title: PF055-25

description:
Matched RNAseq, untargeted metabolomics, and O-link (from supernatants)
processed data file:
Experiment8_Immunocult_Counts.csv
Processed data file column headers with technical replicate IDs:
B08_S4_L001_R1_001.fastq.gz
B08_S4_L002_R1_001.fastq.gz
B08_S4_L003_R1_001.fastq.gz
B08_S4_L004_R1_001.fastq.gz

tag: reactivation hours


title: siMitf-2


title: brown adipocytes_ISO2

value: brown adipocytes

value: ISO

tag: time


title: RNAseq_D7_P14_Arm_MemoryPrecursor_3

city: Bethesda

first: Tuoqi

last: Wu

state: MD

address: 49 Convent Dr.

institute: National Institute of Allergy and Infectious Diseases

data_processing:
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 mm10 using TopHat 2.1.0.
Genome_build: mm10

source_name: CD8 P14

extract_protocol:
50,000 P14 cells were sorted and resuspended in Qiazol (Qiagen). Total RNA was extracted with miRNeasy Mini kit (Qiagen). mRNA was selected using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB). RNAseq libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB) and NEBNext Multiplex Oligos for (NEB) according to manufacturer’s instruction.
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 3000  according to the manufacturer's protocols.

treatment_protocol:
Cells from spleen were obtained by mechanical disruption. Isolated cells were further sorted based on their surface markers.
For acute viral infections, mice were intravenously (i.v.) injected with 2×105 plaque-forming unit (PFU) LCMV Armstrong. For chronic viral infections, mice were intravenously (i.v.) injected with 2×106 PFU LCMV clone 13.

tag: tissue

value: Spleen

tag: surface marker

tag: culture condition

value: ex vivo


title: RNAseq_D7_P14_Arm_MemoryPrecursor_2

tag: strain


title: PF055-24

description:
Matched RNAseq, untargeted metabolomics, and O-link (from supernatants)
processed data file:
Experiment8_Immunocult_Counts.csv
Processed data file column headers with technical replicate IDs:
C03_S3_L001_R1_001.fastq.gz
C03_S3_L002_R1_001.fastq.gz
C03_S3_L003_R1_001.fastq.gz
C03_S3_L004_R1_001.fastq.gz

tag: knockdown

tag: drug

tag: donor

tag: plate # (submitted to seqmatic)


title: RNAseq_D7_P14_Arm_ShortLivedEffector_3


title: PF055-23

description:
Matched RNAseq, untargeted metabolomics, and O-link (from supernatants)
processed data file:
Experiment8_Immunocult_Counts.csv
Processed data file column headers with technical replicate IDs:
D07_S2_L001_R1_001.fastq.gz
D07_S2_L002_R1_001.fastq.gz
D07_S2_L003_R1_001.fastq.gz
D07_S2_L004_R1_001.fastq.gz

tag: seqmatic run

tag: date of seqmatic run

tag: sample name (randomized)


title: RNAseq_D7_P14_Arm_ShortLivedEffector_2


title: PF055-22

description:
Matched RNAseq, untargeted metabolomics, and O-link (from supernatants)
processed data file:
Experiment8_Immunocult_Counts.csv
Processed data file column headers with technical replicate IDs:
B01_S12_L001_R1_001.fastq.gz
B01_S12_L002_R1_001.fastq.gz
B01_S12_L003_R1_001.fastq.gz
B01_S12_L004_R1_001.fastq.gz


title: siMitf-1

description:
PolyA RNA
processed data: siMITF_siSOX10_gene_expression_table.xls

tag: strain/background

value: In vitro cultured Braf/Pten melanoma cells

tag: sirna


title: siC-3

tag: cell type

value: Control


title: RNAseq_D7_P14_Arm_ShortLivedEffector_1


title: PF055-26

description:
Matched RNAseq, untargeted metabolomics, and O-link (from supernatants)
processed data file:
Experiment8_Immunocult_Counts.csv
Processed data file column headers with technical replicate IDs:
C04_S5_L001_R1_001.fastq.gz
C04_S5_L002_R1_001.fastq.gz
C04_S5_L003_R1_001.fastq.gz
C04_S5_L004_R1_001.fastq.gz

value: Primary human CD4+ T cells

tag: re-activation

value: Immunocult CD3/CD28 (1:100)

tag: experiment number


title: BMP-LOF_exp3_st9p_polyA-RNA_rep3

description: BMP loss-of-function, stage 9+ (late blastula), experiment 3, poly(A)+ RNA, biological replicate 3

value: wild-type (out-bred Nigerian)

tag: developmental stage

tag: treatment

tag: chip antibody


title: BMP-LOF_exp3_st8p_polyA-RNA_rep3

description: BMP loss-of-function, stage 8+ (mid-blastula transition), experiment 3, poly(A)+ RNA, biological replicate 3


title: BMP-LOF_exp3_st9p_polyA-RNA_rep2

description: BMP loss-of-function, stage 9+ (late blastula), experiment 3, poly(A)+ RNA, biological replicate 2


title: siC-1


title: RNAseq_D7_P14_Cl13_ProgenitorLike_2

tag: tissue

tag: surface marker

tag: culture condition


title: PF055-20

description:
Matched RNAseq, untargeted metabolomics, and O-link (from supernatants)
processed data file:
Experiment8_Immunocult_Counts.csv
Processed data file column headers with technical replicate IDs:
B04_S10_L001_R1_001.fastq.gz
B04_S10_L002_R1_001.fastq.gz
B04_S10_L003_R1_001.fastq.gz
B04_S10_L004_R1_001.fastq.gz

tag: reactivation hours

tag: knockdown

tag: drug


title: BMP-LOF_exp3_st9p_polyA-RNA_rep1

description: BMP loss-of-function, stage 9+ (late blastula), experiment 3, poly(A)+ RNA, biological replicate 1

tag: strain


title: siC-2


title: BMP-LOF_exp3_st8p_polyA-RNA_rep2

description: BMP loss-of-function, stage 8+ (mid-blastula transition), experiment 3, poly(A)+ RNA, biological replicate 2


title: PF055-19

description:
Matched RNAseq, untargeted metabolomics, and O-link (from supernatants)
processed data file:
Experiment8_Immunocult_Counts.csv
Processed data file column headers with technical replicate IDs:
D08_S9_L001_R1_001.fastq.gz
D08_S9_L002_R1_001.fastq.gz
D08_S9_L003_R1_001.fastq.gz
D08_S9_L004_R1_001.fastq.gz

tag: donor

tag: plate # (submitted to seqmatic)

tag: seqmatic run

tag: date of seqmatic run


title: BMP-LOF_exp3_st8p_polyA-RNA_rep1

description: BMP loss-of-function, stage 8+ (mid-blastula transition), experiment 3, poly(A)+ RNA, biological replicate 1


title: RNAseq_D7_P14_Cl13_ProgenitorLike_1


title: BMP-LOF_exp3_st10p_polyA-RNA_rep1

description: BMP loss-of-function, stage 10+ (early gastrula), experiment 3, poly(A)+ RNA, biological replicate 1

value: 10+ (early gastrula)


title: Nodal-LOF_exp3_st10p_polyA-RNA_rep3

description: Nodal loss-of-function, stage 10+ (early gastrula), experiment 3, poly(A)+ RNA, biological replicate 3

value: treatment with SB431542 (Nodal inhibition)


title: RNAseq_D7_P14_Cl13_TerminallyExhausted_2


title: PF055-18

description:
Matched RNAseq, untargeted metabolomics, and O-link (from supernatants)
processed data file:
Experiment8_Immunocult_Counts.csv
Processed data file column headers with technical replicate IDs:
C01_S8_L001_R1_001.fastq.gz
C01_S8_L002_R1_001.fastq.gz
C01_S8_L003_R1_001.fastq.gz
C01_S8_L004_R1_001.fastq.gz

tag: cell type

tag: sample name (randomized)


title: RNAseq_D7_P14_Arm_MemoryPrecursor_1


title: PF055-21

description:
Matched RNAseq, untargeted metabolomics, and O-link (from supernatants)
processed data file:
Experiment8_Immunocult_Counts.csv
Processed data file column headers with technical replicate IDs:
D01_S11_L001_R1_001.fastq.gz
D01_S11_L002_R1_001.fastq.gz
D01_S11_L003_R1_001.fastq.gz
D01_S11_L004_R1_001.fastq.gz

tag: re-activation

value: shmTOR

tag: experiment number


title: RNAseq_D7_P14_Cl13_TerminallyExhausted_1


title: PF055-16

description:
Matched RNAseq, untargeted metabolomics, and O-link (from supernatants)
processed data file:
Experiment8_Immunocult_Counts.csv
Processed data file column headers with technical replicate IDs:
D06_S6_L001_R1_001.fastq.gz
D06_S6_L002_R1_001.fastq.gz
D06_S6_L003_R1_001.fastq.gz
D06_S6_L004_R1_001.fastq.gz


title: RNAseq_D7_P14_Cl13_2


title: PF055-15

description:
Matched RNAseq, untargeted metabolomics, and O-link (from supernatants)
processed data file:
Experiment8_Immunocult_Counts.csv
Processed data file column headers with technical replicate IDs:
B02_S5_L001_R1_001.fastq.gz
B02_S5_L002_R1_001.fastq.gz
B02_S5_L003_R1_001.fastq.gz
B02_S5_L004_R1_001.fastq.gz

value: shNT CTL


title: Nodal-LOF_exp3_st10p_polyA-RNA_rep2

description: Nodal loss-of-function, stage 10+ (early gastrula), experiment 3, poly(A)+ RNA, biological replicate 2

tag: developmental stage

tag: treatment


title: PF055-14

description:
Matched RNAseq, untargeted metabolomics, and O-link (from supernatants)
processed data file:
Experiment8_Immunocult_Counts.csv
Processed data file column headers with technical replicate IDs:
C07_S4_L001_R1_001.fastq.gz
C07_S4_L002_R1_001.fastq.gz
C07_S4_L003_R1_001.fastq.gz
C07_S4_L004_R1_001.fastq.gz


title: Nodal-LOF_exp3_st10p_polyA-RNA_rep1

description: Nodal loss-of-function, stage 10+ (early gastrula), experiment 3, poly(A)+ RNA, biological replicate 1

tag: chip antibody


title: RNAseq_D7_P14_Cl13_1

tag: tissue

tag: surface marker


title: RNAseq_D7_P14_Cl13_3

tag: culture condition


title: RNAseq_D7_P14_Arm_3


title: Nodal-LOF_exp3_st9p_polyA-RNA_rep2

description: Nodal loss-of-function, stage 9+ (late blastula), experiment 3, poly(A)+ RNA, biological replicate 2

value: 9+ (late blastula)


title: Nodal-LOF_exp3_st9p_polyA-RNA_rep1

description: Nodal loss-of-function, stage 9+ (late blastula), experiment 3, poly(A)+ RNA, biological replicate 1


title: PF055-12

description:
Matched RNAseq, untargeted metabolomics, and O-link (from supernatants)
processed data file:
Experiment8_Immunocult_Counts.csv
Processed data file column headers with technical replicate IDs:
B06_S2_L001_R1_001.fastq.gz
B06_S2_L002_R1_001.fastq.gz
B06_S2_L003_R1_001.fastq.gz
B06_S2_L004_R1_001.fastq.gz

tag: reactivation hours

tag: knockdown


title: PF055-13

description:
Matched RNAseq, untargeted metabolomics, and O-link (from supernatants)
processed data file:
Experiment8_Immunocult_Counts.csv
Processed data file column headers with technical replicate IDs:
A05_S3_L001_R1_001.fastq.gz
A05_S3_L002_R1_001.fastq.gz
A05_S3_L003_R1_001.fastq.gz
A05_S3_L004_R1_001.fastq.gz

value: Untransduced

tag: drug


title: Nodal-LOF_exp3_st9p_polyA-RNA_rep3

description: Nodal loss-of-function, stage 9+ (late blastula), experiment 3, poly(A)+ RNA, biological replicate 3

tag: strain


title: RNAseq_D7_P14_Arm_2


title: ChIPseq_H3K4me1_dTAD_plusdox

data_processing:
ChIP-seq analysis. Each sample’s reads were aligned to the mouse (mm10) genome using Bowtie2 followed by removal of PCR duplicates using Samtools. Peak calling was performed using MACS with the following parameters: --bw 300 -p 1e-3. Similar results were obtained by performing peak calling using QESEQ with the following parameters: -s 100 -c 15 -p 0.01. Peak analysis was performed using bedtools. For triplicate experiments, peaks called in 2 of the 3 replicates were further considered. For duplicate experiments, common peaks between the 2 replicates were further considered. In addition, the peak lists were filtered (intersect –v option) for sites overlapping to peaks detected in the uninduced control ChIP-seq and in the mouse ChIP-seq black-list. Density maps were generated with SeqMiner using the enrichment file enr.sgr produced by QESEQ. Bigwig files for visualization on IGV were generated by converting the wig files obtained from MACS  using the Kent tool Wig-to-BigWig.
HiChIP analysis. Paired-end samples were processed using the HiC-Pro pipeline. Contact matrices were generated for 10Kb bin pairs using default parameters in HiC-Pro to map the reads to the mm10 genome, remove duplicate reads, assign reads to Mbol restriction fragments, and acquire valid interactions. Statistically significant bin pairs and number of contacts were determined using the Fit-Hi-C contact caller using default settings and interaction distance less than 2 Mb.   Generation of Contact Matrix Heat Maps. Raw contact matrices from the HiC-Pro pipeline were normalized by read depth. The resulting normalized matrices were used to generate heat maps. The matrix acquired for the condition with no addition of doxycycline (non-induced) was subtracted from the matrices for 1-day and 6-day in doxycycline conditions. This enhanced the visualization of the heat maps for contacts specific to the manipulated condition. Similarly, the matrix for the Ldb1 knockdown sample was subtracted from the shSCR matrix to emphasize loss of contacts with the knockdown of Ldb1. R Bioconductor package “HiTC” was used to assist the generation of the contact heat maps.
Genome_build: mm10
Supplementary_files_format_and_content: ChIP-seq: processed files represent author-curated list of peaks obtained by removing Encode blacklist and peaks detected in non-induced samples or input
Supplementary_files_format_and_content: HiChIP: processed files represent .hic matrix

value: differentiating mES cells

tag: time

value: day4 of differentiation

tag: purification

value: PDGFRα+FLK1- sorted

tag: doxycycline-treatment

tag: antibody

value: ab8895 (Abcam)


title: Nodal-LOF_exp3_st8p_polyA-RNA_rep3

description: Nodal loss-of-function, stage 8+ (mid-blastula transition), experiment 3, poly(A)+ RNA, biological replicate 3

value: 8+ (mid-blastula transition)


title: ChIPseq_H3K4me1_dTAD_nodox

tag: cell type

value: not treated


title: PF055-11

description:
Matched RNAseq, untargeted metabolomics, and O-link (from supernatants)
processed data file:
Experiment8_Immunocult_Counts.csv
Processed data file column headers with technical replicate IDs:
A08_S12_L001_R1_001.fastq.gz
A08_S12_L002_R1_001.fastq.gz
A08_S12_L003_R1_001.fastq.gz
A08_S12_L004_R1_001.fastq.gz

tag: re-activation

tag: donor

tag: plate # (submitted to seqmatic)

tag: seqmatic run

tag: date of seqmatic run

tag: sample name (randomized)


title: Nodal-LOF_exp3_st8p_polyA-RNA_rep2

description: Nodal loss-of-function, stage 8+ (mid-blastula transition), experiment 3, poly(A)+ RNA, biological replicate 2

tag: developmental stage

tag: treatment

tag: chip antibody


title: RNAseq_D7_P14_Arm_1

tag: tissue

value: Spleen

tag: surface marker

tag: culture condition

value: ex vivo


title: PF055-17

description:
Matched RNAseq, untargeted metabolomics, and O-link (from supernatants)
processed data file:
Experiment8_Immunocult_Counts.csv
Processed data file column headers with technical replicate IDs:
B05_S7_L001_R1_001.fastq.gz
B05_S7_L002_R1_001.fastq.gz
B05_S7_L003_R1_001.fastq.gz
B05_S7_L004_R1_001.fastq.gz

value: Primary human CD4+ T cells

tag: reactivation hours

tag: knockdown

tag: drug

tag: experiment number


title: ChIPseq_H3K4me1_dTAD_Ldb1_plusdox

tag: cell type

tag: time

tag: purification

tag: doxycycline-treatment

tag: antibody


title: PF055-10

description:
Matched RNAseq, untargeted metabolomics, and O-link (from supernatants)
processed data file:
Experiment8_Immunocult_Counts.csv
Processed data file column headers with technical replicate IDs:
A04_S11_L001_R1_001.fastq.gz
A04_S11_L002_R1_001.fastq.gz
A04_S11_L003_R1_001.fastq.gz
A04_S11_L004_R1_001.fastq.gz

tag: re-activation

value: Immunocult CD3/CD28 (1:100)

tag: donor

tag: plate # (submitted to seqmatic)

tag: seqmatic run

tag: date of seqmatic run


title: Nodal-LOF_exp3_st8p_polyA-RNA_rep1

description: Nodal loss-of-function, stage 8+ (mid-blastula transition), experiment 3, poly(A)+ RNA, biological replicate 1

tag: strain

value: wild-type (out-bred Nigerian)

tag: developmental stage

tag: treatment

tag: chip antibody


title: RNAseq_D4.5_P14_Cl13_3

tag: tissue

tag: surface marker

tag: culture condition


title: ChIPseq_H3K4me1_dTAD_Ldb1_nodox

tag: cell type


title: RNAseq_D4.5_P14_Cl13_2


title: PF055-09

description:
Matched RNAseq, untargeted metabolomics, and O-link (from supernatants)
processed data file:
Experiment8_Immunocult_Counts.csv
Processed data file column headers with technical replicate IDs:
B03_S10_L001_R1_001.fastq.gz
B03_S10_L002_R1_001.fastq.gz
B03_S10_L003_R1_001.fastq.gz
B03_S10_L004_R1_001.fastq.gz

tag: reactivation hours

tag: knockdown

tag: drug

tag: sample name (randomized)

tag: experiment number


title: uninj_exp2_st10p_polyA-RNA_rep3

description: uninjected, stage 10+ (early gastrula), experiment 2, poly(A)+ RNA, biological replicate 3

value: 10+ (early gastrula)


title: ChIPseq_H3K4me3_6day

tag: time

value: day9 of differentiation

tag: purification

tag: doxycycline-treatment

tag: antibody

value: ab8580 (Abcam)


title: ChIPseq_H3K4me1_6day


title: RNAseq_D4.5_P14_Cl13_1

tag: strain


title: uninj_exp2_st10p_polyA-RNA_rep2

description: uninjected, stage 10+ (early gastrula), experiment 2, poly(A)+ RNA, biological replicate 2

tag: developmental stage


title: uninj_exp2_st10p_polyA-RNA_rep1

description: uninjected, stage 10+ (early gastrula), experiment 2, poly(A)+ RNA, biological replicate 1

tag: treatment


title: lc_F&IM_R3

source_name: floral and inflorescence meristems (F&IM)

tag: genotype

value: lc mutant in LA1589 background

tag: cultivar


title: uninj_exp2_st9p_polyA-RNA_rep3

description: uninjected, stage 9+ (late blastula), experiment 2, poly(A)+ RNA, biological replicate 3

value: 9+ (late blastula)

tag: chip antibody


title: lc_2dpi_R3

source_name: 2dpi floral buds

tag: tissue

value: 2dpi floral buds


title: PF055-07

description:
Matched RNAseq, untargeted metabolomics, and O-link (from supernatants)
processed data file:
Experiment8_Immunocult_Counts.csv
Processed data file column headers with technical replicate IDs:
D03_S8_L001_R1_001.fastq.gz
D03_S8_L002_R1_001.fastq.gz
D03_S8_L003_R1_001.fastq.gz
D03_S8_L004_R1_001.fastq.gz

tag: cell type

tag: re-activation

value: shmTOR

tag: donor

tag: plate # (submitted to seqmatic)

tag: seqmatic run

tag: date of seqmatic run


title: ID236 MEP

source_name: Blood

value: megakaryocyte-erythrocyte progenitors

tag: donor age

value: 57 years

tag: donor sex

value: female


title: ChIPseq_H3K27Ac_6day

value: differentiating mES cells

tag: time

tag: purification

value: PDGFRα+FLK1- sorted

tag: doxycycline-treatment

value: ab4729 (Abcam)


title: RNAseq_D4.5_P14_Arm_3

tag: strain

value: Spleen

tag: surface marker

tag: culture condition

value: ex vivo


title: PF055-05

description:
Matched RNAseq, untargeted metabolomics, and O-link (from supernatants)
processed data file:
Experiment8_Immunocult_Counts.csv
Processed data file column headers with technical replicate IDs:
D04_S6_L001_R1_001.fastq.gz
D04_S6_L002_R1_001.fastq.gz
D04_S6_L003_R1_001.fastq.gz
D04_S6_L004_R1_001.fastq.gz

value: Primary human CD4+ T cells

value: Immunocult CD3/CD28 (1:100)

tag: reactivation hours

tag: knockdown

tag: drug

tag: sample name (randomized)

tag: experiment number


title: RNAseq_D4.5_P14_Arm_2

tag: tissue


title: uninj_exp2_st9p_polyA-RNA_rep2

description: uninjected, stage 9+ (late blastula), experiment 2, poly(A)+ RNA, biological replicate 2

value: wild-type (out-bred Nigerian)

tag: developmental stage

tag: treatment

tag: chip antibody


title: ChIPseq_H3K27me3_6day

tag: cell type

value: day9 of differentiation

tag: antibody

value: 07-449 (EMD Millipore)


title: PF055-04

description:
Matched RNAseq, untargeted metabolomics, and O-link (from supernatants)
processed data file:
Experiment8_Immunocult_Counts.csv
Processed data file column headers with technical replicate IDs:
C08_S5_L001_R1_001.fastq.gz
C08_S5_L002_R1_001.fastq.gz
C08_S5_L003_R1_001.fastq.gz
C08_S5_L004_R1_001.fastq.gz

tag: re-activation

tag: donor

tag: plate # (submitted to seqmatic)

tag: seqmatic run

tag: date of seqmatic run


title: PF055-03

description:
Matched RNAseq, untargeted metabolomics, and O-link (from supernatants)
processed data file:
Experiment8_Immunocult_Counts.csv
Processed data file column headers with technical replicate IDs:
A01_S4_L001_R1_001.fastq.gz
A01_S4_L002_R1_001.fastq.gz
A01_S4_L003_R1_001.fastq.gz
A01_S4_L004_R1_001.fastq.gz

value: Untransduced


title: uninj_exp2_st8p_polyA-RNA_rep3

description: uninjected, stage 8+ (mid-blastula transition), experiment 2, poly(A)+ RNA, biological replicate 3

tag: strain

value: 8+ (mid-blastula transition)


title: RNAseq_D4.5_P14_Arm_1

tag: surface marker

tag: culture condition


title: uninj_exp2_st9p_polyA-RNA_rep1

description: uninjected, stage 9+ (late blastula), experiment 2, poly(A)+ RNA, biological replicate 1

value: 9+ (late blastula)


title: scRNA_D7_BMC_WT_GP33

data_processing:
Raw sequencing data were processed with CASAVA 1.8.2 to generate FastQ files. Alignment, filtering, barcode counting, and unique molecular identifier (UMI) counting were performed using Cell Ranger v1.2.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files for  histone modification ChIP-seq

extract_protocol:
The scRNA-seq libraries were generated using Chromium Single Cell 3’ Library & Gel Bead Kit v2 (10X Genomic) according to manufacturer’s protocol. Briefly, 10,000-15,000 live cells were FACS-sorted and used to generate single-cell gel-bead in emulsion (GEM). After reverse transcription, GEMs were disrupted. Barcoded cDNA was isolated and amplified by PCR (12 cycles). Following fragmentation, end repair, and A-tailing, sample indexes were added during index PCR (8 cycles).
Indexed libraries were multiplexed and sequenced on Illumina HiSeq 3000 instruments according to the manufacturer's instructions (26 cycles of Read 1, 8 cycles of i7 Index, and 98 cycles of Read2).


title: scRNA_D7_BMC_TOXKO_GP33


title: scRNA_D7_P14_Cl13_2


title: PF055-01

description:
Matched RNAseq, untargeted metabolomics, and O-link (from supernatants)
processed data file:
Experiment8_Immunocult_Counts.csv
Processed data file column headers with technical replicate IDs:
C05_S2_L001_R1_001.fastq.gz
C05_S2_L002_R1_001.fastq.gz
C05_S2_L003_R1_001.fastq.gz
C05_S2_L004_R1_001.fastq.gz

tag: reactivation hours

tag: knockdown

tag: drug


title: SJAMLM7040256_C1

city: Memphis

first: Michael

last: Walsh

state: TN

address: 262 Danny Thomas Place

department: Clinical Applications Core Tech

institute: St. Jude's Childrens Research Hospital

data_processing:
Illumina bcl2fastq 1.8.4 software used for basecalling.
Sequenced reads were aligned to GRCh37-lite using the Strongarm (internal unpublished) mapping pipeline with default parameters.
Fragments Per Kilobase Transcript expression levels were estimated as Fragments Per Kilobase of transcript per Million mapped fragments (FPKM); gene FPKMs were computed by summing the transcript FPKMs for each gene using Cuffdiff2.
Genome_build: GRCh37-lite
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: AML

growth_protocol: Cells were cultured in RPMI1640 media supplemented with 10% fetal bovine serum.  M07e cells were supplemented with 10ng/mL interleukin-3 and M-MOK cells were supplemented with 10ng/mL GM-CSF.

extract_protocol:
Cells were harvested, spun down, and RNA was isolated from cell pellets using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells growing in logrithmic phase were used for sequencing

tag: cell line


title: SJAMLM7040259_C1

value: WSU-AML


title: scRNA_D7_P14_Arm_2

tag: tissue


title: SJAML040258_C1


title: PF055-08

description:
Matched RNAseq, untargeted metabolomics, and O-link (from supernatants)
processed data file:
Experiment8_Immunocult_Counts.csv
Processed data file column headers with technical replicate IDs:
D05_S9_L001_R1_001.fastq.gz
D05_S9_L002_R1_001.fastq.gz
D05_S9_L003_R1_001.fastq.gz
D05_S9_L004_R1_001.fastq.gz

value: shmTOR

tag: sample name (randomized)

tag: experiment number


title: scRNA_D4.5_P14_Cl13_2


title: SJAML040254_C1


title: SJAMLM7040255_C1

value: M-MOK


title: SJAML040257_C1


title: PF052-104

description:
Matched RNAseq, untargeted metabolomics, and O-link (from supernatants)
processed data file:
Experiment6_PlateBound_Counts.csv
Processed data file column headers with technical replicate IDs:
D08_S14_L001_R1_001.fastq.gz
D08_S14_L002_R1_001.fastq.gz
D08_S14_L003_R1_001.fastq.gz
D08_S14_L004_R1_001.fastq.gz

tag: cell type

value: Plate bound CD3/CD28 (100ng/mL)


title: PF055-06

description:
Matched RNAseq, untargeted metabolomics, and O-link (from supernatants)
processed data file:
Experiment8_Immunocult_Counts.csv
Processed data file column headers with technical replicate IDs:
A07_S7_L001_R1_001.fastq.gz
A07_S7_L002_R1_001.fastq.gz
A07_S7_L003_R1_001.fastq.gz
A07_S7_L004_R1_001.fastq.gz


title: uninj_exp2_st8p_polyA-RNA_rep2

description: uninjected, stage 8+ (mid-blastula transition), experiment 2, poly(A)+ RNA, biological replicate 2

tag: developmental stage

tag: treatment

tag: chip antibody


title: uninj_exp2_st8p_polyA-RNA_rep1

description: uninjected, stage 8+ (mid-blastula transition), experiment 2, poly(A)+ RNA, biological replicate 1


title: PF052-102

description:
Matched RNAseq, untargeted metabolomics, and O-link (from supernatants)
processed data file:
Experiment6_PlateBound_Counts.csv
Processed data file column headers with technical replicate IDs:
B05_S12_L001_R1_001.fastq.gz
B05_S12_L002_R1_001.fastq.gz
B05_S12_L003_R1_001.fastq.gz
B05_S12_L004_R1_001.fastq.gz

tag: re-activation

value: shNT CTL

tag: donor

tag: plate # (submitted to seqmatic)


title: SJAML040253_C1


title: scRNA_D7_P14_Cl13_1

tag: strain


title: scRNA_D4.5_P14_Arm_2

tag: surface marker


title: SJAMLM7040252_C1

value: CMY


title: cMO_exp2_st10p_polyA-RNA_rep2

description: standard control morphant, stage 10+ (early gastrula), experiment 2, poly(A)+ RNA, biological replicate 2

value: 10+ (early gastrula)

value: injection of control MO


title: cMO_exp2_st10p_polyA-RNA_rep3

description: standard control morphant, stage 10+ (early gastrula), experiment 2, poly(A)+ RNA, biological replicate 3


title: PF055-02

description:
Matched RNAseq, untargeted metabolomics, and O-link (from supernatants)
processed data file:
Experiment8_Immunocult_Counts.csv
Processed data file column headers with technical replicate IDs:
A06_S3_L001_R1_001.fastq.gz
A06_S3_L002_R1_001.fastq.gz
A06_S3_L003_R1_001.fastq.gz
A06_S3_L004_R1_001.fastq.gz

tag: seqmatic run

tag: date of seqmatic run


title: PF052-101

description:
Matched RNAseq, untargeted metabolomics, and O-link (from supernatants)
processed data file:
Experiment6_PlateBound_Counts.csv
Processed data file column headers with technical replicate IDs:
C05_S11_L001_R1_001.fastq.gz
C05_S11_L002_R1_001.fastq.gz
C05_S11_L003_R1_001.fastq.gz
C05_S11_L004_R1_001.fastq.gz

tag: reactivation hours

tag: knockdown


title: cMO_exp2_st9p_polyA-RNA_rep3

description: standard control morphant, stage 9+ (late blastula), experiment 2, poly(A)+ RNA, biological replicate 3


title: scRNA_D7_P14_Arm_1

value: Spleen

tag: culture condition

value: ex vivo


title: SJAMLM7040251_C1

tag: cell line

value: CMS


title: PF052-103

description:
Matched RNAseq, untargeted metabolomics, and O-link (from supernatants)
processed data file:
Experiment6_PlateBound_Counts.csv
Processed data file column headers with technical replicate IDs:
C04_S13_L001_R1_001.fastq.gz
C04_S13_L002_R1_001.fastq.gz
C04_S13_L003_R1_001.fastq.gz
C04_S13_L004_R1_001.fastq.gz

value: Primary human CD4+ T cells

tag: drug

tag: sample name (randomized)


title: PF052-100

description:
Matched RNAseq, untargeted metabolomics, and O-link (from supernatants)
processed data file:
Experiment6_PlateBound_Counts.csv
Processed data file column headers with technical replicate IDs:
C02_S10_L001_R1_001.fastq.gz
C02_S10_L002_R1_001.fastq.gz
C02_S10_L003_R1_001.fastq.gz
C02_S10_L004_R1_001.fastq.gz

tag: cell type

tag: experiment number


title: cMO_exp2_st9p_polyA-RNA_rep2

description: standard control morphant, stage 9+ (late blastula), experiment 2, poly(A)+ RNA, biological replicate 2

value: wild-type (out-bred Nigerian)

tag: developmental stage

tag: treatment


title: SJAMLM7040250_C1

value: CMK


title: SJAMLM7040249_C1


title: PF052-99

description:
Matched RNAseq, untargeted metabolomics, and O-link (from supernatants)
processed data file:
Experiment6_PlateBound_Counts.csv
Processed data file column headers with technical replicate IDs:
B03_S9_L001_R1_001.fastq.gz
B03_S9_L002_R1_001.fastq.gz
B03_S9_L003_R1_001.fastq.gz
B03_S9_L004_R1_001.fastq.gz

tag: re-activation


title: scRNA_D4.5_P14_Arm_1

tag: tissue


title: cMO_exp2_st8p_polyA-RNA_rep3

description: standard control morphant, stage 8+ (mid-blastula transition), experiment 2, poly(A)+ RNA, biological replicate 3

tag: chip antibody


title: PF052-96

description:
Matched RNAseq, untargeted metabolomics, and O-link (from supernatants)
processed data file:
Experiment6_PlateBound_Counts.csv
Processed data file column headers with technical replicate IDs:
D03_S6_L001_R1_001.fastq.gz
D03_S6_L002_R1_001.fastq.gz
D03_S6_L003_R1_001.fastq.gz
D03_S6_L004_R1_001.fastq.gz

tag: donor

tag: plate # (submitted to seqmatic)


title: scRNA_D4.5_P14_Cl13_1

tag: strain

tag: surface marker


title: cMO_exp2_st8p_polyA-RNA_rep2

description: standard control morphant, stage 8+ (mid-blastula transition), experiment 2, poly(A)+ RNA, biological replicate 2


title: SKIIP siRNA + NaCl rep2

city: Barcelona

first: Francesc

last: Posas

address: Carrar Baldiri Reixac 10

country: Spain

institute: Cell Signaling Group, IRB Barcelona

data_processing:
RNA-sequencing reads were mapped to the hg19 genome using VAST-TOOLS “align” program (vast-tools align  -sp Hsa -c 15 -o vast_out --IR_version 2 --expr). Replicates were merged using “vast-tools merge” (-sp Hsa) and the table provided in INCLUSION_GEO.tsv was created by “vast-tools combine” (-sp Hsa). Differential splicing analysis was also performed using VAST-TOOLS (vast-tools compare --min_dPSI 15 --min_range 5 --print_dPSI –no_plot).
Genome_build: hg19
Supplementary_files_format_and_content: Results for each pre-determined alternative splicing event analysed by VAST-TOOLS have been stored in INCLUSION_GEO.tsv via the “combine” function. Further details and explanations can be found at https://github.com/vastgroup/vast-tools#combine-output-format

source_name: HeLa whole cell

growth_protocol: HeLa cells were maintained in Dulbecco’s modified Eagle’s Medium supplemented with 10% fetal calf serum (Sigma), 1 mM sodium pyruvate, 2 mM L-glutamine, 100 U/ml Penicillin and 100 μg/ml Streptomycin (GibCO) and were cultured in a 5% CO2 humidified incubator at 37ºC.

extract_protocol:
Total RNA was isolated using the RNAspin Mini Kit (GE Healthcare). An additional treatment with DNAse was performed using the TURBO DNA-free Kit  (Ambion inc).    Quality assessment of Total RNA samples were analyzed using the Agilent Bioanalyzer 2100 and the RNA 6000 LabChip Kit (Agilent) with the Eukaryote Total RNA Nano Assay.
Stranded mRNA-seq libraries (TruSeq) were prepared from 0.5 ng RNA

treatment_protocol:
siRNA protocol: HeLa cells were transiently transfected with SKIIP or scrambled stealth siRNAs (20 nM) using Lipofectamine RNAiMAX (Invitrogen).
72h after siRNA transfection, cells were incubated (or not) with 100 mM NaCl for 3 hours and treated (or not) with 10 μM SB203502 (SB) for 30 minutes prior to NaCl addition.

value: HeLa

tag: sirnatreatment

value: SKIIP siRNA

tag: sirnatreatment time

value: untreated

tag: pre_treatment time

value: 100 mM NaCl

value: 3 hours


title: SKIIP siRNA rep2

tag: cell line


title: cMO_exp2_st8p_polyA-RNA_rep1

description: standard control morphant, stage 8+ (mid-blastula transition), experiment 2, poly(A)+ RNA, biological replicate 1

value: 8+ (mid-blastula transition)


title: SKIIP siRNA rep1