title: F2 Sample 33


title: F2 Sample 29 (Technical Replicate 1)

status: Public on Mar 15 2017

type: SRA

city: Salt Lake City

first: Richard

middle: M

last: Clark

state: Utah

department: Department of Biology

country: USA

institute: University of Utah

library_source: transcriptomic

data_processing:
Following transfer of the flowcell to an Illumina HiSeq 2000 instrument, a 50 cycle single-end sequence run was performed, and the resulting reads were aligned to the A. thaliana TAIR 10 reference genome and annotation using the Bowtie2 (2.1.0.0) and TopHat 2 (2.0.8b) mapping pipeline. Reads were sorted using SAMtools 0.1.18.0.
Read counts for genes in the TAIR 10 annotation were obtained using HTSeq 0.6.0 with --stranded no.
Genome_build: TAIR 10
Supplementary_files_format_and_content: Tab-delimited text files with counts of reads per gene from alignments as assessed with HTSeq 0.6.0.

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: aerial shoot

growth_protocol: F2 seeds were stratified for 5 days in 0.1 % agarose at 4°C. Plants were germinated and grown 2 plants per pot in 8 cm2 pots on Sunshine LA4P Mix (Sun Gro Horticulture, Bellevue, WA, USA) at 16°C constant temperature with a 16 hour light photoperiod. Plants were thinned to one plant per pot at the 5 true leaf stage and aerial portions of the plants were harvested at the 9 true leaf stage between 7.5 and 8.5 hours into the photoperiod.

extract_protocol:
Briefly, individual frozen plants were ground in liquid nitrogen using a mortar and pestle and RNA was isolated using PureLink Plant RNA Reagent (#12322-012, Invitrogen, Carlsbad, CA, USA) following the manufacturers instructions. Precipitated RNA was resuspended in RNAsecure Resuspension Solution (#AM7010, Ambion; Life Technologies, Carlsbad, CA, USA) following manufacturers guidelines to prevent RNA degradation. Contaminating genomic DNA was removed by incubating samples with Turbo DNase (#AM2238, Ambion) for 15 min at 37°C. Finally, RNA was precipitated using 2.5 vol 100% ethanol, 0.1 volume 5M Ammonium Acetate and 1µl glycogen (5 mg/ml) and resuspended in RNase-free water.
RNA-seq libraries were constructed using the Illumina TruSeq RNA Sample Preparation Kit V2 (# 15026495 Rev. C). Briefly, poly-A mRNA was purified from 1 µg of isolated total RNA using poly-T oligo-attached magnetic beads. Purified RNA was fragmented into 120-210 bp fragments (average size ~155 bp) using divalent cations at 94°C for 8 minutes. After fragmentation, first strand cDNA synthesis was performed using random primers and reverse transcriptase, followed by second strand cDNA synthesis using DNA polymerase I and RNase H. The cDNA fragments then went through end repair and overhang A addition reactions followed by the ligation of the RNA Adapters. Finally, the products were purified and enriched using 12 PCR cycles to create the final cDNA sequencing library.

tag: Stage

value: 9 true leaves

tag: accession

value: F2:8230 x 6195 (female x male)

tag: tissue

value: aerial shoot


title: WT EF3h rep2

city: Shanghai

first: Hongxing

last: Yang

address: 3888 Chenhua Rd, Songjiang District

country: China

institute: Shanghai Chenshan Botanical Garden

data_processing:
RNA-seq reads were aligned to the Arabidopsis thaliana reference genome using TopHat (version 2.0.13)
Uniquely aligned reads were counted for each annotated gene using the program htseq-count from the python package HTSeq
Genome_build: TAIR10
Supplementary_files_format_and_content: gene_readCount.txt: Tab-delimited text file with each row representing a gene and each column a sample; sample names were shown on the head line (Abbr.: RL, rosette leaf; EF, early flower; LF, late flower)

molecule: total RNA

source_name: flower buds at stages 1-9

growth_protocol: Seeds were sown into soil before stratified at 4 0C for two days, and cultivated under standard growth conditions (22 0C, 16/8 h day/night photoperiod, 60% humidity).

extract_protocol:
Plant materials were ground in liquid nitrogen, and total RNA was extracted with Trizol.
The cDNA libraries were constructed and sequenced with Illumina HiSeq3000.

treatment_protocol: Flowering plants were treated at 37 0C for 3 hours, and the control were taken at 22C. After heat shock, early flower (EF), late flower (LF) and rosette leaf (RL) were collected immediately and put into the liquid nitrogen.

tag: genotype

value: Wild-type

tag: treatment

value: treated at 37C for 3h

value: flower bud

tag: developmental stage

value: flower stages 1-9

tag: ecotype


title: F2 Sample 27


title: WT EF3h rep1


title: F2 Sample 28


title: F2 Sample 26


title: F2 Sample 25


title: WT EF0h rep2

value: control


title: WT EF0h rep3


title: F2 Sample 24


title: F2 Sample 23


title: F2 Sample 22


title: WT LF3h rep1

source_name: flower buds at stages 10-12

value: flower stages 10-12


title: WT RL3h rep3

source_name: rosette leaves at flower stages 1-9

value: rosette leaf


title: WT RL3h rep1


title: WT RL3h rep2


title: F2 Sample 21


title: F2 Sample 20


title: WT RL0h rep3


title: WT RL0h rep1


title: F2 Sample 16


title: WT RL0h rep2


title: SS-4-cDC1

city: Zwijnaarde

first: Liesbet

last: Martens

address: Technologiepark 927

department: VIB Inflammation Research Center

country: Belgium

institute: VIB-University of Ghent

description: cDC1s in steady state

data_processing:
FastQC v0.11.4 is used to check the quality of the samples
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Trimmomatic v0.35 with parameters ILLUMINACLIP:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:35
Sequenced reads were then mapped to mm10 transcriptome using Tophat2 v2.1.0 with parameters --library-type fr-unstranded --min-intron-length 50 --no-coverage-search
The mapping files were then filtered using samtools v0.1.18 (samtools view with parameters -bq 20) and sorted using samtools sort
Reads were counted using HTSeqCount v0.6.1p1 with parameters -f bam -m intersection-strict -s no -a 10 -t exon -i gene_id
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files including raw counts (output HTSeqCount) for each sample

organism: Mus musculus

source_name: Heart

growth_protocol: Hearts were harvested from mice aged between 8 and 12 weeks

extract_protocol:
Hearts were digested in RMPI containing 20mg/ML Liberase and 10U/ml DNase (37oC for 45 minutes). Single cell suspensions were filtered through a 100mM strainer and stained with antibodies to allow cDC1s,cDC2s, moDCs and MFs to be isolated by FACS.
RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 4 ng of total RNA was used as input for the SMART-Seq v4 Ultra Low Input RNA protocol (version “040215”) from Clontech Laboratories, Inc. Subsequently, 1ng of purified cDNA was sheared to 300bp using the Covaris M220. From the sheared material, sequencing libraries were prepared with the NEBNext Ultra DNA Library Prep Kit for Illumina (version 3.0 -8/15), according to the manufacturer’s protocol including a size selection to 250bp insert size with the following minor modifications: only half of the library is subjected to a 15 cycle PCR in the final library amplification step. Sequence-libraries of each sample were equimolarly pooled and sequenced on 2 NextSeq500 flow-cells at 1x75 bp with a v2 high-output kit.

treatment_protocol: Myocardial infarction (MI) was induced by permanently ligating the left anterior descending coronary artery during surgery.

tag: strain

value: Balb/c

value: Heart

tag: state

value: Steady State (SS)

tag: cell type


title: F2 Sample 19


title: F2 Sample 13 (Technical Replicate 1)


title: SS-4-CD11cpos

description: moDCs in steady state

value: CD11c positive monocyte-derived cells


title: F2 Sample 18


title: F2 Sample 12


title: F2 Sample 15


title: F2 Sample 14


title: SS-4-CD11cneg

description: Macrophages in steady state

value: CD11c negative monocyte-derived cells


title: F2 Sample 17


title: SS-3-cDC1

description: cDC1s in steady state


title: F2 Sample 9


title: WT EF0h rep1


title: F2 Sample 11


title: F2 Sample 8


title: F2 Sample 10 (Technical Replicate 1)


title: SS-3-CD11cneg

description: Macrophages in steady state


title: SS-2-cDC2

description: cDC2s in steady state


title: SS-2-cDC1

description: cDC1s in steady state


title: SS-3-CD11cpos

description: moDCs in steady state


title: SS-2-CD11cpos

description: moDCs in steady state


title: SS-1-cDC1

description: cDC1s in steady state


title: F2 Sample 7


title: F2 Sample 6 (Technical Replicate 1)


title: F2 Sample 4


title: F2 Sample 2


title: SS-4-cDC2

description: cDC2s in steady state


title: SS-1-CD11cneg

description: Macrophages in steady state


title: SS-2-CD11cneg

description: Macrophages in steady state


title: F2 Sample 5


title: SS-3-cDC2

description: cDC2s in steady state


title: SS-1-cDC2

description: cDC2s in steady state


title: MI-4-CD11cneg

description: Macrophages in MI state

value: Myocardial Infarction (MI)


title: F2 Sample 3


title: SS-1-CD11cpos

description: moDCs in steady state


title: miRXplore_52

city: Albuquerque

first: Christos

last: Argyropoulos

state: New Mexico

address: 901 University Blvd SE, Suite 150

department: Department of Internal Medicine

institute: University of New Mexico School of Medicine

description:
mirxplore_libraries.xlsx
160926_miRX_10_S58_R1_001

data_processing:
Conversion from BCL to fastq files and demultiplexing was done with bcl2fastq2 v2.17
Adapter trimming was done using Trimmomatic-0.36 in SE mode with settings ILLUMINACLIP:<adapter_file.txt>:2:30:2
Adapter trimming was done using prinseq-lite 0.20.3 -out_format 3 -min_len 18 -max_len 75 -ns_max_n 0
Fastq files were converted to fasta files using FASTX Toolkit v0.0.14 fastq_to_fasta with settings -Q33 -r
miRNA sequences were counted using grep with the following settings LC_ALL=C grep -F -o -f <list_of_sequences.txt>
output files were converted to fasta format with the following command: awk '{print ">" NR; print $0}' input > output.fa
fasta files were collapsed using FASTX Toolkit v0.0.14 fastx_collapser
collapsed fasta files were output as tables using FASTX Toolkit v0.0.14 fasta_formatter -t
Supplementary_files_format_and_content: Excel tables with read counts for each sequence present in the input pool.  Mirxplore_libraries.xlsx includes 1 sheet containing 32 legacy libraries, 1 sheet for 58 libraries sequenced 160811 (run_1) and a separate sheet for the same libraries re-sequenced 160926 (run_2).  Each table includes the name and sequence of each oligo present in the pool and the read counts for each sequence in every library.  Column colors indicate which batch the library was made with (blue=batch 1, orange=batch 2, green= batch 3).  286_libraries.xlsx includes 1 sheet containing 48 libraries sequenced 160811 (run_1) and 1 sheet containing the same libraries re-sequenced 160926 (run_2).  Each table includes the name and sequence of each oligo present in the pool and the subpool the oligo was included in for ratiometric pools.  The top two rows indicate whether the library was made with equimolar or ratiometric input samples and the total RNA input amount.  Column colors indicate which batch the library was made with (blue=batch 1, orange=batch 2, green= batch 3).

organism: synthetic construct

source_name: miRXplore equimolar pool

extract_protocol: 3’ ligation was carried out in thin-walled PCR tubes containing dried pellets of polyethelyne glycol (PEG) to give the indicated final PEG concentration (15%-25%) when resuspended in 10uL.  For each library, the indicated amount of input RNA (0.1 femtomoles – 100 femtomoles) in 6uL of water was added to the PCR tube along with 1uL of 3’ adapter such that the final amount of adapter in the ligation reaction was as indicated (10 picomoles – 50 picomoles) (3’ adapter sequence: /5rApp/(N:25252525)(N)(N)(N)TGGAATTCTCGGGTGCCAAGG/3ddC/) Tubes containing RNA, adapter and PEG were denatured for 2 minutes at 70C then chilled on ice.  To each tube, 1uL of 10X T4 RNA ligase reaction buffer, 1uL of RNase inhibitor, and 1uL of T4 RNA ligase 2 truncated KQ were added and tubes were incubated for 2 hours at 25C.  Excess 3’ adapter was removed enzymatically by addition of 1ug of E. coli single strand binding protein and incubation for 10 minutes at 25C, followed by treatment with 1uL of 5’ deadenylase for 1 hour at 30C, then treatment with 1uL of RecJ for 1 hour at 37C.  In a separate tube, the indicated 5’ adapter (5’ adapter v1 sequence: rGrUrUrCrArGrArGrUrUrCrUrArCrArGrUrCrCrGrArCrGrArUrCr(N:25252525)r(N)r(N)r(N), 5’ adapter v3 sequence: G*T*T*C*A*G*A*G*T*T*C*T*A*C*A*G*T*C*C*G*A*C*rGrArUrCr(N:25252525)r(N)r(N)r(N)) was denatured for 2 minutes at 70C and chilled on ice.  1uL of 5’ adapter to yield the indicated final amount of 5’ adapter (10 picomoles – 135 picomoles), 1uL of 1mM ATP and 1uL of T4 RNA ligase 1 was added to each tube and incubated at either 25C or 37C  for 1-2 hours as indicated.  For reverse transcription, 6uL of ligated RNA and 1uL of reverse transcription primer (10uM; GCCTTGGCACCCGAGAATTCCA) were added to a new tube and denatured at 70C for 2 minutes then chilled on ice.  To each tube, 2uL of 5X first strand reaction buffer, 1uL of 100mM DTT, 0.5 uL of 12.5mM dNTP mix, 1uL of RNase inhibitor and 1uL of SuperScript III reverse transcriptase were added and the reaction was incubated at 55C for 1 hour followed by 70C for 15 minutes.  To remove excess 5’ adapter, 1uL of RiboShredder RNase blend was added and incubated at 37C for 15 minutes.  For PCR amplification #1, 25uL of 2X PCR master mix, 2uL of Illumina forward PCR primer (20uM; sequence: AATGATACGGCGACCACCGAGATCTACACGTTCAGAGTTCTACAGTCCGA) and 2uL of Illumina indexed reverse PCR primer (20uM; sequence: CAAGCAGAAGACGGCATACGAGATXXXXXXGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA, where XXXXXX indicates barcode), and 7.5uL of water was added to the cDNA.  Libraries were amplified for 4 cycles.  PCR reactions were cleaned using a PCR purification column and eluted in 20uL of elution buffer.  For size selection #1, 5uL of loading buffer was added to each purified PCR and libraries were loaded on a 3% agarose gel and size selected on a PippinHT automated electrophoresis instrument.  The range of 127-156bp was collected.  Eluted DNA was concentrated in a vacuum concentrator until the volume was less than 22.5uL.  For PCR amplification #2, each library was transferred to a new PCR tube and the volume was adjusted to 22.5uL with water.  25uL of PCR master mix and 2.5uL of universal primer cocktail (20uM each primer; Forward primer sequence: AATGATACGGCGACCACCGAG, Reverse primer sequence: CAAGCAGAAGACGGCATACGA) was added to each tube.  Libraries were amplified for a further 8-15 cycles.  PCR reactions were cleaned using a PCR purification column and eluted in 20uL of elution buffer.  For size selection #2, 5uL of loading buffer was added to each tube and libraries were loaded on a 3% agarose gel and size selected on a PippinHT automated electrophoresis instrument.  The range of 127-156bp was collected.  Eluted DNA was concentrated in a vacuum concentrator until the volume was approximately 15uL.  1uL of each library was loaded onto a Bioanalyzer DNA 1000 chip to assess size and purity of the finished library.

tag: pool type

value: equimolar

tag: input amount

value: 10 femtomoles

tag: percent peg in ligation

tag: 3' adapter amount (picomoles)

tag: 5' adapter version

tag: 5' adapter amount (picomoles)

tag: 5' ligation time

value: 1 hour

tag: 5' ligation temperature (degrees c)


title: F2 Sample 1

tag: Stage

value: 9 true leaves

tag: accession

value: F2:8230 x 6195 (female x male)

value: aerial shoot


title: miRXplore_49

description:
mirxplore_libraries.xlsx
160926_miRX_7_S55_R1_001


title: miRXplore_50

description:
mirxplore_libraries.xlsx
160926_miRX_8_S56_R1_001


title: miRXplore_51

description:
mirxplore_libraries.xlsx
160926_miRX_9_S57_R1_001


title: MI-3-CD11cpos

description: moDCs in MI state

tag: tissue


title: MI-4-CD11cpos

description: moDCs in MI state


title: 286_ratiometric_B_15

description:
286_libraries.xlsx
160926_Ratio_B_7_S53_R1_001

source_name: 286 miRNA ratiometric pool B

value: ratiometric

value: 100 femtomoles


title: MI-3-cDC2

description: cDC2s in MI state


title: MI-4-cDC1

description: cDC1s in MI state


title: 286_ratiometric_B_16

description:
286_libraries.xlsx
160926_Ratio_B_8_S54_R1_001


title: 286_ratiometric_A_16

description:
286_libraries.xlsx
160926_Ratio_A_8_S51_R1_001

source_name: 286 miRNA ratiometric pool A


title: 286_ratiometric_B_14

description:
286_libraries.xlsx
160926_Ratio_B_6_S52_R1_001


title: MI-2-cDC2

description: cDC2s in MI state


title: 286_ratiometric_A_15

description:
286_libraries.xlsx
160926_Ratio_A_7_S50_R1_001


title: 286_ratiometric_A_14

description:
286_libraries.xlsx
160926_Ratio_A_6_S49_R1_001


title: MI-3-cDC1

description: cDC1s in MI state


title: 286_equimolar_60

description:
286_libraries.xlsx
160926_288_equimolar_28_S44_R1_001

source_name: 286 miRNA equimolar pool


title: MI-2-cDC1

description: cDC1s in MI state


title: MI-2-CD11cneg

description: Macrophages in MI state


title: MI-2-CD11cpos

description: moDCs in MI state


title: 286_equimolar_64

description:
286_libraries.xlsx
160926_288_equimolar_32_S48_R1_001

value: 0.1 femtomoles


title: MI-1-cDC2

description: cDC2s in MI state


title: 286_equimolar_63

description:
286_libraries.xlsx
160926_288_equimolar_31_S47_R1_001


title: 286_equimolar_59

description:
286_libraries.xlsx
160926_288_equimolar_27_S43_R1_001


title: MI-1-cDC1

description: cDC1s in MI state


title: Lag3_islet.3

city: Pittsburgh

first: Maria

last: Chikina

state: PA

address: 3501 5th ave

institute: University of Pittsburgh

description: cytoplasmic RNA

data_processing:
adapter trimmed
aligned with tophat2 default parameters
quantified with cufflincks
counts processed by Deseq2
normalized counts produces by Deseq2 with median ratio size factor calculation
Genome_build: mm10
Supplementary_files_format_and_content: all counts and normalized counts after filtering for genes with all 0 counts

source_name: islet

extract_protocol:
none provided by the submitter
none provided by the submitter

tag: genotype

tag: replicate

value: islet


title: MI-1-CD11cpos

description: moDCs in MI state


title: Wt_NDL.2

description: cytoplasmic RNA

source_name: NDL

value: Wt

value: NDL


title: 286_equimolar_61

description:
286_libraries.xlsx
160926_288_equimolar_29_S45_R1_001

value: 1 femtomole


title: miRXplore_48

description:
mirxplore_libraries.xlsx
160926_miRX_6_S40_R1_001


title: miRXplore_45

description:
mirxplore_libraries.xlsx
160926_miRX_3_S37_R1_001


title: Wt_NDL.3

description: cytoplasmic RNA


title: Lag3_NDL.2

description: cytoplasmic RNA


title: MI-3-CD11cneg

description: Macrophages in MI state

value: Balb/c

value: Heart


title: 286_equimolar_62

description:
286_libraries.xlsx
160926_288_equimolar_30_S46_R1_001


title: MI-1-CD11cneg

description: Macrophages in MI state

value: CD11c negative monocyte-derived cells


title: 286_equimolar_58

description:
286_libraries.xlsx
160926_288_equimolar_26_S42_R1_001


title: 286_equimolar_57

description:
286_libraries.xlsx
160926_288_equimolar_25_S41_R1_001


title: miRXplore_47

description:
mirxplore_libraries.xlsx
160926_miRX_5_S39_R1_001


title: Wt_islet.2

description: cytoplasmic RNA


title: Wt_islet.3

description: cytoplasmic RNA


title: Wt_islet.1

description: cytoplasmic RNA


title: 286_ratiometric_B_13

description:
286_libraries.xlsx
160926_Ratio_B_5_S36_R1_001


title: Lag3_islet.2

description: cytoplasmic RNA


title: Lag3_islet.1

description: cytoplasmic RNA


title: 286_ratiometric_A_13

description:
286_libraries.xlsx
160926_Ratio_A_5_S34_R1_001


title: Wt_NDL.1

description: cytoplasmic RNA


title: miRXplore_46

description:
mirxplore_libraries.xlsx
160926_miRX_4_S38_R1_001


title: 286_ratiometric_B_12

description:
286_libraries.xlsx
160926_Ratio_B_4_S35_R1_001


title: Lag3_NDL.3

description: cytoplasmic RNA


title: 286_equimolar_53

description:
286_libraries.xlsx
160926_288_equimolar_21_S30_R1_001


title: 286_equimolar_55

description:
286_libraries.xlsx
160926_288_equimolar_23_S32_R1_001


title: 286_equimolar_56

description:
286_libraries.xlsx
160926_288_equimolar_24_S33_R1_001


title: 286_equimolar_52

description:
286_libraries.xlsx
160926_288_equimolar_20_S29_R1_001


title: 286_equimolar_51

description:
286_libraries.xlsx
160926_288_equimolar_19_S28_R1_001


title: 286_equimolar_54

description:
286_libraries.xlsx
160926_288_equimolar_22_S31_R1_001


title: 286_equimolar_50

description:
286_libraries.xlsx
160926_288_equimolar_18_S27_R1_001


title: 286_equimolar_49

description:
286_libraries.xlsx
160926_288_equimolar_17_S26_R1_001


title: 286_equimolar_48

description:
286_libraries.xlsx
160926_288_equimolar_16_S25_R1_001


title: 286_equimolar_47

description:
286_libraries.xlsx
160926_288_equimolar_15_S24_R1_001


title: Lag3_NDL.1

description: cytoplasmic RNA


title: 286_equimolar_46

description:
286_libraries.xlsx
160926_288_equimolar_14_S23_R1_001


title: 286_equimolar_45

description:
286_libraries.xlsx
160926_288_equimolar_13_S22_R1_001


title: miRXplore_43

description:
mirxplore_libraries.xlsx
160926_miRX_1_S19_R1_001


title: 286_ratiometric_B_11

description:
286_libraries.xlsx
160926_Ratio_B_3_S18_R1_001


title: D2_24hr_VP24_VP35

city: Galveston

first: Alexander

last: Bukreyev

state: Texas

address: 301 University Boulevard

institute: University of Texas Medical Branch at Galveston

data_processing:
Illumina bcl2fastq-1.8.4 used for base calling with 1 mismatch allowed in the index read
Alignment to human hg19 reference using Tophat v2.0.2, Bowtie2 version 2.0.0.7, with settings -p 8 -M  --no-novel-juncs
hg19 reference and annotation (November, 2012) downloaded from Illumina iGenome website.
Gfold V1.0.7 with default parameters (doi: 10.1093/bioinformatics/bts515) analysis of expression levels using the UCSC hg19.gtf annotation file  PubMed PMID: 22923299.)
Gfold estimation with default parameters of log2 fold differences between each infected sample compared to the appropriate mock infected control.
Genome_build: hg19
Supplementary_files_format_and_content: Tab delimited table of RPKM values determined by the Gfold program
Supplementary_files_format_and_content: Tab delimited table of Gfold values (estimated log2 fold differences between samples)

organism: Homo sapiens

source_name: Donor2 dendritic cells

extract_protocol:
Total cellular RNA was extracted using  Trizol Reagent (Life Technologies, CA) according to the manufacturer’s recommendations
polyA+ libraries were prepared from 1 ug of total RNA using Illumina's True_Seq RNA kit using standard protocols

tag: phenotype

value: 24hr infected with mutant VP24_VP35 virus


title: D2_24hr_VP35

value: 24hr infected with mutant VP35 virus


title: 286_ratiometric_A_11

description:
286_libraries.xlsx
160926_Ratio_A_3_S14_R1_001


title: 286_equimolar_44

description:
286_libraries.xlsx
160926_288_equimolar_12_S21_R1_001

value: equimolar


title: D1_24hr_VP24_VP35

source_name: Donor1 dendritic cells


title: miRXplore_44

description:
mirxplore_libraries.xlsx
160926_miRX_2_S20_R1_001

value: 10 femtomoles

value: 1 hour


title: 286_equimolar_43

description:
286_libraries.xlsx
160926_288_equimolar_11_S11_R1_001


title: D1_24hr_Mock

value: 24hr Mock infected


title: D2_24hr_VP24

value: 24hr infected with mutant VP24 virus


title: 286_ratiometric_B_10

description:
286_libraries.xlsx
160926_Ratio_B_2_S17_R1_001

value: ratiometric


title: 286_ratiometric_B_9

description:
286_libraries.xlsx
160926_Ratio_B_1_S16_R1_001

value: 100 femtomoles


title: D1_24hr_VP35


title: 286_ratiometric_A_10

description:
286_libraries.xlsx
160926_Ratio_A_2_S13_R1_001


title: D2_24hr_WT

value: 24hr infected with wild-type virus


title: D1_24hr_VP24


title: D2_8hr_VP35

value: 8hr infected with mutant VP35 virus


title: 286_ratiometric_A_12

description:
286_libraries.xlsx
160926_Ratio_A_4_S15_R1_001


title: D2_24hr_Mock


title: D2_8hr_VP24_VP35

value: 8hr infected with mutant VP24_VP35 virus


title: 286_equimolar_42

description:
286_libraries.xlsx
160926_288_equimolar_10_S10_R1_001

value: 0.1 femtomoles


title: D2_8hr_VP24

value: 8hr infected with mutant VP24 virus


title: 286_equimolar_41

description:
286_libraries.xlsx
160926_288_equimolar_9_S9_R1_001

value: 1 femtomole


title: 286_equimolar_40

description:
286_libraries.xlsx
160926_288_equimolar_8_S8_R1_001


title: 286_ratiometric_A_9

description:
286_libraries.xlsx
160926_Ratio_A_1_S12_R1_001


title: 286_equimolar_39

description:
286_libraries.xlsx
160926_288_equimolar_7_S7_R1_001


title: D1_24hr_WT


title: D2_8hr_Mock

value: 8hr Mock infected


title: 286_equimolar_38

description:
286_libraries.xlsx
160926_288_equimolar_6_S6_R1_001


title: D2_8hr_WT

value: 8hr infected with wild-type virus


title: D1_8hr_VP24_VP35


title: 286_equimolar_36

description:
286_libraries.xlsx
160926_288_equimolar_4_S4_R1_001


title: D1_8hr_VP35


title: D1_8hr_VP24


title: 286_equimolar_37

description:
286_libraries.xlsx
160926_288_equimolar_5_S5_R1_001


title: 286_equimolar_34

description:
286_libraries.xlsx
160926_288_equimolar_2_S2_R1_001


title: 286_equimolar_35

description:
286_libraries.xlsx
160926_288_equimolar_3_S3_R1_001


title: 286_equimolar_33

description:
286_libraries.xlsx
160926_288_equimolar_1_S1_R1_001


title: D1_8hr_Mock


title: F2 Sample 57

value: 9 true leaves

value: F2:8230 x 6195 (female x male)

value: aerial shoot


title: D1_8hr_WT


title: miRXplore_41

description:
mirxplore_libraries.xlsx
160811_miRX_9_S57_R1_001

value: equimolar

value: 10 femtomoles


title: miRXplore_40

description:
mirxplore_libraries.xlsx
160811_miRX_8_S56_R1_001

value: 1 hour


title: miRXplore_42

description:
mirxplore_libraries.xlsx
160811_miRX_10_S58_R1_001


title: miRXplore_39

description:
mirxplore_libraries.xlsx
160811_miRX_7_S55_R1_001


title: 286_ratiometric_B_8

description:
286_libraries.xlsx
160811_Ratio_B_8_S54_R1_001


title: 286_ratiometric_B_7

description:
286_libraries.xlsx
160811_Ratio_B_7_S53_R1_001


title: 286_ratiometric_B_6

description:
286_libraries.xlsx
160811_Ratio_B_6_S52_R1_001


title: 286_ratiometric_A_8

description:
286_libraries.xlsx
160811_Ratio_A_8_S51_R1_001


title: 286_equimolar_31

description:
286_libraries.xlsx
160811_288_equimolar_31_S47_R1_001


title: 286_ratiometric_A_7

description:
286_libraries.xlsx
160811_Ratio_A_7_S50_R1_001


title: 286_equimolar_30

description:
286_libraries.xlsx
160811_288_equimolar_30_S46_R1_001


title: 286_equimolar_32

description:
286_libraries.xlsx
160811_288_equimolar_32_S48_R1_001


title: 286_ratiometric_A_6

description:
286_libraries.xlsx
160811_Ratio_A_6_S49_R1_001


title: Tcf1 deficient DN3 thymocytes 1

city: Iowa City

first: Thomas

middle: B

last: Bair

state: IA

address: 335 EMRB

institute: University of Iowa

description: Tcf1 deficient DN3 thymocytes

data_processing:
tophat2 alginment vv2.1.1
featureCount v 1.5.0-p3
DESEQ2 v 3.4
Genome_build: mm9
Supplementary_files_format_and_content: csv files that contain gene name followed by unnormalized count values from the output of featureCount

source_name: DN3 thymocytes

extract_protocol:
Thymocytes were isolated and surface-stained to identify DN3 cells. The DN3 cells were then sorted and total RNA was extracted using standard Qiagen RNease columns
RNA libraries were prepared for sequencing using stardard Illumina protocol

value: Lck-cre+ Tcf1 fl/fl

value: thymus

tag: cell phenotypes

value: CD4-, CD8-, CD44 low, CD25 high


title: p45 deficient DN3 thymocytes 2

description: p45 deficient DN3 thymocytes


title: p45 deficient DN3 thymocytes 1

description: p45 deficient DN3 thymocytes


title: 286_equimolar_28

description:
286_libraries.xlsx
160811_288_equimolar_28_S44_R1_001


title: 286_equimolar_29

description:
286_libraries.xlsx
160811_288_equimolar_29_S45_R1_001


title: 286_equimolar_27

description:
286_libraries.xlsx
160811_288_equimolar_27_S43_R1_001


title: control DN3 thymocytes 2

description: control DN3 thymocytes

value: wild type


title: Tcf1 deficient DN3 thymocytes 2

description: Tcf1 deficient DN3 thymocytes


title: 286_equimolar_25

description:
286_libraries.xlsx
160811_288_equimolar_25_S41_R1_001

value: 100 femtomoles


title: 286_equimolar_26

description:
286_libraries.xlsx
160811_288_equimolar_26_S42_R1_001


title: miRXplore_38

description:
mirxplore_libraries.xlsx
160811_miRX_6_S40_R1_001


title: miRXplore_36

description:
mirxplore_libraries.xlsx
160811_miRX_4_S38_R1_001


title: control DN3 thymocytes 1

description: control DN3 thymocytes


title: miRXplore_37

description:
mirxplore_libraries.xlsx
160811_miRX_5_S39_R1_001


title: miRXplore_35

description:
mirxplore_libraries.xlsx
160811_miRX_3_S37_R1_001


title: 286_ratiometric_B_5

description:
286_libraries.xlsx
160811_Ratio_B_5_S36_R1_001

value: ratiometric


title: WT

city: Gainesville

first: Dawei

last: Dai

state: Florida

address: 2550 Hull Rd

department: Horticultural Sciences

institute: University of Florida

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to B73 RefGen_v2 using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of transcript per Million mapped reads were calculated. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of fragments falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Ensembl plants release-19 zea_mays
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Zea mays

source_name: kernel

extract_protocol:
RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: endosperm

tag: age

value: 18 DAP

value: WT


title: dek37


title: 286_ratiometric_B_4

description:
286_libraries.xlsx
160811_Ratio_B_4_S35_R1_001


title: 286_equimolar_23

description:
286_libraries.xlsx
160811_288_equimolar_23_S32_R1_001

value: 0.1 femtomoles


title: 286_equimolar_20

description:
286_libraries.xlsx
160811_288_equimolar_20_S29_R1_001

value: 1 femtomole


title: 286_equimolar_22

description:
286_libraries.xlsx
160811_288_equimolar_22_S31_R1_001


title: 286_equimolar_21

description:
286_libraries.xlsx
160811_288_equimolar_21_S30_R1_001


title: 286_equimolar_24

description:
286_libraries.xlsx
160811_288_equimolar_24_S33_R1_001


title: 286_equimolar_15

description:
286_libraries.xlsx
160811_288_equimolar_15_S24_R1_001


title: 286_equimolar_16

description:
286_libraries.xlsx
160811_288_equimolar_16_S25_R1_001


title: 286_equimolar_13

description:
286_libraries.xlsx
160811_288_equimolar_13_S22_R1_001


title: 286_equimolar_14

description:
286_libraries.xlsx
160811_288_equimolar_14_S23_R1_001


title: 286_equimolar_12

description:
286_libraries.xlsx
160811_288_equimolar_12_S21_R1_001


title: 286_equimolar_17

description:
286_libraries.xlsx
160811_288_equimolar_17_S26_R1_001


title: 286_ratiometric_A_5

description:
286_libraries.xlsx
160811_Ratio_A_5_S34_R1_001


title: 286_equimolar_18

description:
286_libraries.xlsx
160811_288_equimolar_18_S27_R1_001


title: miRXplore_33

description:
mirxplore_libraries.xlsx
160811_miRX_1_S19_R1_001


title: 286_equimolar_19

description:
286_libraries.xlsx
160811_288_equimolar_19_S28_R1_001


title: 286_ratiometric_B_2

description:
286_libraries.xlsx
160811_Ratio_B_2_S17_R1_001


title: 286_ratiometric_A_3

description:
286_libraries.xlsx
160811_Ratio_A_3_S14_R1_001


title: 286_ratiometric_A_4

description:
286_libraries.xlsx
160811_Ratio_A_4_S15_R1_001


title: H1 human embryonic stem cell line

city: Baltimore

first: Andrew

middle: P

last: Feinberg

state: MD

address: 855 N. Wolfe St., Rangos 570

department: Center for Epigenetics

institute: Johns Hopkins

description:
SAMN04571863
SRP072141
SRX1651660

library_source: genomic

data_processing:
base calls and demultiplexing: bcl2fastq v1.8.4
Trim Galore! v0.3.6
Bismark v0.12.3
ITEX
Genome_build: hg19
Supplementary_files_format_and_content: bigWig format. Diverse content: output from processing pipeline described in manuscript

molecule: genomic DNA

source_name: H1 stem cells

extract_protocol:
Epicentre DNA extraction kit
Illumina TruSeq, NEBNext

tag: cancer / normal

value: normal

tag: passage

value: unknown


title: 286_ratiometric_B_1

description:
286_libraries.xlsx
160811_Ratio_B_1_S16_R1_001

tag: pool type

tag: input amount


title: 286_ratiometric_A_1

description:
286_libraries.xlsx
160811_Ratio_A_1_S12_R1_001

tag: percent peg in ligation

tag: 3' adapter amount (picomoles)


title: 286_ratiometric_B_3

description:
286_libraries.xlsx
160811_Ratio_B_3_S18_R1_001

tag: 5' adapter version

tag: 5' adapter amount (picomoles)


title: lung cancer

description:
SAMN04568439
SRP072078
SRX1651659

source_name: lung tissue

value: cancer


title: 286_equimolar_10

description:
286_libraries.xlsx
160811_288_equimolar_10_S10_R1_001

value: equimolar

tag: 5' ligation time

tag: 5' ligation temperature (degrees c)


title: lung normal

description:
SAMN04568438
SRP072078
SRX1651658


title: DB3CD90pos

city: Chapel Hill

first: Jonathan

middle: S

last: Serody

state: NC

address: 125 Mason Farm Rd.

department: Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

data_processing:
Alignment to mm9 reference genome using MapSplice version 2.0.1.9
Translate sorted genome alignment file (reordered) to transtriptome coordinates
Filter large indels and inserts greater than 10K bases from transcript file
Gene and isoform expression were calculated with RSEM version 1.1.13
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file represents normalized gene expression

source_name: Innate Lymphoid Cells

growth_protocol: Cells were cultured for six days in complete media with rIL-7 and rIL-33 (10ng/ml)

extract_protocol:
RNA was extracted from cultured ILC2s using the RNEasy mini kit (Qiagen)
mRNA sequencing libraries were prepared according to the TruSeq protocol (Illumina)

tag: strain

value: Innate Lymphoid Cells

tag: cell population


title: miRXplore_34

description:
mirxplore_libraries.xlsx
160811_miRX_2_S20_R1_001

value: 10 femtomoles

value: 1 hour


title: DB2CD90pos

tag: tissue


title: 286_ratiometric_A_2

description:
286_libraries.xlsx
160811_Ratio_A_2_S13_R1_001


title: indiv6-lung-cancer

description:
SAMN04568437
SRP072078
SRX1651657


title: DB3CD90neg


title: DB1CD90pos


title: indiv6-lung-normal

description:
SAMN04568436
SRP072078
SRX1651655


title: 286_equimolar_8

description:
286_libraries.xlsx
160811_288_equimolar_8_S8_R1_001


title: 286_equimolar_7

description:
286_libraries.xlsx
160811_288_equimolar_7_S7_R1_001


title: 286_equimolar_6

description:
286_libraries.xlsx
160811_288_equimolar_6_S6_R1_001


title: 286_equimolar_5

description:
286_libraries.xlsx
160811_288_equimolar_5_S5_R1_001


title: 286_equimolar_11

description:
286_libraries.xlsx
160811_288_equimolar_11_S11_R1_001


title: 286_equimolar_4

description:
286_libraries.xlsx
160811_288_equimolar_4_S4_R1_001


title: indiv5-lung-normal

description:
SAMN04568434
SRP072078
SRX1649893


title: indiv5-lung-cancer

description:
SAMN04568435
SRP072078
SRX1651654


title: 286_equimolar_3

description:
286_libraries.xlsx
160811_288_equimolar_3_S3_R1_001


title: DB1CD90neg


title: 286_equimolar_2

description:
286_libraries.xlsx
160811_288_equimolar_2_S2_R1_001


title: splenic DCs_3

city: Braunschweig

first: Michael

last: Beckstette

state: Lower Saxony

address: Inhoffenstrase 7

department: Molecular Infection Biology

country: Germany

institute: Helmholtz Centre for Infection Research

data_processing:
library quality assessment using FastQC
alignment vs. reference genome using Tophat2 (V1.20) with default parametrization
read count quantification using htseq-count (http://www.huber.embl.de/users/anders/HTSeq) and subsequent RPKM normalization
Detection of differentially expressed genes using DeSEQ2 with raw count data and default parametrization
Genome_build: GRCm38
Supplementary_files_format_and_content: htseqcounts*.tab files: tab-delimited format with raw read counts per gene; htseqcounts*.rpkm files: tab-delimited format with RPKM normalized read counts per gene; DESeq2_genes_diffexp*.csv: CSV files with differentially expressed genes

source_name: spleen

extract_protocol:
Total RNA was isolated from purified APCs with RNAeasy Plus mini kit (Qiagen).
Purification of poly‑A containing mRNA was done using poly‑T oligo attached magnetic beads (Illumina). Following the purification, the mRNA was used for library preparation using Script Seq v2 Library preparation kit (Illumina).

value: BALB/c

tag: genotype/variation

tag: cell type

value: splenic dendritic cells

value: 4-6 weeks


title: splenic DCs_2

value: wild type


title: 286_equimolar_1

description:
286_libraries.xlsx
160811_288_equimolar_1_S1_R1_001

value: 100 femtomoles


title: indiv2-liver-cancer

description:
SAMN04568431
SRP072078
SRX1649881

source_name: liver tissue


title: indiv3-liver-normal

description:
SAMN04568432
SRP072078
SRX1649884


title: 286_equimolar_9

description:
286_libraries.xlsx
160811_288_equimolar_9_S9_R1_001


title: splenic DCs_1


title: indiv1-liver-cancer

description:
SAMN04568429
SRP072078
SRX1649877


title: miRXplore_32

description:
mirxplore_libraries.xlsx
miRxplore_q_S43_R1_001


title: DB2CD90neg


title: thymic DCs_1

source_name: thymus

value: thymic dendritic cells


title: miRXplore_30

description:
mirxplore_libraries.xlsx
miRxplore_o_S41_R1_001


title: miRXplore_31

description:
mirxplore_libraries.xlsx
miRxplore_p_S42_R1_001


title: indiv3-liver-cancer

description:
SAMN04568433
SRP072078
SRX1649891


title: mTECs_3

value: medullary thymic epithelial cells


title: mTECs_2


title: indiv1-liver-normal

description:
SAMN04568428
SRP072078
SRX1648637


title: mTECs_1


title: miRXplore_27

description:
mirxplore_libraries.xlsx
miRxplore_l_S38_R1_001


title: indiv2-liver-normal

description:
SAMN04568430
SRP072078
SRX1649880


title: CD4-82yo-indiv5

description:
SAMN04568411
SRP072075
SRX1648565

source_name: CD4+ lymphocytes sorted from peripheral blood


title: miRXplore_29

description:
mirxplore_libraries.xlsx
miRxplore_n_S40_R1_001

source_name: miRXplore equimolar pool


title: thymic DCs_2


title: miRXplore_28

description:
mirxplore_libraries.xlsx
miRxplore_m_S39_R1_001


title: Rpb1-PAR-CLIP

city: Göttingen

first: Carlo

last: Bäjen

address: Am Fassberg 11

department: Molecular Biology

institute: Max Planck Institute for Biophysical Chemistry

data_processing:
PAR-CLIP: Adapter sequences are first trimmed from the raw sequencing files. The quality filter then discards all reads containing unidentified nucleotides (N), Phreds scores below 30, reads shorter than 15 nucleotides (nt), or reads that are flagged by Illumina’s internal chastity filter. Quality-trimmed reads are aligned to the S. cerevisiae genome (sacCer3, version 64.2.1) using the short read aligner Bowtie (version 1.1.1) with a maximum of one mismatch and taking unique matches only (options: -q -p 4 -S -sam -nohead -v 1 -e 70 -l 28 -y -a -m 1 -best -strata -phred33 -quals). The resulting SAM files are then converted into BAM and PileUp files using SAMTools.
ChIP-seq: Paired-end reads were aligned to the S. cerevisiae genome (sacCer3, version 64.2.1) using the short read aligner Bowtie (version 2.2.3) with options: ––p 8 --no-discordant. SAMTools was used to quality filter SAM files. Alignments with MAPQ smaller than 7 (-q 7) were skipped. Duplicate reads were removed. The BEDTools toolset was used to obtain coverage tracks that were subsequently imported into R/Bioconductor where further processing of the data was carried out.
4tU-seq: Paired-end 50 base reads with additional 6 base reads of barcodes were obtained for labeled RNA. Reads were demultiplexed and aligned to the S. cerevisiae genome (sacCer3, version 64.2.1) using STAR (version 2.3.0). SAMTools was used to quality filter SAM files. Alignments with MAPQ smaller than 7 (-q 7) were skipped and only proper pairs (-f99, -f147, -f83, -f 163) were selected. Further processing of the RNA-Seq data was carried out using the R/Bioconductor environment
Readthrough index (RI): Was defined as the ratio of normalized read counts falling into the (pA+50bp, pA+500bp) region over normalized read counts falling into the (pA-500bp, pA-50bp) region. Excluding a region of 50 bp up- and downstream of the pA site increased the robustness of our analysis. We then compared the RIs of samples with nuclear depletion (or mutants) and the untreated ones (or wild-type) to characterize the amount of termination defects.
Genome_build: sacCer3, version 64.2.1
Supplementary_files_format_and_content: RIs for each factor and transcript are summarized in .txt files.

organism: Saccharomyces cerevisiae

source_name: Yeast cell extract

growth_protocol: Cells expressing the TAP-tagged or FRB-tagged protein were grown at 30 °C and 160 rpm. While ChIP and 4tU-seq were performed in YPD, the PAR-CLIP experiments were carried out in CSM minimal medium (Formedium) supplemented with 10 mg/l uracil, 100 µM 4-thiouracil and 2 % glucose.

extract_protocol:
CLIP and ChIP: Cells were lysed by bead beating and the lysate was sonicated in a Covaris S220 system. Immunoprecipitation was performed at 4 °C with rabbit IgG-conjugated Protein G magnetic Dynabeads.
4tU-seq: Total RNA was extracted and labeled RNA purified. 100 ng of labeled RNA was used as input for the Ovation Universal RNA-Seq System Library Kit (NuGen) and processed following the manufacturer’s protocol. ChIP-seq: Purified DNA from IP and input samples was RNase digested and used for ChIP-seq library perparation with the NEB-Next ChIP-seq Library Reagent Set for Illumina Sequencing (NEB) in combination with Multiplex Oligos (NEB) according to the manufacturers protocol.

treatment_protocol: ChIP: 1% formaldehyde for 20 min at 20°C and subsequently quenched with 375 mM glycine for 10 min. PAR-CLIP: 900 µM 4-thiouracil were added and cells were grown further for 4 h before they were UV-irradiated with an energy dose of 12 J/cm2 at 365 nm. 4tU-seq: the cultures were supplemented with rapamycin (1 μg/ml) and labeled for 60 min.

tag: strain background

value: expressing the TAP-tagged protein

tag: method

value: PAR-CLIP

tag: molecule subtype

value: crosslinked RNA


title: thymic DCs_3

tag: age


title: miRXplore_25

description:
mirxplore_libraries.xlsx
miRxplore_j_S36_R1_001

tag: pool type

value: 0.1 femtomoles


title: CD4-86yo-indiv6

description:
SAMN04568412
SRP072075
SRX1648566

tag: cancer / normal

value: normal

tag: passage


title: CD4-82yo-indiv4

description:
SAMN04568410
SRP072075
SRX1648434


title: miRXplore_24

description:
mirxplore_libraries.xlsx
miRxplore_i_S35_R1_001

tag: input amount

tag: percent peg in ligation

tag: 3' adapter amount (picomoles)


title: fibro-P33

description:
SAMN04568406
SRP072075
SRX1648630

source_name: human neonatal foreskin fibroblasts


title: miRXplore_26

description:
mirxplore_libraries.xlsx
miRxplore_k_S37_R1_001

tag: 5' adapter version

tag: 5' adapter amount (picomoles)

tag: 5' ligation time


title: WT_4tUseq

description: library strategy: 4tU-seq

value: expressing the FRB-tagged protein


title: CD4-18yo-indiv1

description:
SAMN04568407
SRP072075
SRX1648319


title: CD4-25yo-indiv2

description:
SAMN04568408
SRP072075
SRX1648432


title: Rpb1-ChIP_Rat1no_input 2

data_processing:
PAR-CLIP: Adapter sequences are first trimmed from the raw sequencing files. The quality filter then discards all reads containing unidentified nucleotides (N), Phreds scores below 30, reads shorter than 15 nucleotides (nt), or reads that are flagged by Illumina’s internal chastity filter. Quality-trimmed reads are aligned to the S. cerevisiae genome (sacCer3, version 64.2.1) using the short read aligner Bowtie (version 1.1.1) with a maximum of one mismatch and taking unique matches only (options: -q -p 4 -S -sam -nohead -v 1 -e 70 -l 28 -y -a -m 1 -best -strata -phred33 -quals). The resulting SAM files are then converted into BAM and PileUp files using SAMTools.
ChIP-seq: Paired-end reads were aligned to the S. cerevisiae genome (sacCer3, version 64.2.1) using the short read aligner Bowtie (version 2.2.3) with options: ––p 8 --no-discordant. SAMTools was used to quality filter SAM files. Alignments with MAPQ smaller than 7 (-q 7) were skipped. Duplicate reads were removed. The BEDTools toolset was used to obtain coverage tracks that were subsequently imported into R/Bioconductor where further processing of the data was carried out.
4tU-seq: Paired-end 50 base reads with additional 6 base reads of barcodes were obtained for labeled RNA. Reads were demultiplexed and aligned to the S. cerevisiae genome (sacCer3, version 64.2.1) using STAR (version 2.3.0). SAMTools was used to quality filter SAM files. Alignments with MAPQ smaller than 7 (-q 7) were skipped and only proper pairs (-f99, -f147, -f83, -f 163) were selected. Further processing of the RNA-Seq data was carried out using the R/Bioconductor environment
Readthrough index (RI): Was defined as the ratio of normalized read counts falling into the (pA+50bp, pA+500bp) region over normalized read counts falling into the (pA-500bp, pA-50bp) region. Excluding a region of 50 bp up- and downstream of the pA site increased the robustness of our analysis. We then compared the RIs of samples with nuclear depletion (or mutants) and the untreated ones (or wild-type) to characterize the amount of termination defects.
Genome_build: sacCer3, version 64.2.1
Supplementary_files_format_and_content:
*.bed: Paired-end reads were aligned using Bowtie (2.2.3) and filtered with SAMTools. Alignments with MAPQ smaller than 7 were skipped and BEDTools was used to obtain coverage tracks.
*normalized_q95.table: Reads were aligned using Bowtie (1.1.1.). The resulting SAM files are then converted into BAM and PileUp files using SAMTools. The P-value calculation was performed for any genomic T site, given the total number of reads covering the site (”coverage”) and given the fraction of these reads which show the T-to-C mismatch (P-value cut-off of 0.005 and a minimum coverage threshold of 4). The frequency of T-to-C transitions was subsequently normalized by RNA-seq.
*fragmentcoverageRatiotable_*.txt:  The readthrough index (RI) was defined as the ratio of normalized read counts falling into the (pA+50bp, pA+500bp) region over normalized read counts falling into the (pA-500bp, pA-50bp) region. Excluding a region of 50 bp up- and downstream of the pA site increased the robustness of the analysis.The RIs of samples with nuclear depletion (or mutants) and the untreated ones (or wild-type) were finally compared to characterize the amount of termination defects.

value: chromatin


title: miRXplore_23

description:
mirxplore_libraries.xlsx
miRxplore_h_S34_R1_001

value: equimolar

tag: 5' ligation temperature (degrees c)


title: fibro-P31

description:
SAMN04568405
SRP072075
SRX1648571


title: Rpb1-ChIP_Rat1no_input 1


title: fibro-P10

description:
SAMN04568404
SRP072075
SRX1648570


title: Rpb1-ChIP_Rat1no 2


title: Rpb1-ChIP_Rat1no 1


title: CD4-25yo-indiv3

description:
SAMN04568409
SRP072075
SRX1648433


title: miRXplore_22

description:
mirxplore_libraries.xlsx
mirxplore_h_S10_R1_001

value: 1 femtomole


title: Rpb1-ChIP_Rat1aa_input 2


title: Rpb1-ChIP_Rat1aa_input 1


title: miRXplore_21

description:
mirxplore_libraries.xlsx
miRxplore_g_S33_R1_001

value: 1 hour


title: SD2_BM_2937_CD19

city: Montreal

first: Magalie

last: Celton

state: Quebec

address: 2950, Chemin de Polytechnique

country: Canada

institute: IRIC

data_processing:
Basecalls performed using CASAVA 1.8.2
Sequenced reads were trimmed for adaptor sequence and mapped to the reference genome using CASAVA 1.8.2
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using CASAVA 1.8.2.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file includes RPKM values. Columns are: Chromosome, Start location, Stop location, Gene, RPKM.

source_name: bone marrow

growth_protocol: Human CD34+ cord blood cells were positively selected (CD34  cells). Cells were transduced with a retrovirus containing GFP and the human MLL-AF9 fusion gene and were maintained for  in vitro culture for 80-90 days (CD34-MLL-AF9 cells).  Transduced cells were expanded in myeloid promoting culture with 15% FSC +IL3 +SCF for 4 weeks. After ~30 days of expansion cells (10 x106/mouse) from each donor sample were injected into multiple NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ (NSG) immunodeficient mice. Mice were analyzed after ~20-24 weeks and the bone marrow was harvested (Model AML MLL_AF9 samples).

extract_protocol:
mRNA was isolated from TRIzol extraction protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: bone marrow

tag: sample type

value: CD34 MLL-AF9 were injected into multiple NGS immunodeficient mice


title: B_ALL 4067


title: miRXplore_20

description:
mirxplore_libraries.xlsx
mirxplore_g_S9_R1_001


title: Ysh1_4tUseq

description: library strategy: 4tU-seq

tag: genotype/variation


title: miRXplore_19

description:
mirxplore_libraries.xlsx
miRxplore_f_S32_R1_001


title: Rpb1-ChIP_Rat1aa 2

tag: strain background


title: Rpb1-ChIP_Rat1aa 1


title: SD2_BM_2936_CD19


title: SD2_BM_2934_CD19


title: Spt5KOW_4tUseq

data_processing:
library strategy: 4tU-seq
PAR-CLIP: Adapter sequences are first trimmed from the raw sequencing files. The quality filter then discards all reads containing unidentified nucleotides (N), Phreds scores below 30, reads shorter than 15 nucleotides (nt), or reads that are flagged by Illumina’s internal chastity filter. Quality-trimmed reads are aligned to the S. cerevisiae genome (sacCer3, version 64.2.1) using the short read aligner Bowtie (version 1.1.1) with a maximum of one mismatch and taking unique matches only (options: -q -p 4 -S -sam -nohead -v 1 -e 70 -l 28 -y -a -m 1 -best -strata -phred33 -quals). The resulting SAM files are then converted into BAM and PileUp files using SAMTools.
ChIP-seq: Paired-end reads were aligned to the S. cerevisiae genome (sacCer3, version 64.2.1) using the short read aligner Bowtie (version 2.2.3) with options: ––p 8 --no-discordant. SAMTools was used to quality filter SAM files. Alignments with MAPQ smaller than 7 (-q 7) were skipped. Duplicate reads were removed. The BEDTools toolset was used to obtain coverage tracks that were subsequently imported into R/Bioconductor where further processing of the data was carried out.
4tU-seq: Paired-end 50 base reads with additional 6 base reads of barcodes were obtained for labeled RNA. Reads were demultiplexed and aligned to the S. cerevisiae genome (sacCer3, version 64.2.1) using STAR (version 2.3.0). SAMTools was used to quality filter SAM files. Alignments with MAPQ smaller than 7 (-q 7) were skipped and only proper pairs (-f99, -f147, -f83, -f 163) were selected. Further processing of the RNA-Seq data was carried out using the R/Bioconductor environment
Readthrough index (RI): Was defined as the ratio of normalized read counts falling into the (pA+50bp, pA+500bp) region over normalized read counts falling into the (pA-500bp, pA-50bp) region. Excluding a region of 50 bp up- and downstream of the pA site increased the robustness of our analysis. We then compared the RIs of samples with nuclear depletion (or mutants) and the untreated ones (or wild-type) to characterize the amount of termination defects.
Genome_build: sacCer3, version 64.2.1
Supplementary_files_format_and_content:
*.bed: Paired-end reads were aligned using Bowtie (2.2.3) and filtered with SAMTools. Alignments with MAPQ smaller than 7 were skipped and BEDTools was used to obtain coverage tracks.
*normalized_q95.table: Reads were aligned using Bowtie (1.1.1.). The resulting SAM files are then converted into BAM and PileUp files using SAMTools. The P-value calculation was performed for any genomic T site, given the total number of reads covering the site (”coverage”) and given the fraction of these reads which show the T-to-C mismatch (P-value cut-off of 0.005 and a minimum coverage threshold of 4). The frequency of T-to-C transitions was subsequently normalized by RNA-seq.
*fragmentcoverageRatiotable_*.txt:  The readthrough index (RI) was defined as the ratio of normalized read counts falling into the (pA+50bp, pA+500bp) region over normalized read counts falling into the (pA-500bp, pA-50bp) region. Excluding a region of 50 bp up- and downstream of the pA site increased the robustness of the analysis.The RIs of samples with nuclear depletion (or mutants) and the untreated ones (or wild-type) were finally compared to characterize the amount of termination defects.

value: Spt5 mutants lacking the fifth KOW domain

value: labeled/ total RNA


title: SD2_BM_2933_EGFP


title: Spt5CTR_4tUseq

value: Spt5 mutants lacking the C-terminal repeat (CTR)


title: miRXplore_17

description:
mirxplore_libraries.xlsx
miRxplore_d_S30_R1_001


title: miRXplore_16

description:
mirxplore_libraries.xlsx
mirxplore_d_S6_R1_001

value: 2 hours


title: miRXplore_15

description:
mirxplore_libraries.xlsx
miRxplore_c_S29_R1_001


title: 2565


title: miRXplore_14

description:
mirxplore_libraries.xlsx
mirxplore_c_S5_R1_001


title: miRXplore_13

description:
mirxplore_libraries.xlsx
miRxplore_b_S28_R1_001


title: Spt5_4tUseq


title: fibro-P7

description:
SAMN04568403
SRP072075
SRX1648569


title: fibro-P4

description:
SAMN04568402
SRP072075
SRX1648568


title: miRXplore_12

description:
mirxplore_libraries.xlsx
miRxplore_a_S27_R1_001


title: 2566


title: Spt5-PAR-CLIP

data_processing:
library strategy: PAR-CLIP
PAR-CLIP: Adapter sequences are first trimmed from the raw sequencing files. The quality filter then discards all reads containing unidentified nucleotides (N), Phreds scores below 30, reads shorter than 15 nucleotides (nt), or reads that are flagged by Illumina’s internal chastity filter. Quality-trimmed reads are aligned to the S. cerevisiae genome (sacCer3, version 64.2.1) using the short read aligner Bowtie (version 1.1.1) with a maximum of one mismatch and taking unique matches only (options: -q -p 4 -S -sam -nohead -v 1 -e 70 -l 28 -y -a -m 1 -best -strata -phred33 -quals). The resulting SAM files are then converted into BAM and PileUp files using SAMTools.
ChIP-seq: Paired-end reads were aligned to the S. cerevisiae genome (sacCer3, version 64.2.1) using the short read aligner Bowtie (version 2.2.3) with options: ––p 8 --no-discordant. SAMTools was used to quality filter SAM files. Alignments with MAPQ smaller than 7 (-q 7) were skipped. Duplicate reads were removed. The BEDTools toolset was used to obtain coverage tracks that were subsequently imported into R/Bioconductor where further processing of the data was carried out.
4tU-seq: Paired-end 50 base reads with additional 6 base reads of barcodes were obtained for labeled RNA. Reads were demultiplexed and aligned to the S. cerevisiae genome (sacCer3, version 64.2.1) using STAR (version 2.3.0). SAMTools was used to quality filter SAM files. Alignments with MAPQ smaller than 7 (-q 7) were skipped and only proper pairs (-f99, -f147, -f83, -f 163) were selected. Further processing of the RNA-Seq data was carried out using the R/Bioconductor environment
Readthrough index (RI): Was defined as the ratio of normalized read counts falling into the (pA+50bp, pA+500bp) region over normalized read counts falling into the (pA-500bp, pA-50bp) region. Excluding a region of 50 bp up- and downstream of the pA site increased the robustness of our analysis. We then compared the RIs of samples with nuclear depletion (or mutants) and the untreated ones (or wild-type) to characterize the amount of termination defects.
Genome_build: sacCer3, version 64.2.1
Supplementary_files_format_and_content:
*.bed: Paired-end reads were aligned using Bowtie (2.2.3) and filtered with SAMTools. Alignments with MAPQ smaller than 7 were skipped and BEDTools was used to obtain coverage tracks.
*normalized_q95.table: Reads were aligned using Bowtie (1.1.1.). The resulting SAM files are then converted into BAM and PileUp files using SAMTools. The P-value calculation was performed for any genomic T site, given the total number of reads covering the site (”coverage”) and given the fraction of these reads which show the T-to-C mismatch (P-value cut-off of 0.005 and a minimum coverage threshold of 4). The frequency of T-to-C transitions was subsequently normalized by RNA-seq.
*fragmentcoverageRatiotable_*.txt:  The readthrough index (RI) was defined as the ratio of normalized read counts falling into the (pA+50bp, pA+500bp) region over normalized read counts falling into the (pA-500bp, pA-50bp) region. Excluding a region of 50 bp up- and downstream of the pA site increased the robustness of the analysis.The RIs of samples with nuclear depletion (or mutants) and the untreated ones (or wild-type) were finally compared to characterize the amount of termination defects.


title: 2563


title: Spt4_4tUseq


title: 2555


title: Pcf11-ChIP_input 2


title: miRXplore_18

description:
mirxplore_libraries.xlsx
miRxplore_e_S31_R1_001


title: miRXplore_11

description:
mirxplore_libraries.xlsx
mirx-b_S4_R1_001


title: Pcf11-ChIP_input 1


title: Pcf11-ChIP 1


title: Pcf11-ChIP 2


title: Pcf11_4tUseq


title: Rtt103-ChIP_input 2


title: miRXplore_10

description:
mirxplore_libraries.xlsx
mirx-a_S3_R1_001


title: miRXplore_8

description:
mirxplore_libraries.xlsx
mirx-4N-l_S26_R1_001

value: 10 femtomoles


title: miRXplore_9

description:
mirxplore_libraries.xlsx
mirx-20peg_S32_R1_001


title: miRXplore_6

description:
mirxplore_libraries.xlsx
mirx_f_S9_R1_001


title: miRXplore_7

description:
mirxplore_libraries.xlsx
mirx_g_S10_R1_001


title: Rtt103-ChIP_input 1

value: expressing the TAP-tagged protein


title: miRXplore_4

description:
mirxplore_libraries.xlsx
mirx_d_S4_R1_001


title: miRXplore_5

description:
mirxplore_libraries.xlsx
mirx_e_S5_R1_001


title: Rtt103-ChIP 2


title: Rtt103-ChIP 1


title: miRXplore_3

description:
mirxplore_libraries.xlsx
mirx_c_S3_R1_001


title: miRXplore_2

description:
mirxplore_libraries.xlsx
mirx_b_S2_R1_001


title: miRXplore_1

description:
mirxplore_libraries.xlsx
mirx_a_S1_R1_001


title: Rtt103-PAR-CLIP


title: Rtt103_4tUseq


title: Rai1-ChIP_input 1


title: Rai1-ChIP_input 2


title: Spt5-ChIP_Input1


title: Spt5-ChIP_Input2


title: DNase_Naked_DNA

city: Cambridge

first: Shmulik

last: Motola

state: MA

address: 77 Mass Ave.

institute: MIT

description: Dnase-Seq

data_processing:
Pair-end, 36-bp reads from each sample were aligned to the mouse genome (mm9) using TopHat and Bowtie.  Gene expression was quantified as fragments per kilobase of exon model per million mapped fragments (FPKM,) using Cufflinks (version 1.0.3).
Differential expression for calorie restricted-treated or high-fat diet-treated biological replicates compared to normal diet-treated mice was determined using the Cufflinks tool Cuffdiff.  The criteria for differential expression were: genes with FPKMs ≥ 0.1 in at least one of the tested conditions, whose absolute log2 fold-changes between conditions were ≥ 0.5, and whose FDR-adjusted p-values for significance of differential expression were ≥ 0.05
Processed data file are in the format of Cufflinks output.
ChIP-seq reads were aligned against the mm9 reference mouse genome. Enriched genomic regions were identified by MACS v1.468 using an IgG control, and the resulting peaks were filtered to have an enrichment p-value of <1e-10. Peaks were mapped to gene symbols using the UCSC mm9 annotation database
Genome_build: mm9
Supplementary_files_format_and_content: Processed data file are in the format of Cufflinks output for RNA-seq and bed files for ChIP- and Dnase-seq

source_name: C57Black mouse maintained on a normal diet

growth_protocol: At the age of 8 weeks, male C57BL/6J mice fed normal diet, high-fat diet or calorie restricted diet for 16 weeks.

extract_protocol: Mice were fasted overnight and the livers were harvested for the extraction of total RNA using the RNeasy Mini Kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions.  DNA was eliminated by on-column RNase-free DNase treatment.  RNA quality was verified (RNA integrity number >8.5) using a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).  Messenger RNA was isolated, converted to cDNA, and amplified using the mRNA Purification Kit (Illumina, San-Diego, CA) according to the manufacturer’s instructions. An Illumina library was built and used to generate clusters on the Illumina flow cell according to the Illumina protocol and sequenced using a Genome Analyzer II (Illumina). Alternatively, livers were crosslinked and used for ChIP-seq using various antibodies. For DNase-seq - livers were digested with DNaseI following by sequencing.

treatment_protocol: Chow diet (Prolab Isopro RMH 3000, LabDiet, St. Louis, MO), high-fat/high-carbohydrate diet (TD.93075; Harlan Laboratories, South Easton, MA), Calorie restricted diet (40% calorie restriction).

tag: strain

tag: gender

value: male


title: DNase_HFD

description: Dnase-Seq

source_name: C57Black mouse maintained on a high fat diet


title: DNase_ND

description: Dnase-Seq


title: HFD_IgG_PPARa

tag: chip antibody

value: IgG


title: DNase_CR

description: Dnase-Seq

source_name: C57Black mouse maintained on a calorie restricted diet


title: Spt5-ChIP_IP2

tag: molecule subtype


title: Rai1-ChIP 2


title: Spt5-ChIP_IP1


title: CR_IgG_PPARa


title: HFD_IgG_RXRa


title: CR_IgG_RXRa


title: Rai1_4tUseq


title: Rai1-PAR-CLIP

value: crosslinked RNA


title: Rai1-ChIP 1


title: LiCl_St9_2

city: Los Angeles

first: Edward

last: De Robertis

state: CA

address: 615 Charles E. Young Drive South

department: Biological chemistry

institute: HHMI/UCLA

data_processing:
After sequencing, adaptors were first trimmed from the RNA reads and RNA reads of low quality filtered. The clean RNA reads were mapped using Tophat (Version 2.09, default parameters) against the Xenopus laevis JGI9.1 (Xenbase) transcript sequences.
Transcripts counts were normalized using DESeq package in R . RPKM (Reads Per Kilobase per Million mapped reads) for transcripts was calculated in R.
Human gene names were assigned to transcripts using an annotation file obtained by blasting the JGI9.1 peptide sequences to human reference protein sequences.
Genome_build: Xenopus Laevis J-strain Version 9.1
Supplementary_files_format_and_content: Excel tables that include RPKM and fold induction values of genes for each sample
Supplementary_files_format_and_content: Supplemental Table S1 - Complete table of all sequenced libraries  (~43000 transcripts) (correct names, new order to match figures).xlsx
Supplementary_files_format_and_content: Supplemental Table S2 - Early dorsal bCatenin Signature (123 genes) expression values (in RPKM) throughout all libraries sequenced.xlsx
Supplementary_files_format_and_content: Supplemental Table S3 -  Complete table of all stage 9 sequenced libraries.xlsx

organism: Xenopus laevis

source_name: LiCl treatment which expands organizer;Same batch with WE_St9_5

growth_protocol: The embryos were cultured in 0.1x Marc's Modified Ringers (MMR) and staged according to Nieuwkoop and Faber (1967).

extract_protocol:
RNA from  whole embryos or dorsal halves or ventrla halves was isolated with an Absolutely RNA miniprep Kit (Agilent).
Libraries were constructed with the Illumina TruSeq RNA Library Preparation Kit V2 according to manufacturer’s protocol. Briefly, 1 µg total RNA from whole embryos, dorsal halves or ventral halves was used for input RNA. Then mRNA was purified through polyA+ selection. After fragmentation of the mRNA, first strand and second strand synthesis, double strand cDNA (ds cDNA) was obtained. The ds cDNA was then further processed for A-tailing, end repair and ligation of appropriate adaptors. Finally, the ds cDNA with adaptors was amplified by PCR to generate libraries. After measurement of the length and concentration of the libraries by Bioanalyser and Qubit, the libraries were sent for sequencing on Illumina Hi-Seq 2000 using standard methods to generate 100-bp single end reads by the Broad Stem Cell Research Center at UCLA.

treatment_protocol: MO and mRNAs were injected at 2-4 cell stage; Embryos were treated with LiCl at 32 cell stage; Dorsal and ventral halves were dissected at stage 8 in 1x Barth’s solution and cultured to stage 10.5 in 0.3 x Barth's solution.

value: Nasco

value: whole embryo

tag: developmental stage


title: bCatMO_St9_2

source_name: b-catenin knockdown which prevents organizer formation;Same batch with WE_St9_5


title: HFD2_PPARa_ChIP

value: PPARα


title: HFD2_RXRa_ChIP

value: RXRα


title: WE_St9_5

source_name: whole embryo


title: Rat1-ChIP_input 1

value: chromatin


title: CR2_PPARa_ChIP


title: Sia_St9_1

source_name: Embryos injected marginally with 100 pg sia mRNA;Same batch with WE_St9_4


title: CR2_RXRa_ChIP


title: Rat1-ChIP 2


title: LiCl_St9_1

source_name: LiCl treatment which expands organizer;Same batch with WE_St9_4


title: Rat1-ChIP 1


title: HFD1_PPARa_ChIP


title: bCatMO_St9_1

source_name: b-catenin knockdown which prevents organizer formation;Same batch with WE_St9_4


title: WE_St9_4


title: Rat1_4tUseq

value: expressing the FRB-tagged protein


title: Rat1-PAR-CLIP


title: CR1_PPARa_ChIP


title: Sia_St9_2

source_name: Embryos injected marginally with 100 pg sia mRNA;Same batch with WE_St9_5


title: Cer_St9_3

source_name: whole embryo injected with xCer L mRNA;Same batch with WE_St9_3


title: HFD1_RXRa_ChIP


title: Rat1-ChIP_input 2


title: RNA_seq_CR2


title: Wnt8_St9_3

source_name: whole embryo injected with xWnt8 mRNA;Same batch with WE_St9_3


title: RNA_seq_HFD2


title: Cer_St9_2

source_name: whole embryo injected with xCer L mRNA;Same batch with WE_St9_2


title: RNA_seq_CR3


title: RNA_seq_HFD1


title: WE_St9_3


title: RNA_seq_CR1


title: Wnt8_St9_2

source_name: whole embryo injected with xWnt8 mRNA;Same batch with WE_St9_2


title: Cer_St9_1

source_name: whole embryo injected with xCer L mRNA;Same batch with WE_St9_1


title: WE_St9_2


title: RNA_seq_ND2


title: Wnt8_St9_1

source_name: whole embryo injected with xWnt8 mRNA;Same batch with WE_St9_1


title: RNA_seq_ND3


title: WE_St9_1


title: RNA_seq_ND1


title: CR1_RXRa_ChIP


title: Wnt8_St10.5_2

source_name: whole embryo injected with xWnt8 mRNA, st10.5;Same batch with WE_St10.5_5


title: Cer_St10.5_2

source_name: whole embryo injected with xCer L mRNA, st10.5;Same batch with WE_St10.5_5


title: Wnt8_St10.5_3

source_name: whole embryo injected with xWnt8 mRNA, st10.5;Same batch with WE_St10.5_6


title: WE_St10.5_6

source_name: whole embryo at st10.5


title: WE_St10.5_5


title: Wnt8_St10.5_1

source_name: whole embryo injected with xWnt8 mRNA, st10;Same batch with WE_St10.5_4


title: Cer_St10.5_1

source_name: whole embryo injected with xCer L mRNA, st10;Same batch with WE_St10.5_4


title: Vhalf_St10.5_5

source_name: Vental halves of embryos cut at st8 and developed until st10.5

value: ventral half embryo


title: WE_St10.5_4


title: Cer_St10.5_3

source_name: whole embryo injected with xCer L mRNA, st10.5;Same batch with WE_St10.5_6


title: Dhalf_St10.5_5

source_name: Dorsal halves of embryos cut at st8 and developed until st10.5

value: dorsal half embryo


title: Vhalf_St10.5_4


title: Dhalf_St10.5_3


title: Dhalf_St10.5_4


title: Dhalf_St10.5_2


title: LiCl_St10.5_2

source_name: LiCl treatment which expands organizer;Same batch with WE_St10.5_3


title: Vhalf_St10.5_2


title: WE_St10.5_3

source_name: WE=whole embryo at early gastrula


title: Dhalf_St10.5_1


title: WE_St10.5_2


title: Sia_St10.5_1

source_name: Embryos injected marginally with 100 pg sia mRNA;Same batch with WE_St10.5_2


title: bCatMO_St10.5_2

source_name: b-catenin knockdown which prevents organizer formation;Same batch with WE_St10.5_2


title: bCatMO_St10.5_1

source_name: b-catenin knockdown which prevents organizer formation;Same batch with WE_St10.5_1


title: WE_St10.5_1


title: Vhalf_St10.5_3


title: Sia_St10.5_2

source_name: Embryos injected marginally with 100 pg sia mRNA;Same batch with WE_St10.5_3


title: bCatMO_St10.5_3

source_name: b-catenin knockdown which prevents organizer formation;Same batch with WE_St10.5_3


title: inbred pigmented (J Strain) offspring

city: Boston

first: Leonid

last: Peshkin

address: 200 Longwood Ave

department: Systems Biology

institute: Harvard Medical School

description: JJ

data_processing:
Casava version 1.8.2 was used for base calling, samples were adapter/quality trimmed using Trimmomatic.
Ribosomal reads were removed and remaining high quality paired reads were aligned to reference set using tophat,
allowing up to 5 mismatches, read-gap length of 3, and edit-distance of 5.  We used samtools mpileup tool to discard any ambiguous or low quality maps
and processed the output with bcftools (Li et al., 2009)  to obtain and characterize variant calls by depth and quality.
The variants were further annotated as synonymous or missense using SNPeff  software and further qualified as benign or damaging using PolyPhen-2 web server.
Genome_build: JGI v9.1; http://gbrowse.xenbase.org/fgb2/gbrowse/xl9_1/
Supplementary_files_format_and_content: variant call files (vcf) containing variant call positions; polymorphism data: where the sequences differ from the reference genome (JGI v9.1)
Supplementary_files_format_and_content: LaevisBB.ovr30.vcf - the Variant Call File for the B-strain
Supplementary_files_format_and_content: LaevisJJ.ovr30.vcf - the Variant Call File for the J-strain
Supplementary_files_format_and_content: LaevisF1.ovr30.vcf - the Variant Call File for the F1 samples
Supplementary_files_format_and_content: Xlav91.name.L.S.tsv - the list of paired allo-alleles with respective gene names
Supplementary_files_format_and_content: xenopus4.pph.humvar - the raw output of PolyPhen annotation, one line per SNP
Supplementary_files_format_and_content: pph.perGene.HV.withSynCnts.txt - the aggregated result of PolyPhen annotation, one line per gene

source_name: Xenopus laevis, whole embryos

growth_protocol: embryos were raised in 0.1 X MMR containing gentamycin

extract_protocol:
total RNA was extracted using TRIzol and phase-lock tubes
libraries were constructed using RNA enriched for mRNA by rRNA depletion using the EpiCenter RiboZero kit and the EpiCenter ScripSeq kit V2 using 50ng input RNA, and 12 cycles amplification

treatment_protocol: embryos were snap frozen in liquid nitrogen at the desired stage, and stored at -80 until extraction

value: inbred pigmented; BxB

tag: developmental timepoint

value: stage NF 42

value: whole embryos


title: inbred albino x inbred pigmented (J Strain) offspring (ie mating two different inbred populations)

description: XX

value: offspring from inbred albino x inbred pigmented mating (ie two different inbred populations); BxJ, JxB


title: MtbRaGyr

city: Bangalore

first: Valakunja

last: Nagaraja

state: Karnataka

address: C V Raman Avenue

department: Department of Microbiology and Cell Biology

country: India

institute: Indian Institute of Science (IISc)

description: Chromatin immunoprecipitation against Gyrase A subunit

data_processing:
Data processing Illumina Casava1.7 software used for basecalling.
Sequenced reads were mapped to M.tb H37Rv genome (NCBI accession NC_000962.2)
Mapping done using the Bowtie2 program (Version = 2.0.5) with default parameters
Coverage calculated using Bedtools (Version : 2.17.0)
Genome_build: M.tb H37Rv genome (NCBI accession NC_000962.2)
Supplementary_files_format_and_content: *.txt: Coverage calculated using Bedtools (Version : 2.17.0). Column 4: Genome coordinates, Column 5: Read depth.

organism: Mycobacterium tuberculosis H37Ra

source_name: Log/exponential phase Mtb H37Ra cells

growth_protocol: Mycobacterium tuberculosis H37Ra was grown at 37°C in 7H9 broth (Difco) supplemented with 0.2% glycerol, 0.05% Tween 80 and 10% albumin-dextrose-catalase (ADC, Middlebrook) or on 7H10 plates supplemented with 0.5% glycerol and 10% oleic acid-albumin-dextrose-catalase (OADC, Middlebrook). Logarithmic-phase cultures (exponential phase) were harvested at an optical density (OD600) of 0.4-0.6.

extract_protocol:
Crosslinked bacteria cells were sonicated and protein-DNA complexes were isolated with No antibody (Mock) or anti-TopoI or anti-gyrA antibodies.
Libraries were prepared according to Illumina's instructions.

treatment_protocol: M. tuberculosis cultures, either in exponential or stationary phase, were cross-linked with 1% formaldehyde for ten minutes at 37°C.

value: anti-gyrA (generated in-house, lot# VNMUH1996)

tag: growth phase

value: Exponential


title: inbred albino offspring

description: BB

value: inbred albino; JxJ


title: Mock

description: Mock immunoprecipitation (Control)


title: NOMO1-cntl

data_processing:
Basecalls performed using TOPHAT
Sequenced reads were  mapped to the reference genome using TOPHAT
Fragments Per Kilobase Of Exon Per Million Fragments Mapped
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file includes FPKM values. Columns are: Chromosome, Start location, Stop location, Gene, FPKM

source_name: NOMO1, MLL-AF9 AML cell line

growth_protocol: For lentiviral production, HEK 293T cells were used. The day prior to transfection, 2.5 X 106 cells were seeded in DMEM media (Gibco) containing 10% FBS, 1% penicillin/streptomycin and 10mM HEPES. The co-transfection was performed using 6μg of DNA for each vector. Cells were incubated at 37oC, 5% CO2 overnight and the media was changed the following day and lentiviral particles were collected 36h post-transfection.

tag: manipulation of cell lines, lentivirus kd

value: lentivirus scramble

tag: cell line


title: NOMO1-shRET

value: lentivirus RET-KD


title: LiCl_St10.5_1

source_name: LiCl treatment which expands organizer;Same batch with WE_St10.5_1

value: Nasco


title: Vhalf_St10.5_1


title: mRNA_A549_siKLF10+TGFb_B

status: Public on Mar 14 2017

city: Goettingen

first: Steven

middle: A.

last: Johnsen

address: Robert-Koch-Straße 40

department: Department of General, Visceral and Pediatric Surgery

institute: University Medical Center Goettingen

data_processing:
The FASTQ  files were mapped to the human genome (assembly hg19) using TopHat Gapped-read mapper for RNA-seq data with very-sensitive BOWTIE2 settings on Galaxy Platform (Version 0.9). The read counting was performed via HTSeq (version 0.6.0) with following parameters: -f bam -r pos -s reverse -a 10 -t exon -m union. The count files were subsequently subjected for differential analysis using the DESeq2 Package on R (Bioconductor version 3.2.2).
Genome_build: hg19
Supplementary_files_format_and_content: The provided mRNA-Seq analysis files in .csv format represent the differential gene expression analysis results obtained by DESeq2.

growth_protocol: A549 and Panc1 cells were maintained in phenol red-free Dulbecco’s Modified Eagle’s Media/F12 (DMEM/F12; Invitrogen) supplemented with 10% fetal bovine serum and 1x penicillin/streptomycin (Sigma-Aldrich) at 37°C under 5% CO2.

extract_protocol:
The total cell RNA was isolated with standard TRIzol extraction protocol.
For mRNA-Seq, 1 µg of total cell RNA was subjected to mRNA enrichment by NEXTflex Poly(A) Beads Protocol which was then used for library preparation with NEXTflex Rapid Directional mRNA-Seq from Bioo Scientific.

treatment_protocol: A549 and Panc1 cells were treated with 5 ng/ml TGFβ (R&D systems) for 72 hours.

tag: immortalization type

value: SV40 large T antigen immortalized


title: mRNA_A549_siKLF10_A


title: mRNA_A549_siKLF10_B


title: Monomac1-cntl

source_name: Monomac, MLL-AF9 AML cell line

value: Monomac


title: Kg1a-shRET

source_name: Kg1a, AML cell line


title: Kg1a-cntl


title: MtbRaTopoI

description: Chromatin immunoprecipitation against Topoisomerase I

value: anti-TopoI, monoclonal (generated in-house, lot# VNMNL2012)


title: Thp1-cntl

source_name: Thp1, MLL-AF9 AML cell line


title: Thp1-shRet


title: mRNA_A549_TGFb_A


title: mRNA_A549_siCont_B


title: mRNA_A549_siKLF10+TGFb_A


title: mRNA_A549_siCont_A


title: mRNA_Panc1_siKLF10+TGFb_C


title: mRNA_Panc1_siKLF10+TGFb_A


title: mRNA_Panc1_siKLF10+TGFb_B


title: mRNA_Panc1_siKLF10_B


title: mRNA_Panc1_siKLF10_A


title: mRNA_Panc1_siKLF10_C


title: mRNA_Panc1_TGFb_C


title: mRNA_A549_TGFb_B


title: Monomac1-shRET


title: mRNA_Panc1_TGFb_B


title: A549_H3K9ac_siKLF10+TGFb_A

data_processing:
The FASTQ files were mapped to the human reference genome (assembly hg19) using BOWTIE2 with very-sensitive presets in end-to-end mode on Galaxy Platform (version 2.2.6). The resulting BAM files of ChIPs were deduplicated with RmDup Samtools (Galaxy version 2.0). The corresponding BAM files of the replicates were merged. The merged BAM files were normalized to fragments (reads) per kilobase per million (RPKM) using the bamCoverage tool on Deeptools Galaxy (version 1.1.4) with removal of duplicates (ignoreDuplicates).
Genome_build: hg19
Supplementary_files_format_and_content: bigwig represent the normalized RPKM values of ChIP-seq signal

growth_protocol: A549 cells were maintained in phenol red-free Dulbecco’s Modified Eagle’s Media/F12 (DMEM/F12; Invitrogen) supplemented with 10% fetal bovine serum and 1x penicillin/streptomycin (Sigma-Aldrich) at 37°C under 5% CO2.

extract_protocol:
The ChIP was performed with 15 min (for KLF10) and 10 min (for histone modifications) crosslinking in 1 % formaldehyde in PBS. Following chromatin shearing , 1µg antibody was used for immunoprecipitation overnight. The immunocomplexes were incubated 2 additional hours with protein A sepharose beads and subjected to washes. After reversing the cross-linking, the DNA was isolated by standard phenol-chloroform-isoamyl extraction procedure.
ChIP-Seq libraries were prepared with MicroPlex Library Preparation Kit following the manufacturer's instructions.

treatment_protocol: A549 cells were treated with 5 ng/ml TGFβ (R&D systems) for 72 hours

tag: fraction

value: ChIP DNA

tag: chip antibody( company, cat.#, clone)

value: Diagenode, C15410004


title: mRNA_Panc1_siCont_A


title: mRNA_Panc1_siCont_C


title: A549_H3K9ac_TGFb_A


title: A549_H3K27ac_siKLF10+TGFb_C

value: Diagenode, C15410196


title: A549_H3K27ac_siKLF10+TGFb_A


title: A549_H3K27ac_TGFb_C


title: A549_H3K9ac_Control_B


title: A549_H3K9ac_siKLF10_B


title: A549_H3K9ac_TGFb_B


title: A549_H3K9ac_siKLF10+TGFb_B


title: A549_H3K27ac_siKLF10+TGFb_B


title: A549_H3K27ac_siKLF10_A


title: A549_H3K27ac_Control_C


title: A549_H3K9ac_Control_A.


title: A549_H3K27ac_Control_B


title: A549_H3K27ac_siKLF10_C


title: mRNA_Panc1_TGFb_A


title: mRNA_Panc1_siCont_B


title: A549_KLF10_C

value: Abcam, ab184182


title: A549_KLF10_A


title: A549_KLF10_B


title: A549_H3K9ac_siKLF10_A


title: A549_H3K27ac_TGFb_A


title: A549_H3K27ac_TGFb_B


title: A549_Input_A


title: mRNA_PANC1_TGFb+4SC-202_A

growth_protocol: L3.6 cells were maintained in Minimum Essential Media (MEM, Invitrogen) supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin (Sigma-Aldrich) as previously described (Herreros-Villanueva et al., 2013). BXPC3 cells were grown in RPMI-1640 media supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin. PANC1 cells were grown in DMEM/F14 media supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin.

treatment_protocol: Cells were treated with DMSO or 4SC-202 (1 µg/ml) and/or TGFβ (5 ng/ml) for 24 or 72 hours.


title: mRNA_PANC1_TGFb+4SC-202_C


title: mRNA_PANC1_4SC-202_B


title: mRNA_PANC1_TGFb_A


title: mRNA_PANC1_4SC-202_C


title: mRNA_PANC1_TGFb+4SC-202_B


title: mRNA_PANC1_TGFb_B


title: mRNA_PANC1_4SC-202_A


title: mRNA_BXPC3_4SC-202_C


title: mRNA_PANC1_DMSO_C


title: mRNA_PANC1_TGFb_C


title: mRNA_PANC1_DMSO_B


title: mRNA_PANC1_DMSO_A


title: mRNA_BXPC3_4SC-202_A


title: mRNA_BXPC3_4SC-202_B


title: mRNA_BXPC3_DMSO_C


title: A549_H3K27ac_Control_A


title: mRNA_L3.6_4SC-202_C


title: A549_Input_B


title: mRNA_BXPC3_DMSO_A


title: A549_Input_C


title: mRNA_BXPC3_DMSO_B


title: mRNA_L3.6_4SC-202_A


title: mRNA_L3.6_DMSO_B


title: mRNA_L3.6_DMSO_C


title: 4SC-202_H3K4me3_A

description:
ChIP DNA
processed data file: Merged_4SC-202_H3K4me3.bigwig

growth_protocol: L3.6 cells were maintained in Minimum Essential Media (MEM, Invitrogen) supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin (Sigma-Aldrich) as previously described (Herreros-Villanueva et al., 2013).

extract_protocol:
The ChIP was performed with 10 min crosslinking in 1 % formaldehyde in PBS. Following chromatin shearing , 1-2µg antibody was used for immunoprecipitation overnight. The immunocomplexes were incubated 2 additional hours with protein A sepharose beads and subjected to washes. After reversing the cross-linking, the DNA was isolated by standard phenol-chloroform-isoamyl extraction procedure.
ChIP-Seq libraries were prepared with MicroPlex Library Preparation Kit following the manufacturer's instructions.

treatment_protocol: Cells were treated with DMSO or 4SC-202 (1 µg/ml) for 24 hours

tag: chip antibody (company, cat.#, clone)

value: Diagenode, C15410003


title: mRNA_L3.6_DMSO_A


title: DMSO_H3K4me3_C

description:
ChIP DNA
processed data file: Merged_DMSO_H3K4me3.bigwig


title: DMSO_H3K4me3_B


title: 4SC-202_H3K27ac_A

description:
ChIP DNA
processed data file: Merged_4SC-202_H3K27ac.bigwig


title: DMSO_H3K27ac_C

description:
ChIP DNA
processed data file: Merged_DMSO_H3K27ac.bigwig


title: DMSO_H3K27ac_B


title: 4SC-202_Input_C

description: genomic DNA

value: none (input)


title: DMSO_H3K4me3_A


title: 4SC-202_Input_B

description: genomic DNA


title: DMSO_H3K27ac_A


title: 4SC-202_H3K27ac_B


title: DMSO_Input_B

description: genomic DNA


title: DMSO_Input_A

description: genomic DNA


title: Lgr5_high_751P_10_SCBC-39

city: Barcelona

first: Gustavo

last: Rodriguez-Esteban

state: Catalonia

address: C. Baldiri Reixac, 4; Barcelona Science Park

department: Development

country: Spain

institute: Centro Nacional de Análisis Genómico

description: Lgr5 GFP/+ mice

data_processing:
Illumina Real-Time Analysis (RTA) 1.18.66.3 software used for basecalling.
Sequenced reads were filtered for low-complexity or low-quality sequence.
Libraries were mapped as single-end reads with the GEMTools 1.7.0 RNA pipeline on the mouse reference genome.
Gene quantification was performed using UMI corrected transcript information to correct for amplification biases.
Genome_build: Gencode release M8, assembly GRCm38.p4
Supplementary_files_format_and_content: Tab-separated values (.tsv) file containing gene expression values (rows) as UMI counts (MARS-Seq) for each cell (columns).

source_name: small intestinal epithelium

growth_protocol: Lgr5::EGFP-IRES-Cre-ERT2 mice were obtained from the laboratory of Dr. Hans Clevers. Cyp1a1::H2B-YFP mice were obtained from the laboratory of Dr. Douglas J. Winton. Mice were housed and bred according to IRB Barcelona and PCB institutional guidelines.

extract_protocol:
Intestinal crypt cells were purified as previously described (Merlos-Suárez et al., 2011). Proximal small intestines (duodenum and jejunum) were dissected from age and sex-matched mice and cut open longitudinally. They were later incubated with HBSS EDTA (8 mM) for 5 min at room temperature. After this incubation, intestines were shaken vigorously to remove villi and the first supernatant was discarded. The intestines were then incubated with HBSS EDTA on ice for 15 min, after which shaking was repeated. This yielded the first crypt fraction. This process was repeated twice and after microscopic inspection of the samples the fractions enriched in crypts were kept (usually fractions 2 and 3). These fractions were then pooled together for each mouse, centrifuged at 1200 rpm for 5 min (4 ºC) and filtered through a 70 μm mesh (BD Biosciences) to further remove villi. Filtered fractions were enzymatically disaggregated by adding dispase (0.4 mg/mL, Gibco) and incubated for 20 min at 37ºC. The media was then supplemented with 5% FBS (Gibco) to neutralize dispase and the samples were filtered through a 40 μm mesh. For intestinal LRC analysis in compound mice, single cells were stained with an APC-conjugated antibody raised against EphB2 (Clone mAb 2H9, 6 µg/mL, BD). Cells were stained with DAPI (1 µg/mL, Sigma Aldrich) to exclude dead cells. The single-cell preparations of small intestinal crypts were analyzed by flow cytometry in a FACS Aria 2.0 (BD). Data was analyzed with FACSDiva software (BD) or FlowJo for EdU retention assays.
Isolation of single cells, cDNA synthesis and amplification were performed on the C1 mRNA Seq HT IFCs (Fluidigm) with the SMARTer Ultra Low RNA Kit (Clonetech). 400 capture sites on a C1 HT IFC medium chip (10-17μm). Spike-in artificial transcripts (ERCC RNA Spike-In Mix, Ambion) from The External RNA Controls Consortium were added during sample preparation as internal control to supported subsequent quality control steps (Baker et al., 2005). Quantity and quality of cDNA were assessed with a High Sensitivity DNA Chip (Agilent Technologies). Libraries were generated by Nextera XT DNA Sample Prep Kit (Illumina) and sequenced on a HiSeq 2500 (Illumina) using 100-bp mode of Truseq Rapid SBS kit v2. Sequencing was carried out as paired-end reads. Read one (12 bp) contained cell and unique molecular barcodes (Islam et al., 2014; Kivioja et al., 2012); read two (85 bp) contained the transcript sequence. Primary data analysis was carried out with the standard Illumina pipeline. Fluidigm C1 HT-Seq technology includes a two-level indexing system, which allows the multiplexed sequencing of multiple single cells and library pools. Here, we processed 10 libraries (up to 40 cells per library) of Lgr5-high cells.

treatment_protocol: For lineage tracing from the Lgr5GFP/+ model, 1 dose of diluted Tamoxifen (2 mg/kg) was used to ensure tracing from single cell conditions.

tag: cell type

value: Lgr5 intestinal stem cells (ISCs)


title: 4SC-202_Input_A

description: genomic DNA


title: Lgr5_high_751P_10_SCBC-36

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_10_SCBC-38

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_10_SCBC-37

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_10_SCBC-35

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_10_SCBC-34

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_10_SCBC-33

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_10_SCBC-32

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_10_SCBC-31

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_10_SCBC-30

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_10_SCBC-29

description: Lgr5 GFP/+ mice


title: DMSO_Input_C

description: genomic DNA


title: Lgr5_high_751P_10_SCBC-40

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_10_SCBC-28

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_10_SCBC-27

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_10_SCBC-26

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_10_SCBC-25

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_10_SCBC-23

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_10_SCBC-20

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_10_SCBC-21

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_10_SCBC-24

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_10_SCBC-18

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_10_SCBC-16

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_10_SCBC-17

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_10_SCBC-14

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_10_SCBC-15

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_10_SCBC-12

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_10_SCBC-13

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_10_SCBC-11

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_10_SCBC-10

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_10_SCBC-09

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_10_SCBC-06

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_10_SCBC-05

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_10_SCBC-04

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_10_SCBC-22

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_10_SCBC-19

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_10_SCBC-01

description: Lgr5 GFP/+ mice


title: 4SC-202_H3K4me3_C


title: Lgr5_high_751P_10_SCBC-03

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_10_SCBC-02

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_09_SCBC-39

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_09_SCBC-34

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_09_SCBC-37

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_09_SCBC-35

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_09_SCBC-36

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_09_SCBC-31

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_09_SCBC-33

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_09_SCBC-29

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_09_SCBC-28

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_09_SCBC-30

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_10_SCBC-08

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_09_SCBC-27

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_09_SCBC-26

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_09_SCBC-25

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_10_SCBC-07

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_09_SCBC-24

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_09_SCBC-23

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_09_SCBC-40

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_09_SCBC-20

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_09_SCBC-38

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_09_SCBC-22

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_09_SCBC-21

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_09_SCBC-17

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_09_SCBC-18

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_09_SCBC-16

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_09_SCBC-15

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_09_SCBC-14

description: Lgr5 GFP/+ mice


title: A549_H3K27ac_siKLF10_B


title: Lgr5_high_751P_09_SCBC-11

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_09_SCBC-10

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_09_SCBC-12

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_09_SCBC-19

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_09_SCBC-32

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_09_SCBC-08

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_09_SCBC-05

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_09_SCBC-03

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_09_SCBC-06

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_09_SCBC-01

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_09_SCBC-04

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_09_SCBC-02

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_08_SCBC-40

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_08_SCBC-36

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_08_SCBC-35

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_08_SCBC-39

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_08_SCBC-33

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_08_SCBC-34

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_09_SCBC-13

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_08_SCBC-30

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_08_SCBC-37

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_09_SCBC-07

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_08_SCBC-31

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_09_SCBC-09

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_08_SCBC-27

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_08_SCBC-29

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_08_SCBC-28

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_08_SCBC-32

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_08_SCBC-25

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_08_SCBC-23

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_08_SCBC-21

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_08_SCBC-22

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_08_SCBC-18

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_08_SCBC-16

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_08_SCBC-17

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_08_SCBC-15

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_08_SCBC-14

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_08_SCBC-20

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_08_SCBC-19

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_08_SCBC-13

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_08_SCBC-11

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_08_SCBC-12

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_08_SCBC-10

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_08_SCBC-08

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_08_SCBC-26

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_08_SCBC-09

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_08_SCBC-06

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_08_SCBC-04

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_08_SCBC-03

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_08_SCBC-05

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_08_SCBC-07

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_08_SCBC-38

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_08_SCBC-24

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_08_SCBC-01

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_08_SCBC-02

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_07_SCBC-38

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_07_SCBC-37

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_07_SCBC-39

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_07_SCBC-36

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_07_SCBC-40

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_07_SCBC-34

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_07_SCBC-33

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_07_SCBC-31

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_07_SCBC-32

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_07_SCBC-30

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_07_SCBC-29

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_07_SCBC-35

description: Lgr5 GFP/+ mice


title: mRNA_L3.6_4SC-202_B


title: Lgr5_high_751P_07_SCBC-28

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_07_SCBC-27

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_07_SCBC-26

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_07_SCBC-25

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_07_SCBC-23

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_07_SCBC-24

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_07_SCBC-21

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_07_SCBC-22

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_07_SCBC-19

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_07_SCBC-20

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_07_SCBC-18

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_07_SCBC-17

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_07_SCBC-12

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_07_SCBC-11

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_07_SCBC-10

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_07_SCBC-13

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_07_SCBC-16

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_07_SCBC-14

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_07_SCBC-15

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_07_SCBC-09

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_07_SCBC-07

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_07_SCBC-06

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_07_SCBC-04

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_07_SCBC-05

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_07_SCBC-02

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_07_SCBC-03

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_06_SCBC-40

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_06_SCBC-38

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_06_SCBC-36

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_06_SCBC-35

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_06_SCBC-34

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_06_SCBC-39

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_06_SCBC-32

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_06_SCBC-37

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_06_SCBC-31

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_06_SCBC-29

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_06_SCBC-26

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_06_SCBC-30

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_06_SCBC-23

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_06_SCBC-22

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_06_SCBC-25

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_06_SCBC-28

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_06_SCBC-21

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_06_SCBC-20

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_07_SCBC-08

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_06_SCBC-24

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_06_SCBC-27

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_06_SCBC-19

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_07_SCBC-01

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_06_SCBC-17

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_06_SCBC-18

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_06_SCBC-16

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_06_SCBC-33

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_06_SCBC-15

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_06_SCBC-14

description: Lgr5 GFP/+ mice


title: Lgr5_high_751P_06_SCBC-12

description: Lgr5 GFP/+ mice