title: Hematopoietic stem cell (HSC) 259


title: Hematopoietic stem cell (HSC) 264

status: Public on Apr 28 2022

type: SRA

city: Dresden

first: Alexander

last: Gerbaulet

state: Saxony

address: Fetscherstr. 74

department: Institute for Immunology

country: Germany

institute: Medical Faculty TU Dresden

library_source: transcriptomic

data_processing:
Alignment of the samples with GSNAP (version 2018–07-04) to the mm10 reference, and using Ensembl 87 for the support of splicesite detection
featureCounts (version1.6.2) was used to assign the reads to genes with the help of Ensembl 87 annotation
Genome_build: mm10

molecule: polyA RNA

organism: Mus musculus

source_name: bone marrow

extract_protocol:
Whole bone marrow cells were isolated by crushing long bones with mortar and pestle using PBS/2% FCS/2 mM EDTA and filtered through a 100 µm mesh. After erythrocyte lysis in hypotonic NH4Cl-buffer, cells were filtered through a 40 µm mesh. Hematopoietic lineage+ cells were removed with the lineage cell depletion kit (Miltenyi Biotec). Cells were incubated with antibodies in PBS / 2% FCS for 30 min, washed twice with PBS / 2% FCS. Single BM HSPC cells were sorted on an BD ARIA II SORP flow cytometer. Single hematopoietic stem and progenitor cells were index-sorted into 384 well plates containing 0.5 µl of nuclease free water with 0.2% Triton-X 100 and 4 U murine RNase Inhibitor (NEB), spun down and frozen at -80°C. After thawing, 0.5 µl of a primer mix were added (5 mM dNTP (Invitrogen), 0.5 µM dT-primer (C6 aminolinkerAAGCAGTGGTATCAACGCAGAGTCGACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTVN), 1 U RNase Inhibitor (NEB)). RNA was denatured for 3 minutes at 72°C and the reverse transcription (RT) was performed at 42°C for 90 min after filling up to 10 µl with RT buffer mix for a final concentration of 1x superscript II buffer (Invitrogen), 1 M betaine, 5 mM DTT, 6 mM MgCl2, 1 µM TSO-primer (AAGCAGTGGTATCAACGCAGAGTACATrGrGrG), 9 U RNase Inhibitor and 90 U Superscript II. After synthesis, the reverse transcriptase was inactivated at 70°C for 15 min. The cDNA was amplified using Kapa HiFi HotStart Readymix (Peqlab) at a final 1x concentration and 0.1 µM UP-primer (AAGCAGTGGTATCAACGCAGAGT) under following cycling conditions: initial denaturation at 98°C for 3 min, 23 cycles [98°C 20 sec, 67°C 15 sec, 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA was purified using 1x volume of hydrophobic Sera-Mag SpeedBeads (GE Healthcare) resuspended in a buffer consisting of 10 mM Tris, 20 mM EDTA, 18.5 % (w/v) PEG 8000 and 2 M sodium chloride solution. The cDNA was eluted in 12 µl nuclease free water and the concentration of the samples was measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates (Corning) using AccuBlue Broad range chemistry (Biotium).
For library preparation up to 700 pg cDNA was desiccated and rehydrated in 1 µl Tagmentation mix (1x TruePrep Tagment Buffer L, 0.1 µl TruePrep Tagment Enzyme V50; from TruePrep DNA Library Prep Kit V2 for Illumina; Vazyme) and tagmented at 55°C for 5 min. Subsequently, Illumina indices are added during PCR (72°C 3 min, 98°C 30 sec, 13 cycles [98°C 10 sec, 63°C 20 sec, 72°C 1 min], 72°C 5 min) with 1x concentrated KAPA Hifi HotStart Ready Mix and 300 nM dual indexing primers. After PCR, libraries are quantified with AccuBlue Broad range chemistry, equimolarly pooled and purified twice with 1x volume Sera-Mag SpeedBeads. This was followed by Illumina 50 bp paired-end sequencing on a Novaseq6000 aiming at an average sequencing depth of 0.5 mio reads per cell.

tag: col1a1 genotype

tag: rosa26 genotype

value: rtTA/rtTA

tag: doxycyclin induction

value: induced


title: Restricted hematopoietic progenitor 1 (HPC-1) 144

description:
raw_counts+metadata.csv
counts_filtered.csv
counts_filtered_normalized_log.csv
cell_metadata_filtered.csv


title: Hematopoietic stem cell (HSC) 257


title: Hematopoietic stem cell (HSC) 260


title: Hematopoietic stem cell (HSC) 261


title: Hematopoietic stem cell (HSC) 258


title: Multipotent Progenitor (MPP) 233


title: Multipotent Progenitor (MPP) 219


title: Multipotent Progenitor (MPP) 218


title: Multipotent Progenitor (MPP) 216


title: Multipotent Progenitor (MPP) 217


title: Multipotent Progenitor (MPP) 215


title: Multipotent Progenitor (MPP) 213


title: Restricted hematopoietic progenitor 1 (HPC-1) 146


title: Multipotent Progenitor (MPP) 212


title: Multipotent Progenitor (MPP) 214


title: Multipotent Progenitor (MPP) 211


title: Multipotent Progenitor (MPP) 209


title: Restricted hematopoietic progenitor 1 (HPC-1) 147


title: Multipotent Progenitor (MPP) 206


title: Multipotent Progenitor (MPP) 207


title: Multipotent Progenitor (MPP) 205


title: Multipotent Progenitor (MPP) 208


title: Restricted hematopoietic progenitor 1 (HPC-1) 143


title: Restricted hematopoietic progenitor 1 (HPC-1) 142


title: Restricted hematopoietic progenitor 1 (HPC-1) 140


title: Restricted hematopoietic progenitor 1 (HPC-1) 141


title: Restricted hematopoietic progenitor 1 (HPC-1) 138


title: Multipotent Progenitor (MPP) 210


title: Multipotent Progenitor (MPP) 220


title: Restricted hematopoietic progenitor 1 (HPC-1) 137


title: Restricted hematopoietic progenitor 1 (HPC-1) 139


title: Restricted hematopoietic progenitor 1 (HPC-1) 136


title: Restricted hematopoietic progenitor 1 (HPC-1) 133


title: Restricted hematopoietic progenitor 1 (HPC-1) 135


title: Restricted hematopoietic progenitor 1 (HPC-1) 134


title: Restricted hematopoietic progenitor 1 (HPC-1) 132


title: Restricted hematopoietic progenitor 1 (HPC-1) 130


title: Restricted hematopoietic progenitor 1 (HPC-1) 129


title: Restricted hematopoietic progenitor 1 (HPC-1) 131


title: Restricted hematopoietic progenitor 1 (HPC-1) 128


title: E34 Hematopoietic Stem Cell (E34 HSC) 47


title: E34 Hematopoietic Stem Cell (E34 HSC) 46


title: E34 Hematopoietic Stem Cell (E34 HSC) 44


title: E34 Hematopoietic Stem Cell (E34 HSC) 48


title: E34 Hematopoietic Stem Cell (E34 HSC) 43


title: E34 Hematopoietic Stem Cell (E34 HSC) 42


title: E34 Hematopoietic Stem Cell (E34 HSC) 38


title: E34 Hematopoietic Stem Cell (E34 HSC) 39


title: E34 Hematopoietic Stem Cell (E34 HSC) 36


title: E34 Hematopoietic Stem Cell (E34 HSC) 37


title: E34 Hematopoietic Stem Cell (E34 HSC) 41


title: E34 Hematopoietic Stem Cell (E34 HSC) 35


title: E34 Hematopoietic Stem Cell (E34 HSC) 33


title: E34 Hematopoietic Stem Cell (E34 HSC) 40


title: E34 Hematopoietic Stem Cell (E34 HSC) 34


title: Hematopoietic stem cell (HSC) 254


title: Hematopoietic stem cell (HSC) 256


title: Hematopoietic stem cell (HSC) 251


title: Hematopoietic stem cell (HSC) 252


title: Hematopoietic stem cell (HSC) 253


title: Hematopoietic stem cell (HSC) 247


title: Hematopoietic stem cell (HSC) 248


title: Hematopoietic stem cell (HSC) 255


title: Hematopoietic stem cell (HSC) 245


title: Hematopoietic stem cell (HSC) 244


title: Hematopoietic stem cell (HSC) 243


title: Hematopoietic stem cell (HSC) 242


title: E34 Hematopoietic Stem Cell (E34 HSC) 45


title: Megakaryocyte Progenitor (MkP) 157


title: Megakaryocyte Progenitor (MkP) 156


title: Hematopoietic stem cell (HSC) 241


title: Megakaryocyte Progenitor (MkP) 155


title: Megakaryocyte Progenitor (MkP) 154


title: Megakaryocyte Progenitor (MkP) 153


title: Megakaryocyte Progenitor (MkP) 151


title: Megakaryocyte Progenitor (MkP) 149


title: Megakaryocyte Progenitor (MkP) 152


title: Megakaryocyte Progenitor (MkP) 150


title: Megakaryocyte Progenitor (MkP) 147


title: Megakaryocyte Progenitor (MkP) 148


title: Megakaryocyte Progenitor (MkP) 145


title: Megakaryocyte Progenitor (MkP) 146


title: Megakaryocyte Progenitor (MkP) 144


title: Hematopoietic stem cell (HSC) 240


title: Hematopoietic stem cell (HSC) 246


title: Megakaryocyte Progenitor (MkP) 142


title: Megakaryocyte Progenitor (MkP) 143


title: Hematopoietic stem cell (HSC) 238


title: Hematopoietic stem cell (HSC) 239


title: Hematopoietic stem cell (HSC) 249


title: Hematopoietic stem cell (HSC) 236


title: Hematopoietic stem cell (HSC) 237


title: Hematopoietic stem cell (HSC) 250


title: Hematopoietic stem cell (HSC) 235


title: Hematopoietic stem cell (HSC) 232


title: Hematopoietic stem cell (HSC) 234


title: Hematopoietic stem cell (HSC) 233


title: Hematopoietic stem cell (HSC) 231


title: Hematopoietic stem cell (HSC) 227


title: Hematopoietic stem cell (HSC) 229


title: Hematopoietic stem cell (HSC) 226


title: Hematopoietic stem cell (HSC) 230


title: Hematopoietic stem cell (HSC) 225


title: lineage- kit+ CD150+ cell 35


title: lineage- kit+ CD150+ cell 34


title: lineage- kit+ CD150+ cell 36


title: lineage- kit+ CD150+ cell 32


title: lineage- kit+ CD150+ cell 37


title: Hematopoietic stem cell (HSC) 228


title: lineage- kit+ CD150+ cell 33


title: lineage- kit+ CD150+ cell 31


title: lineage- kit+ CD41- CD150- cell 41


title: lineage- kit+ CD41- CD150- cell 39


title: lineage- kit+ CD41- CD150- cell 40


title: lineage- kit+ CD41- CD150- cell 38


title: lineage- kit+ CD41- CD150- cell 35


title: Multipotent Progenitor (MPP) 204


title: lineage- kit+ CD41- CD150- cell 34


title: lineage- kit+ CD41- CD150- cell 37


title: lineage- kit+ CD41- CD150- cell 36


title: Multipotent Progenitor (MPP) 203


title: Multipotent Progenitor (MPP) 201


title: Multipotent Progenitor (MPP) 202


title: Multipotent Progenitor (MPP) 200


title: Megakaryocyte Progenitor (MkP) 132


title: Megakaryocyte Progenitor (MkP) 138


title: Megakaryocyte Progenitor (MkP) 141


title: Multipotent Progenitor (MPP) 197


title: Megakaryocyte Progenitor (MkP) 129


title: Multipotent Progenitor (MPP) 190


title: Megakaryocyte Progenitor (MkP) 133


title: Multipotent Progenitor (MPP) 192


title: Multipotent Progenitor (MPP) 198


title: Megakaryocyte Progenitor (MkP) 139


title: Megakaryocyte Progenitor (MkP) 134


title: Megakaryocyte Progenitor (MkP) 136


title: Multipotent Progenitor (MPP) 195


title: Megakaryocyte Progenitor (MkP) 135


title: Multipotent Progenitor (MPP) 199


title: Multipotent Progenitor (MPP) 196


title: Multipotent Progenitor (MPP) 191


title: Multipotent Progenitor (MPP) 194


title: Megakaryocyte Progenitor (MkP) 137


title: Megakaryocyte Progenitor (MkP) 130


title: Megakaryocyte Progenitor (MkP) 131


title: Megakaryocyte Progenitor (MkP) 128


title: Megakaryocyte Progenitor (MkP) 127


title: Megakaryocyte Progenitor (MkP) 125


title: Megakaryocyte Progenitor (MkP) 126


title: Multipotent Progenitor (MPP) 193


title: Megakaryocyte Progenitor (MkP) 140


title: Megakaryocyte Progenitor (MkP) 124


title: Megakaryocyte Progenitor (MkP) 123


title: Megakaryocyte Progenitor (MkP) 116


title: Megakaryocyte Progenitor (MkP) 117


title: Megakaryocyte Progenitor (MkP) 120


title: Megakaryocyte Progenitor (MkP) 121


title: Megakaryocyte Progenitor (MkP) 114


title: Megakaryocyte Progenitor (MkP) 113


title: Multipotent Progenitor (MPP) 180


title: Multipotent Progenitor (MPP) 181


title: Multipotent Progenitor (MPP) 185


title: Megakaryocyte Progenitor (MkP) 112


title: Multipotent Progenitor (MPP) 182


title: Multipotent Progenitor (MPP) 183


title: Megakaryocyte Progenitor (MkP) 111


title: Multipotent Progenitor (MPP) 186


title: Multipotent Progenitor (MPP) 188


title: Multipotent Progenitor (MPP) 184


title: Megakaryocyte Progenitor (MkP) 115


title: Multipotent Progenitor (MPP) 189


title: Megakaryocyte Progenitor (MkP) 119


title: Multipotent Progenitor (MPP) 179


title: Multipotent Progenitor (MPP) 178


title: Multipotent Progenitor (MPP) 177


title: Multipotent Progenitor (MPP) 187


title: Multipotent Progenitor (MPP) 176


title: Multipotent Progenitor (MPP) 175


title: Megakaryocyte Progenitor (MkP) 122


title: Multipotent Progenitor (MPP) 174


title: lineage- kit+ CD150+ cell 30


title: lineage- kit+ CD150+ cell 29


title: lineage- kit+ CD150+ cell 28


title: lineage- kit+ CD150+ cell 26


title: Megakaryocyte Progenitor (MkP) 118


title: lineage- kit+ CD150+ cell 27


title: lineage- kit+ CD41- CD150- cell 31


title: lineage- kit+ CD150+ cell 24


title: lineage- kit+ CD41- CD150- cell 32


title: lineage- kit+ CD150+ cell 25


title: lineage- kit+ CD150+ cell 23


title: lineage- kit+ CD41- CD150- cell 30


title: lineage- kit+ CD41- CD150- cell 27


title: Hematopoietic stem cell (HSC) 224


title: Hematopoietic stem cell (HSC) 221


title: Hematopoietic stem cell (HSC) 222


title: lineage- kit+ CD41- CD150- cell 29


title: lineage- kit+ CD41- CD150- cell 26


title: lineage- kit+ CD41- CD150- cell 28


title: Hematopoietic stem cell (HSC) 223


title: Hematopoietic stem cell (HSC) 215


title: Hematopoietic stem cell (HSC) 219


title: Hematopoietic stem cell (HSC) 220


title: Hematopoietic stem cell (HSC) 216


title: Hematopoietic stem cell (HSC) 217


title: Hematopoietic stem cell (HSC) 213


title: Hematopoietic stem cell (HSC) 212


title: Hematopoietic stem cell (HSC) 214


title: Hematopoietic stem cell (HSC) 211


title: Megakaryocyte Progenitor (MkP) 110


title: Megakaryocyte Progenitor (MkP) 109


title: Hematopoietic stem cell (HSC) 210


title: lineage- kit+ CD41- CD150- cell 25


title: Megakaryocyte Progenitor (MkP) 105


title: Megakaryocyte Progenitor (MkP) 101


title: Megakaryocyte Progenitor (MkP) 100


title: Megakaryocyte Progenitor (MkP) 107


title: Megakaryocyte Progenitor (MkP) 95


title: Hematopoietic stem cell (HSC) 218


title: Megakaryocyte Progenitor (MkP) 108


title: Megakaryocyte Progenitor (MkP) 104


title: Hematopoietic stem cell (HSC) 205


title: Megakaryocyte Progenitor (MkP) 96


title: Hematopoietic stem cell (HSC) 206


title: Hematopoietic stem cell (HSC) 202


title: Hematopoietic stem cell (HSC) 204


title: Hematopoietic stem cell (HSC) 200


title: Hematopoietic stem cell (HSC) 201


title: Hematopoietic stem cell (HSC) 199


title: Hematopoietic stem cell (HSC) 198


title: Hematopoietic stem cell (HSC) 197


title: Hematopoietic stem cell (HSC) 209


title: Hematopoietic stem cell (HSC) 196


title: Hematopoietic stem cell (HSC) 195


title: Megakaryocyte Progenitor (MkP) 102


title: Hematopoietic stem cell (HSC) 192


title: Hematopoietic stem cell (HSC) 193


title: Megakaryocyte Progenitor (MkP) 106


title: Megakaryocyte Progenitor (MkP) 99


title: Hematopoietic stem cell (HSC) 194


title: Hematopoietic stem cell (HSC) 190


title: Megakaryocyte Progenitor (MkP) 98


title: Hematopoietic stem cell (HSC) 191


title: Hematopoietic stem cell (HSC) 189


title: Hematopoietic stem cell (HSC) 207


title: Megakaryocyte Progenitor (MkP) 103


title: Hematopoietic stem cell (HSC) 180


title: Megakaryocyte Progenitor (MkP) 97


title: Hematopoietic stem cell (HSC) 179


title: Hematopoietic stem cell (HSC) 183


title: Hematopoietic stem cell (HSC) 208


title: Hematopoietic stem cell (HSC) 203


title: Hematopoietic stem cell (HSC) 182


title: Hematopoietic stem cell (HSC) 187


title: Hematopoietic stem cell (HSC) 181


title: Restricted hematopoietic progenitor 1 (HPC-1) 127


title: Hematopoietic stem cell (HSC) 177


title: Hematopoietic stem cell (HSC) 178


title: Restricted hematopoietic progenitor 1 (HPC-1) 126


title: Restricted hematopoietic progenitor 1 (HPC-1) 125


title: Restricted hematopoietic progenitor 1 (HPC-1) 124


title: Restricted hematopoietic progenitor 1 (HPC-1) 121


title: Hematopoietic stem cell (HSC) 188


title: Restricted hematopoietic progenitor 1 (HPC-1) 120


title: Hematopoietic stem cell (HSC) 186


title: Restricted hematopoietic progenitor 1 (HPC-1) 119


title: 457_Wang_input_BWX5349_CH_20uMIPTG1h

city: Bloomington

first: Xindan

last: Wang

state: IN

address: 1001 E 3rd St

department: Biology

country: USA

institute: Indiana University at Bloomington

library_source: genomic

data_processing:
Reads from each end of a DNA fragment were represented in each of the two FASTQ files generated by Illumina paired-end sequencing.
For Hi-C, we mapped reads in each FASTQ file back to the genome of A. tumefaciens C58 (NCBI Reference Sequence GCA_000092025.1) or 15955 (NCBI Reference sequence GCA_003666465.1) independently by Bowtie version 2.1.0 to preserve the order of reads. All the processing steps afterwards were performed using an in-house Perl scripts.  For ChIP-seq, we mapped reads in each FASTQ file back to the genome of A. tumefaciens C58 (NCBI Reference Sequence GCA_000092025.1) or Bacillus subtilis PY79 (NCBI Reference Sequence: NC_022898.1)  using CLC genomics workbench 8.0, and exported .csv file.
For Hi-C, the two resulting SAM files were then merged together. Unaligned reads were discarded.
For Hi-C, the A. tumefaciens C58 genome was divided into HindIII restriction fragments. Each aligned read was sorted into its corresponding restriction fragment. We inferred that a DNA fragment resulted from non-ligation or self-ligation if reads from both ends were from the same restriction fragment; these reads were discarded. Only DNA fragments for which the reads came from different restriction fragments were retained and used for construction of a Hi-C contact map.
For Hi-C, the genomes of A. tumefaciens C58 was then divided into bins 10 kb and the remaining reads were allocated to their corresponding bin. We then counted the number of fragments having reads with in different bins. A raw Hi-C contact map is the matrix of read counts in which each entry, mij, indicates the number of fragments with ends mapping to bins i and j. The raw Hi-C contact map/matrix is biased due to the uneven distribution of restriction enzyme sites and, to a lesser extent, differences in GC content and the mappability of individual reads. We normalized raw contact maps using an iterative normalization procedure (Imakaev et al., 2012 PMID: 22941365). Essentially, we converted the number of interactions, or read counts, into Hi-C scores by applying the following equation and iteratively repeating it for the resulting contact map after each cycle:  mij =mij * (total reads) / (total reads in bin i * total reads in bin j). The iterative procedure was repeated until the maximum relative error of the total number of Hi-C scores in a bin was less than 10-5. Resulting matrices were normalized so that Hi-C scores for each row and column sum to 1. Subsequent analysis and visualization was done using R scripts.
Genome_build: A. tumefaciens C58 GCA_000092025.1, A. tumefaciens 15955 GCA_003666465.1, Bacillus subtilis PY79 NC_022898.1
Supplementary_files_format_and_content: Files ending with .matrix.txt: tab-delimited text files of the iteratively-corrected Hi-C contact maps/matrices. Files ending with .csv: comma-separated values files of ChIP-seq results. Files inside the .zip files containing multiple  .csv files which are comma-separated values files of ChIP-seq results.

molecule: genomic DNA

organism: Bacillus subtilis PY79

source_name: Bacillus subtilis PY79

extract_protocol:
Hi-C experiments were performed using HindIII according to previous publications (Le et al, 2013, PMID: 24158908; Wang et al 2015, PMID: 26253537). ChIP-seq experiments were performed using anti-GFP, anti-mCherry antibodies according to previous publication (Graham et al 2014, PMID: 24829297).
Standard library construction protocol was used for Illumina Nextseq550 sequencing platforms. Illumina Truseq indexes were used.

treatment_protocol: Cells were growing in CH medium at 37˚C, IPTG was added to 20uM final concentration for 60 min, fixed by 3% formaldehyde for 30min at room temperature

tag: condition

value: CH, 37˚C, 20uM IPTG for 1h

tag: genotype

value: pelB::Psoj mCherry-parB1At tet, ycgO::Phyperspank mgfpmut3-repBCh2At cat, parS2At cluster at -91 degree


title: Hematopoietic stem cell (HSC) 184


title: Restricted hematopoietic progenitor 1 (HPC-1) 118


title: 456_Wang_ChIP_anti_mCherry_BWX5349_CH_20uMIPTG1h

tag: chip antibody

value: ChIP using anti-mCherry antibodies


title: Hematopoietic stem cell (HSC) 185


title: 453_Wang_ChIP_anti_mCherry_BWX5353_CH_20uMIPTG1h

value: pelB::Psoj mCherry-parB1At tet, ycgO::Phyperspank mgfpmut3-repBCh2At cat, parS2At cluster at -91 degree kan, parS{delta}9, {delta}parBBs spec


title: 455_Wang_ChIP_anti_GFP_BWX5349_CH_20uMIPTG1h

value: ChIP using anti-GFP antibodies


title: Restricted hematopoietic progenitor 1 (HPC-1) 117


title: Restricted hematopoietic progenitor 1 (HPC-1) 115


title: Restricted hematopoietic progenitor 1 (HPC-1) 116


title: Restricted hematopoietic progenitor 1 (HPC-1) 114


title: 454_Wang_input_BWX5353_CH_20uMIPTG1h


title: 451_Wang_ChIP_anti_GFP_BWX5341_CH_20uMIPTG1h

value: pelB::Psoj mCherry-parB1At tet, ycgO::Phyperspank mgfpmut3-repBCh2At cat, {delta}parBBs spec


title: 452_Wang_input_BWX5341_CH_20uMIPTG1h


title: Restricted hematopoietic progenitor 1 (HPC-1) 113


title: 449_Wang_ChIP_anti_GFP_BWX5359_CH_20uMIPTG1h

value: ycgO::Phyperspank mgfpmut3-repBCh2At cat, parS2At cluster at -91 degree kan, {delta}parBBs spec


title: Multipotent Progenitor (MPP) 173


title: 448_Wang_input_BWX5333_CH

treatment_protocol: Cells were growing in CH medium at 37˚C, fixed by 3% formaldehyde for 30min at room temperature

value: CH, 37˚C

value: pelB::Psoj mCherry-parB1At tet, parS2At cluster at -91 degree kan, {delta}parBBs spec


title: Multipotent Progenitor (MPP) 171


title: A4_F88_I1_glc, rep2

city: San Diego

first: Bernhard

middle: O.

last: Palsson

state: California

address: 9500 Gilman Dr

department: Bioengineering

institute: University of California, San Diego

description: Pseudomonas putida KT2440 grown in an M9 medium with 2.5 g/L glucose as a sole carbon source replicate 13

data_processing:
Raw RNA-Seq reads were mapped to the original reference genome using Bowtie and transcript abundance was analyzed using summarizeOverlaps (Lawrence et al., 2013). Calculation of transcripts per million (TPM) and prediction of differentially expressed genes were conducted using DESeq2 (Love et al., 2014).
Genome_build: AE015451.2
Supplementary_files_format_and_content: csv and log tpm

molecule: total RNA

organism: Pseudomonas putida KT2440

growth_protocol: All microbial cultures were conducted at 30 ˚C using the modified minimal M9 medium (4 g/L glucose, 2 g/L (NH4)2SO4, 6.8 g/L Na2HPO4, 3 g/L KH2PO4, 0.5 g/L NaCl, 2 mM MgSO4, 0.1 mM CaCl2, 500 μL/L 2000X trace element solution). The composition of the trace element solution is 4.5 g/L ZnSO4⋅7H2O, 0.7 g/L MnCl2⋅4H2O, 0.3 g/L CoCl2⋅6H2O, 0.2 g/L CuSO4⋅2H2O, 0.4 g/L Na2MoO4⋅2H2O, 4.5 g/L CaCl2⋅2H2O, 3.0 g/L FeSO4⋅7H2O, 1.0 g/L H3BO3, 0.1 g/L KI, 15 g/L disodium ethylenediaminetetraacetate. 2.5 g/L of a carbon source was used for the 12 samples used in the "Aromatic" project.

extract_protocol:
For transcriptomic analysis, cell cultures at the exponential phase (OD600 0.4-0.6) were mixed with two volumes of RNA protect Bacteria Reagent (Qiagen, Hilden, Germany) for stabilization and their total RNA was extracted by using Quick-RNA Fungal/Bacterial Miniprep Kit (Zymo Research). Residual genomic DNA was removed by incubating the samples with DNase I (RNase-free, NEB). Ribosomal RNA was removed by hybridizing with 30-bp oligonucleotides designed to bind the ribosomal RNA of KT2440 specifically and treating with Thermostable RNase H purchased from Lucigen (Middleton, WI, USA). The remaining oligonucleotides were removed by incubating the resulting samples with DNase I (NEB). The samples were purified by using an RNA Clean & Concentrator Kit (Zymo Research). The 12 samples for the “aromatic” project were prepared with several modifications. Collected cells were resuspended in TRIzolTM reagent (ThermoFisher Scientific, Waltham, MA, USA).  Total RNA was isolated using the RNeasy Mini Kit (Qiagen) by following the manufacturer’s instructions. Ribosomal RNA was removed from total RNA using the Ribo-Zero rRNA removal kit (illumina).
Paired-end RNA-Seq libraries were constructed using either KAPA RNA HyperPrep kit from Kapa Biosystems (Wilmington, MA, USA) or ScriptSeqTM Complete kit (illumina, CA, USA).

tag: atcc catalog number

value: Evolved KT2440 A4_F88_I1

tag: treatment (carbon sources)

value: 4 g/L glucose

tag: treatment (supplements)


title: Multipotent Progenitor (MPP) 170


title: Restricted hematopoietic progenitor 1 (HPC-1) 123


title: A3_F85_I1_glc, rep2

description: Pseudomonas putida KT2440 grown in an M9 medium with 2.5 g/L glucose as a sole carbon source replicate 11

value: Evolved KT2440 A3_F85_I1


title: Multipotent Progenitor (MPP) 169


title: Restricted hematopoietic progenitor 1 (HPC-1) 122


title: Multipotent Progenitor (MPP) 168


title: A3_F85_I1_glc, rep1

description: Pseudomonas putida KT2440 grown in an M9 medium with 2.5 g/L glucose as a sole carbon source replicate 10


title: Del_relA_glc, rep1

description: Pseudomonas putida KT2440 grown in an M9 medium with 2.5 g/L glucose as a sole carbon source replicate 8

value: KT2440 relA mutant


title: Multipotent Progenitor (MPP) 167


title: Del_relA_glc, rep2

description: Pseudomonas putida KT2440 grown in an M9 medium with 2.5 g/L glucose as a sole carbon source replicate 9


title: Multipotent Progenitor (MPP) 166


title: Multipotent Progenitor (MPP) 164


title: Wildtype_Flask_changed_aeration, rep1

description: Pseudomonas putida KT2440 grown in an M9 medium with 2.5 g/L glucose as a sole carbon source replicate 6

value: KT2440 wildtype


title: Wildtype_ionic_liquid_mixture, rep2

description: Pseudomonas putida KT2440 grown in an M9 medium with 2.5 g/L glucose as a sole carbon source replicate 5

value: 1% (w/v) triethanolamine acetate and triethylamine hydrogen sulfate


title: Multipotent Progenitor (MPP) 163

value: rtTA/rtTA


title: Multipotent Progenitor (MPP) 162

value: induced


title: Multipotent Progenitor (MPP) 160


title: Multipotent Progenitor (MPP) 161


title: Wildtype_ionic_liquid_mixture, rep1

description: Pseudomonas putida KT2440 grown in an M9 medium with 2.5 g/L glucose as a sole carbon source replicate 4


title: Multipotent Progenitor (MPP) 159


title: Setaria viridis (ME034V) seed head at 16 days after flowering replicate 2

city: Philadelphia

first: Diep

middle: R

last: Ganguly

state: PA

address: 433 S University Ave

department: Department of Biology

institute: University of Pennsylvania

data_processing:
Raw read quality was first diagnosed using FastQC (v0.11.2).
Trim Galore! was used for adapter and low-quality read trimming with PHRED score < 20 (-q 20).
Paired-end alignments were performed using trimmed reads using Subread (v1.6.2) with flags -t 0 and -u to report uniquely mapping reads, prior to sorting, indexing and compressing using Samtools (v1.2).
Transcript quantification was performed at the gene-level with the Setaria viridis gene annotation (v2.1) using featureCounts (with flag -s 0 for non-stranded quantification). This output was utilized for differential gene expression testing with edgeR (quasi-likelihood pipeline).
Genome_build: Setaria viridis v2.1, DOE-JGI, http://phytozome.jgi.doe.gov/
Supplementary_files_format_and_content: .counts: raw counts per gene-level feature for each sample.
Supplementary_files_format_and_content: .csv: matrix of normalized log2 FPKM per gene-level feature across all samples per ecotype

organism: Setaria viridis

source_name: ME034V seed head at 16 days after flowering

growth_protocol: Plants were grown in 1.7 L pots, soil mixture was Debco Green Wizard Premium Potting Mix in a Conviron PGC Flex growth Chamber with approx. 600 uE light intensity, 16 hr photoperiod, and day/night mean temperatures of 28°C / 20 °C, and 55% relative  humidity.

extract_protocol:
Total RNA was extracted using the Aurum™ Total RNA Fatty and Fibrous Tissue Kit.
PolyA RNA-sequencing libraries were generated using the Illumina TruSeq RNA Library Prep Kit v2.

tag: tissue

value: Seed head

tag: ecotype

tag: developmental stage

value: 16 days after flowering


title: Setaria viridis (ME034V) seed head at 16 days after flowering replicate 4


title: Setaria viridis (ME034V) seed head at 16 days after flowering replicate 3


title: 447_Wang_ChIP_anti_mCherry_BWX5333_CH

value: ChIP using anti-mCherry antibodies


title: Multipotent Progenitor (MPP) 158


title: Setaria viridis (ME034V) seed head at 16 days after flowering replicate 1


title: Hematopoietic stem cell (HSC) 176


title: Multipotent Progenitor (MPP) 165


title: Setaria viridis (ME034V) seed head at 8 days after flowering replicate 4

source_name: ME034V seed head at 8 days after flowering

value: 8 days after flowering


title: Setaria viridis (ME034V) seed head at 8 days after flowering replicate 3


title: Setaria viridis (ME034V) seed head at 8 days after flowering replicate 2


title: Hematopoietic stem cell (HSC) 175


title: Hematopoietic stem cell (HSC) 173


title: Hematopoietic stem cell (HSC) 172


title: Setaria viridis (ME034V) seed head at 8 days after flowering replicate 1


title: Multipotent Progenitor (MPP) 172


title: Hematopoietic stem cell (HSC) 170


title: Hematopoietic stem cell (HSC) 171


title: Setaria viridis (ME034V) seed head at anthesis replicate 2

source_name: ME034V seed head at anthesis

value: Anthesis


title: Hematopoietic stem cell (HSC) 169


title: Wildtype_Flask_changed_aeration, rep2

description: Pseudomonas putida KT2440 grown in an M9 medium with 2.5 g/L glucose as a sole carbon source replicate 7


title: Setaria viridis (ME034V) seed head at anthesis replicate 1


title: Hematopoietic stem cell (HSC) 167


title: Hematopoietic stem cell (HSC) 168


title: 450_Wang_input_BWX5359_CH_20uMIPTG1h

value: CH, 37˚C, 20uM IPTG for 1h


title: Setaria viridis (ME034V) seed head at anthesis replicate 3


title: Setaria viridis (ME034V) seed head at 50% emergence replicate 3

source_name: ME034V seed head at 50% emergence

value: 50% seed head emergence


title: Hematopoietic stem cell (HSC) 174


title: Setaria viridis (ME034V) seed head at 50% emergence replicate 2


title: Hematopoietic stem cell (HSC) 165


title: Setaria viridis (ME034V) seed head at 50% emergence replicate 1


title: Hematopoietic stem cell (HSC) 164


title: Setaria viridis (A10) seed head at 16 days after flowering replicate 4

source_name: A10 seed head at 16 days after flowering


title: Hematopoietic stem cell (HSC) 163


title: Hematopoietic stem cell (HSC) 162


title: Hematopoietic stem cell (HSC) 161


title: Restricted hematopoietic progenitor 1 (HPC-1) 111


title: Restricted hematopoietic progenitor 1 (HPC-1) 112


title: Setaria viridis (ME034V) seed head at 50% emergence replicate 4


title: Setaria viridis (A10) seed head at 16 days after flowering replicate 3


title: Setaria viridis (A10) seed head at 16 days after flowering replicate 2


title: Setaria viridis (A10) seed head at 16 days after flowering replicate 1


title: Restricted hematopoietic progenitor 1 (HPC-1) 110


title: Restricted hematopoietic progenitor 1 (HPC-1) 109


title: WR2721+IR_W-Br-6h

type: RNA

city: Beijing

first: Zhang

middle: Xiao

last: Chang

address: Taiping 27 Road

country: China

institute: Beijing Institute of Radiation Medicine

description: This sample was brain sample of mice in the WR2721 administration group 6 hours after irradiation.

hyb_protocol: Hybridization was performed by Bioassay Laboratory of CapitalBio Corporation，Beijing, following their standard operating protocol. See http:www.capitalbio.com.

scan_protocol: Scan  was performed by Bioassay Laboratory of CapitalBio Corporation，Beijing, following their standard operating protocol. See http:www.capitalbio.com.

data_processing:
After data correction, such as normalization of signal value with RMA, SAM4.0 software was used for analysis.
FDR was controlled within 5%, and differential expression genes were screened by 2 or 1.5 times standard.

source_name: C57BL/6J wild mice

label_protocol: Labeling was performed by Bioassay Laboratory of CapitalBio Corporation，Beijing, following their standard operating protocol. See http:www.capitalbio.com.

growth_protocol: Mice were divided into normal control group, drug control group, radiation control group, drug irradiation group, radiation control group. Mice in the radiation control group and drug irradiation group were given 6.5 Gy 60Co γ -ray 30 min after administration.

extract_protocol: Total RNA was extracted from tissues by appropriate methods and purified with NucleoSpin RNA clean-up Kit (Macherey-Nagel, Germany), quantified by spectrophotometer and inspected by formaldehyde denaturing gel electrophoresis.

treatment_protocol: Bone marrow and brain tissues of mice in each group were collected 6 h, 7 days and 14 days after irradiation

value: Brain

tag: treat

tag: time


title: Setaria viridis (ME034V) seed head at anthesis replicate 4


title: Restricted hematopoietic progenitor 1 (HPC-1) 108


title: WR2721+IR_W-Br-7d

description: This sample was brain sample of mice in the WR2721 administration group 7 days after irradiation.


title: Restricted hematopoietic progenitor 1 (HPC-1) 107


title: Setaria viridis (A10) seed head at 8 days after flowering replicate 4

source_name: A10 seed head at 8 days after flowering


title: WR2721_WG-Br-7d

description: This sample was brain sample of mice 7 days after administration of WR2721 without irradiation.


title: Restricted hematopoietic progenitor 1 (HPC-1) 106


title: Restricted hematopoietic progenitor 1 (HPC-1) 104


title: Setaria viridis (A10) seed head at 8 days after flowering replicate 3


title: Restricted hematopoietic progenitor 1 (HPC-1) 105


title: Hematopoietic stem cell (HSC) 166


title: WR2721_WG-Br-6h

description: This sample was brain sample of mice 6 hours after administration of WR2721 without irradiation.


title: TPO+IR_T-Br-7d

description: This sample was brain sample of mice in the TPO administration group 7 days after irradiation.

value: TPO+IR


title: Restricted hematopoietic progenitor 1 (HPC-1) 103


title: Setaria viridis (A10) seed head at 8 days after flowering replicate 2


title: A4_F88_I1_glc, rep1

description: Pseudomonas putida KT2440 grown in an M9 medium with 2.5 g/L glucose as a sole carbon source replicate 12

value: Evolved KT2440 A4_F88_I1


title: TPO+IR_T-Br-6h

description: This sample was brain sample of mice in the TPO administration group 6 hours after irradiation.


title: Restricted hematopoietic progenitor 1 (HPC-1) 102

description:
raw_counts+metadata.csv
counts_filtered.csv
counts_filtered_normalized_log.csv
cell_metadata_filtered.csv


title: Restricted hematopoietic progenitor 1 (HPC-1) 98


title: Restricted hematopoietic progenitor 1 (HPC-1) 100


title: Setaria viridis (A10) seed head at anthesis replicate 3

source_name: A10 seed head at anthesis


title: TPO_TG-Br-7d

description: This sample was brain sample of mice 7 days after administration of TPO without irradiation.

value: TPO


title: Restricted hematopoietic progenitor 1 (HPC-1) 99


title: Setaria viridis (A10) seed head at anthesis replicate 4


title: Restricted hematopoietic progenitor 1 (HPC-1) 97


title: Setaria viridis (A10) seed head at 8 days after flowering replicate 1


title: Multipotent Progenitor (MPP) 157


title: Multipotent Progenitor (MPP) 156


title: Setaria viridis (A10) seed head at anthesis replicate 2


title: TPO_TG-Br-6h

description: This sample was brain sample of mice 6 hours after administration of TPO without irradiation.


title: Nilestriol+IR_E-Br-7d

description: This sample was brain sample of mice in the Nilestriol administration group 7 days after irradiation.

value: Nilestriol+IR


title: Multipotent Progenitor (MPP) 155


title: Multipotent Progenitor (MPP) 153


title: Multipotent Progenitor (MPP) 154


title: Setaria viridis (A10) seed head at anthesis replicate 1


title: Setaria viridis (A10) seed head at 50% emergence replicate 4

source_name: A10 seed head at 50% emergence


title: Multipotent Progenitor (MPP) 152


title: Nilestriol+IR_E-Br-6h

description: This sample was brain sample of mice in the Nilestriol administration group 6 hours after irradiation.


title: Multipotent Progenitor (MPP) 151


title: Setaria viridis (A10) seed head at 50% emergence replicate 3


title: Multipotent Progenitor (MPP) 150


title: Setaria viridis (A10) seed head at 50% emergence replicate 2


title: Multipotent Progenitor (MPP) 149


title: Restricted hematopoietic progenitor 1 (HPC-1) 101


title: CBLB502+IR_C-Br-6h

description: This sample was brain sample of mice in the CBLB502 administration group 6 hours after irradiation.


title: Multipotent Progenitor (MPP) 148


title: Nilestriol_EG-Br-6h

description: This sample was brain sample of mice 6 hours after administration of Nilestriol without irradiation.

value: Nilestriol


title: CBLB502+IR_C-Br-7d

description: This sample was brain sample of mice in the CBLB502 administration group 7 days after irradiation.


title: Multipotent Progenitor (MPP) 145


title: Multipotent Progenitor (MPP) 147


title: Setaria viridis (A10) seed head at 50% emergence replicate 1


title: Multipotent Progenitor (MPP) 146


title: M-miR-512-3p_soraf_3

city: Sevilla

first: Patricia

last: de la Cruz-Ojeda

address: Avda. Manuel Siurot s/n

country: Spain

institute: Institute of Biomedicine of Seville

description: M-miR-512-3p sorafenib rep3

data_processing:
Basecall and demultiplexing was carried out with DRAGEN FASTQ Generation online software (v. 3.8.4)
Secondary analysis, concerning alignment, mapping and differential expression analysis, was carried out using Bluebee® Quantseq pipeline
Reads were mapped to the human genome version GRCh38 using STAR Aligner with modified ENCODE settings
HTSeq-count was used for gene read counting
Differential expression analysis was performed using the DESeq2 method
Assembly: GRCh38
Supplementary files format and content: 2 Matrix tables with raw and normalized gene counts for every gene and every sample

organism: Homo sapiens

growth_protocol: Cells were cultured in minimal essential medium (MEM) with Earle's balanced salts with L-glutamine suplemented with 10% fetal bovine serum, 1% sodium pyruvate, 1% non-essential amino acids and penicillin-streptomycin solution; cells were grown in culture flasks at 37 ºC in a humidified incubator with 5% CO2. Cells were plated at 50.000 cells/cm2 and transfected with Lipofectamine RNAimax after 24h with miR-200c-3p inhibitor, miR-222-5p mimic, miR-512-3p mimic and transfection controls. Media was changed 6 hours later

extract_protocol:
Total RNA was extracted using a miRNeasy mini kit with DNase treatment according to the manufacturer’s instructions(QIAGEN, Germany).
Libraries were prepared using total RNA lysates. Total RNA concentration and quality of the RNA were assessed with Qubit (Qubit™ DNA HS assay) and TapeStation 4150 with the RNA ScreenTape Assay  (Agilent Technologies Genomics, USA), respectively. RNA Integrity Number (RIN) values were > 9 in all the RNA samples. Libraries were constructed from 350 ng of RNA with the QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina with unique dual indexes (set B1), folowing manufacturer instructions (Catalog number 114, Lexogen GmbH, Viena, Austria). Libraries were amplified (cycles 15-19), purified and subjected to quality control with High Sensitivity DNA Qubit® Assay and High Sensitivity D100 ScreenTape Assay (average size 318 bp). Samples were then pooled together at 2 nM, diluted at 750 nM (PhiX 2%) and sequenced in P2  flow cells  in a NextSeq 2000 instrument from Illumina (65 cycles)

treatment_protocol: Sorafenib was added at the concentration of 10 µM at 24 h hours after transfection, and lysates were obtained after 6 and 24 hours after treatment. Control cells were treated in parallel with dimethyl sulfoxide (DMSO), vehicle in wich Sorafenib was dissolved.

tag: cell type

value: Hepatocellular carcinoma cells

tag: cell line

value: Hepatocellular carcinoma (HCC)

tag: transfection

value: Mimic of miR-512-3p 24h

tag: treatment

value: Sorafenib 10 uM 24h


title: Multipotent Progenitor (MPP) 144

tag: col1a1 genotype

tag: rosa26 genotype

value: rtTA/rtTA

value: induced


title: M-miR-512-3p_soraf_2

description: M-miR-512-3p sorafenib rep2


title: Multipotent Progenitor (MPP) 142

tag: doxycyclin induction


title: CBLB502_CG-Br-7d

description: This sample was brain sample of mice 7 days after administration of CBLB502 without irradiation.


title: Multipotent Progenitor (MPP) 143


title: Multipotent Progenitor (MPP) 141


title: CBLB502_CG-Br-6h

description: This sample was brain sample of mice 6 hours after administration of CBLB502 without irradiation.


title: Multipotent Progenitor (MPP) 140


title: WR2721+IR_W-Bm-6h

description: This sample was bone marrow sample of mice in the WR2721 administration group 6 hours after irradiation.

value: Bone marrow


title: WR2721+IR_W-Bm-7d

description: This sample was bone marrow sample of mice in the WR2721 administration group 7 days after irradiation.


title: M-miR-512-3p_soraf_1

description: M-miR-512-3p sorafenib rep1


title: Multipotent Progenitor (MPP) 138


title: Multipotent Progenitor (MPP) 139


title: M-miR-512-3p_control_3

description: M-miR-512-3p control rep3

value: Control (DMSO) 24h


title: Multipotent Progenitor (MPP) 137


title: WR2721_WG-Bm-7d

description: This sample was bone marrow sample of mice 7 days after administration of WR2721 without irradiation.


title: Nilestriol_EG-Br-7d

description: This sample was brain sample of mice 7 days after administration of Nilestriol without irradiation.


title: Multipotent Progenitor (MPP) 136


title: M-miR-512-3p_control_2

description: M-miR-512-3p control rep2


title: WR2721_WG-Bm-6h

description: This sample was bone marrow sample of mice 6 hours after administration of WR2721 without irradiation.


title: Multipotent Progenitor (MPP) 134


title: M-miR-512-3p_control_1

description: M-miR-512-3p control rep1


title: M-miR-222-5p_soraf_3

description: M-miR-222-5p sorafenib rep3

value: Mimic of miR-222-5p 24h


title: Multipotent Progenitor (MPP) 133


title: Multipotent Progenitor (MPP) 132


title: Multipotent Progenitor (MPP) 130


title: Multipotent Progenitor (MPP) 131


title: M-miR-222-5p_soraf_2

description: M-miR-222-5p sorafenib rep2


title: Multipotent Progenitor (MPP) 129


title: Multipotent Progenitor (MPP) 128


title: Multipotent Progenitor (MPP) 127


title: M-miR-222-5p_control_3

description: M-miR-222-5p control rep3


title: M-miR-222-5p_control_2

description: M-miR-222-5p control rep2


title: M-miR-222-5p_control_1

description: M-miR-222-5p control rep1


title: Restricted hematopoietic progenitor 1 (HPC-1) 94


title: Restricted hematopoietic progenitor 1 (HPC-1) 95


title: Restricted hematopoietic progenitor 1 (HPC-1) 96


title: Restricted hematopoietic progenitor 1 (HPC-1) 93


title: Multipotent Progenitor (MPP) 126


title: Restricted hematopoietic progenitor 1 (HPC-1) 92


title: TPO+IR_T-Bm-7d

description: This sample was bone marrow sample of mice in the TPO administration group 7 days after irradiation.


title: TPO+IR_T-Bm-6h

description: This sample was bone marrow sample of mice in the TPO administration group 6 hours after irradiation.


title: TPO_TG-Bm-6h

description: This sample was bone marrow sample of mice 6 hours after administration of TPO without irradiation.


title: MC_24h_soraf_3

description: MimicControl 24h sorafenibenib rep3

value: Mimic Control 24h (M-miR-222-5p, M-miR-512-3p)


title: Nilestriol+IR_E-Bm-6h

description: This sample was bone marrow sample of mice in the Nilestriol administration group 6 hours after irradiation.


title: Nilestriol+IR_E-Bm-7d

description: This sample was bone marrow sample of mice in the Nilestriol administration group 7 days after irradiation.


title: Restricted hematopoietic progenitor 1 (HPC-1) 90

description:
raw_counts+metadata.csv
counts_filtered.csv
counts_filtered_normalized_log.csv
cell_metadata_filtered.csv


title: Restricted hematopoietic progenitor 1 (HPC-1) 91


title: Nilestriol_EG-Bm-7d

description: This sample was bone marrow sample of mice 7 days after administration of Nilestriol without irradiation.


title: Multipotent Progenitor (MPP) 135


title: TPO_TG-Bm-7d

description: This sample was bone marrow sample of mice 7 days after administration of TPO without irradiation.


title: MC_24h_soraf_2

description: MimicControl 24h sorafenibenib rep2


title: Restricted hematopoietic progenitor 1 (HPC-1) 89


title: Restricted hematopoietic progenitor 1 (HPC-1) 88


title: M-miR-222-5p_soraf_1

description: M-miR-222-5p sorafenib rep1


title: MC_24h_soraf_1

description: MimicControl 24h sorafenibenib rep1


title: Restricted hematopoietic progenitor 1 (HPC-1) 87


title: CBLB502+IR_C-Bm-7d

description: This sample was bone marrow sample of mice in the CBLB502 administration group 7 days after irradiation.


title: MC_24h_control_3

description: MimicControl 24h control rep3


title: Restricted hematopoietic progenitor 1 (HPC-1) 85


title: MC_24h_control_2

description: MimicControl 24h control rep2


title: Restricted hematopoietic progenitor 1 (HPC-1) 82


title: Restricted hematopoietic progenitor 1 (HPC-1) 83


title: Restricted hematopoietic progenitor 1 (HPC-1) 84


title: Restricted hematopoietic progenitor 1 (HPC-1) 81


title: MC_24h_control_1

description: MimicControl 24h control rep1


title: Hematopoietic stem cell (HSC) 159


title: Hematopoietic stem cell (HSC) 160


title: Hematopoietic stem cell (HSC) 158


title: Hematopoietic stem cell (HSC) 157


title: I-miR-200c-3p_sorafenib_2

description: I-miR-200c-3p sorafenibenib rep2

value: Inhibitor of miR-200c-3p 6h

value: Sorafenib 10 uM 6h


title: Hematopoietic stem cell (HSC) 156


title: Nilestriol_EG-Bm-6h

description: This sample was bone marrow sample of mice 6 hours after administration of Nilestriol without irradiation.


title: CBLB502+IR_C-Bm-6h

description: This sample was bone marrow sample of mice in the CBLB502 administration group 6 hours after irradiation.


title: MD_D10_rep98

first: Jill

middle: P

last: Mesirov

state: CA

address: 9500 Gilman Drive

department: Medicine

hyb_protocol: Gene expression data was generated by hybridizing labeled RNAs to Affymetrix HT HG-U133A arrays (Affymetrix, Santa Clara, CA). Samples meeting a minimum of 37% p-calls were used in this analysis. A number of samples with borderline 3′/5′ GAPDH and ACTIN ratios were identified but did not contribute to any batch effects in our non-negative matrix factorization (NMF) analysis; these remained in our subsequent analyses. Gene expression data from Kool et al3 and Fattet et al7 were obtained from the Gene Expression Omnibus (GSE10327 and GSE12992, respectively). Gene expression data from Thomson et al4 was downloaded from http://www.stjuderesearch.org/data/medulloblastoma/. All data sets were preprocessed with the Robust Multichip Average (RMA) algorithm to generate the .gct files used in subsequent analyses (Irizarry RA, et al: Biostatistics 4:249-264, 2003).

scan_protocol: standard Affymetrix protocol

data_processing: Briefly, genomic DNA was digested, adaptor-ligated, and amplified by polymerase chain reaction to achieve fragments ranging from 200 to 1,100 base pairs. These fragments were pooled, concentrated, and further fragmented with DNaseI (Affymetrix) followed by labeling, denaturing, and hybridization to arrays in batches of 96 samples. Gene expression data were generated by hybridizing labeled RNAs to Affymetrix U133A2 high-throughput arrays (Affymetrix, Santa Clara, CA). Samples meeting a minimum of 37% p-calls were used in this analysis. Data were preprocessed by using the robust multichip average (Irizarry RA et al: Biostatistics 4:249-264, 2003) to generate the.gct files used in subsequent analyses.

label: biotin

source_name: Brain

label_protocol: standard Affymetrix protocol

growth_protocol: Snap-frozen tumors were obtained from Children's Oncology Group (ACNS02B3; n = 89) and from Children's Hospital Boston (n = 55), University of Washington Medical Center (n = 27), Texas Children's Hospital (n = 24), and Johns Hopkins Medical Center (n = 10). Normal cerebellum (n = 11) was obtained from University of Washington Medical Center and NICHD Brain and Tissue Bank for Developmental Disorders, University of Maryland, Baltimore, MD. All samples were collected with approval from respective institutional review boards, and proper informed consent and/or assent was obtained from all patients or their parents. Tumors were processed at Children's Hospital Boston except for samples from Texas Children's, where similar protocols were used.

extract_protocol: DNA was prepared by using the Puregene DNA Extraction Kit (Gentra Systems, Minneapolis, MN), and total RNA was extracted by using Trizol (Invitrogen, Carlsbad, CA), both per manufacturers' instructions.

value: primary medulloblastoma

tag: subtype

value: classic


title: I-miR-200c-3p_sorafenib_1

description: I-miR-200c-3p sorafenibenib rep1


title: CBLB502_CG-Bm-6h

description: This sample was bone marrow sample of mice 6 hours after administration of CBLB502 without irradiation.


title: MD_D08_rep94


title: MD_C09_rep96.1


title: MD_B11_rep90


title: MD_D11_rep91


title: Hematopoietic stem cell (HSC) 155


title: Hematopoietic stem cell (HSC) 153


title: MD_D09_rep89


title: Restricted hematopoietic progenitor 1 (HPC-1) 86


title: CBLB502_CG-Bm-7d

description: This sample was bone marrow sample of mice 7 days after administration of CBLB502 without irradiation.


title: Hematopoietic stem cell (HSC) 154


title: Hematopoietic stem cell (HSC) 152


title: I-miR-200c-3p_control_2

description: I-miR-200c-3p control rep2

value: Control (DMSO) 6h


title: Hematopoietic stem cell (HSC) 151


title: Hematopoietic stem cell (HSC) 150


title: I-miR-200c-3p_control_1

description: I-miR-200c-3p control rep1


title: MD_E07_rep87


title: MD_E02_rep86.1

value: nodular/desmoplastic


title: I-miR-200c-3p_sorafenib_3

description: I-miR-200c-3p sorafenibenib rep3


title: Hematopoietic stem cell (HSC) 148


title: Hematopoietic stem cell (HSC) 149


title: IC_6h_soraf_3

description: InhibitorControl 6h sorafenib rep3

value: Inhibitor Control 6h (I-miR-200c-3p)


title: Hematopoietic stem cell (HSC) 147


title: MD_A01_rep83

value: NOS


title: Hematopoietic stem cell (HSC) 146


title: MD_A11_rep80


title: Hematopoietic stem cell (HSC) 145


title: IC_6h_soraf_2

description: InhibitorControl 6h sorafenib rep2

value: Hepatocellular carcinoma cells

value: Hepatocellular carcinoma (HCC)


title: Multipotent Progenitor (MPP) 125


title: Multipotent Progenitor (MPP) 120


title: Multipotent Progenitor (MPP) 124


title: Multipotent Progenitor (MPP) 122


title: IC_6h_control_3

description: InhibitorControl 6h control rep3


title: IC_6h_control_2

description: InhibitorControl 6h control rep2


title: Multipotent Progenitor (MPP) 123


title: I-miR-200c-3p_control_3

description: I-miR-200c-3p control rep3


title: Multipotent Progenitor (MPP) 119


title: MD_A10_rep79


title: MD_D06_rep77

value: large cell/anaplastic


title: IC_6h_soraf_1

description: InhibitorControl 6h sorafenib rep1


title: Multipotent Progenitor (MPP) 121

value: rtTA/rtTA


title: MD_E12_rep73


title: IC_6h_control_1

description: InhibitorControl 6h control rep1


title: MD_G03_rep68


title: Multipotent Progenitor (MPP) 116

value: induced


title: Multipotent Progenitor (MPP) 117


title: 470_Wang_HiC_IB173_ATGN

organism: Agrobacterium tumefaciens

source_name: Agrobacterium tumefaciens C58

treatment_protocol: Cells were growing in ATGN at 30˚C, fixed by 3% formaldehyde for 30min at room temperature

tag: condition

value: ATGN, 30˚C

tag: restriction enzyme

value: HindIII

tag: genotype

value: 15955 {delta}popZ


title: Multipotent Progenitor (MPP) 115


title: MD_A11_rep66


title: MD_A05_rep65


title: Multipotent Progenitor (MPP) 112


title: 469_Wang_input_AtWX291_ATGN_halfmMIPTG4h

treatment_protocol: Cells were growing in ATGN at 30˚C, IPTG was added to 0.5mM final concentration for 4h, fixed by 3% formaldehyde for 30min at room temperature

value: ATGN, 30˚C, 0.5mM IPTG for 4h

value: C58, {delta}repBCh2, pSRKKm msfgfp-popZ


title: Multipotent Progenitor (MPP) 111


title: MD_C11_rep6


title: MD_A07_rep75


title: Restricted hematopoietic progenitor 1 (HPC-1) 79


title: 468_Wang_ChIP_anti_GFP_AtWX291_ATGN_halfmMIPTG4h

tag: chip antibody

value: ChIP using anti-GFP antibodies


title: Restricted hematopoietic progenitor 1 (HPC-1) 80


title: Restricted hematopoietic progenitor 1 (HPC-1) 77


title: Restricted hematopoietic progenitor 1 (HPC-1) 75


title: 466_Wang_ChIP_anti_GFP_AtWX289_LB_halfmMIPTG4h

treatment_protocol: Cells were growing in LB at 30˚C for 30h, IPTG was added to 0.5mM final concentration for 4h, fixed by 3% formaldehyde for 30min at room temperature

value: LB, 30˚C, 30h without IPTG, 0.5mM IPTG for 4h

value: C58, {delta}traI, tetRA::gen PtraI-riboswitch-parB1(Atu2828) traR, pSRKKm msfgfp-popZ


title: Restricted hematopoietic progenitor 1 (HPC-1) 74


title: 467_Wang_input_AtWX289_LB_halfmMIPTG4h_4h


title: 465_Wang_input_AtWX289_LB_2mMTheo_1uMAHL_halfmMIPTG4h

treatment_protocol: Cells were growing in LB at 30˚C, AHL was added to 1uM final concentration for 4h and theophylline was added to 2mM final concentration for 4h,  IPTG was added to 0.5mM final concentration for 4h, fixed by 3% formaldehyde for 30min at room temperature

value: LB, 30˚C, 2mM theophylline,1uM AHL, 0.5mM IPTG for 4h


title: Restricted hematopoietic progenitor 1 (HPC-1) 76


title: Restricted hematopoietic progenitor 1 (HPC-1) 78


title: 471_Wang_HiC_IB172_ATGN

value: 15955 {delta}podJ


title: Multipotent Progenitor (MPP) 118


title: MD_A02_rep53

tag: tissue

value: primary medulloblastoma

value: classic


title: Restricted hematopoietic progenitor 1 (HPC-1) 73


title: MD_B04_rep5


title: Multipotent Progenitor (MPP) 114


title: 464_Wang_ChIP_anti_GFP_AtWX289_LB_2mMTheo_1uMAHL_halfmMIPTG4h


title: Multipotent Progenitor (MPP) 113


title: Restricted hematopoietic progenitor 1 (HPC-1) 71


title: 463_Wang_input_AtWX265_ATGN_halfmMIPTG4h

value: C58, pSRKKm msfgfp-podJ


title: 462_Wang_ChIP_anti_GFP_AtWX265_ATGN_halfmMIPTG4h


title: Restricted hematopoietic progenitor 1 (HPC-1) 72


title: Restricted hematopoietic progenitor 1 (HPC-1) 69


title: MD_C01_rep45

value: nodular/desmoplastic


title: MD_A07_rep62


title: Restricted hematopoietic progenitor 1 (HPC-1) 68


title: 461_Wang_input_AtWX236_ATGN_halfmMIPTG4h

value: C58, pSRKGm egfp-gpr


title: MD_B01_rep43


title: Restricted hematopoietic progenitor 1 (HPC-1) 67

value: rtTA/rtTA


title: MD_C10_rep56


title: MD_A08_rep42

value: large cell/anaplastic


title: 460_Wang_ChIP_anti_GFP_AtWX236_ATGN_halfmMIPTG4h


title: MD_B02_rep40


title: 459_Wang_input_AtWX234_ATGN_halfmMIPTG4h

value: C58, pSRKKm msfgfp-popZ


title: MD_B09_rep39


title: 458_Wang_ChIP_anti_GFP_AtWX234_ATGN_halfmMIPTG4h


title: MD_B02_rep32


title: Restricted hematopoietic progenitor 1 (HPC-1) 70

value: induced


title: 445_Wang_HiC_AtWX121_ATGN

value: ATGN, 30˚C

value: HindIII

value: C58, {delta}popZ {delta}podJ


title: Hematopoietic stem cell (HSC) 136


title: Hematopoietic stem cell (HSC) 140


title: Hematopoietic stem cell (HSC) 141


title: Hematopoietic stem cell (HSC) 137


title: Hematopoietic stem cell (HSC) 139


title: Hematopoietic stem cell (HSC) 142


title: Hematopoietic stem cell (HSC) 138


title: Hematopoietic stem cell (HSC) 143


title: Hematopoietic stem cell (HSC) 134


title: 444_Wang_HiC_AtWX110_ATGN

value: C58, {delta}popZ


title: Hematopoietic stem cell (HSC) 133


title: MD_E03_rep28


title: Restricted hematopoietic progenitor 1 (HPC-1) 66


title: 443_Wang_HiC_AtWX283_ATGN

value: C58, {delta}podJ


title: Restricted hematopoietic progenitor 1 (HPC-1) 65


title: MD_G04_rep271.1


title: Hematopoietic stem cell (HSC) 144


title: Hematopoietic stem cell (HSC) 131


title: Hematopoietic stem cell (HSC) 132


title: MD_H09_rep41


title: MD_D10_rep270

value: medulloblastoma


title: 446_Wang_HiC_AtWX286_ATGN

value: C58, {delta}gpr


title: Hematopoietic stem cell (HSC) 129


title: Hematopoietic stem cell (HSC) 128


title: Hematopoietic stem cell (HSC) 135


title: MD_A09_rep31


title: MD_E01_rep27


title: Hematopoietic stem cell (HSC) 127


title: MD_D05_rep264


title: Hematopoietic stem cell (HSC) 126


title: Hematopoietic stem cell (HSC) 124


title: MD_G10_rep259


title: Hematopoietic stem cell (HSC) 125


title: Hematopoietic stem cell (HSC) 123


title: Hematopoietic stem cell (HSC) 122


title: Hematopoietic stem cell (HSC) 121


title: Hematopoietic stem cell (HSC) 119


title: Hematopoietic stem cell (HSC) 118


title: MD_F06_rep223

value: NOS


title: MD_F05_rep211

value: primary medulloblastoma


title: Hematopoietic stem cell (HSC) 120


title: Hematopoietic stem cell (HSC) 117


title: B2Ul_Cy5_vs._B3Un_Cy3

city: New Delhi

first: Nandula

last: Raghuram

state: Delhi

address: Block A

department: USBT

country: India

institute: GGSIP University

hyb_protocol: Scanned on an Agilent  scanner.

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version 10.7).

data_processing: Agilent Feature Extraction Software (v 10.7) was used for background subtraction and LOWESS normalization.

organism: Oryza sativa Indica Group

source_name: Whole rice tissue of 21 old days plant of the genotype Panvel  for low versus normal urea

label_protocol: Cy3 and Cy5 labeling was used

growth_protocol: Rice plants were grown in pots filled with nutrient depleted soil in green house for 21 days

extract_protocol: RNA was extracted from whole tissue (complete shoot and root) by using Trizol method

treatment_protocol: Plants were fertilized with normal (15mM) or low (1.5mM) nitrate or urea as sole n source

tag: age

value: 21 old days grown plant in nutrient depleted soil

value: whole plant tissue (shoot and root)

tag: cultivar

value: Panvel

tag: n source

value: urea

tag: n dose

value: low

value: normal


title: Hematopoietic stem cell (HSC) 130

value: rtTA/rtTA


title: Hematopoietic stem cell (HSC) 115

value: induced


title: Hematopoietic stem cell (HSC) 114


title: MD_H07_rep202

value: classic


title: Hematopoietic stem cell (HSC) 113


title: Megakaryocyte Progenitor (MkP) 94


title: MD_H05_rep200

value: nodular/desmoplastic


title: Megakaryocyte Progenitor (MkP) 93


title: MD_D05_rep24


title: B2Nl_Cy5_vs._B3Nn_Cy3

source_name: Whole rice tissue of 21 old days plant of the genotype Panvel  for low versus normal nitrate

value: nitrate


title: MD_H04_rep199

value: large cell/anaplastic


title: Megakaryocyte Progenitor (MkP) 92


title: A2Nl_Cy5_vs._A1Nn_Cy3

source_name: Whole rice tissue of 21 old days plant of the genotype Nidhi for low versus normal nitrate

value: Nidhi


title: Megakaryocyte Progenitor (MkP) 91


title: MD_G12_rep198


title: MD_G11_rep197


title: Megakaryocyte Progenitor (MkP) 90


title: Megakaryocyte Progenitor (MkP) 89


title: B1Nl_Cy3_vs._B2Nn_Cy5

source_name: Whole rice tissue of 21 old days plant of the genotype Panvel fornormal versus low nitrate


title: A1Nl_Cy3_vs._A2Nn_Cy5

source_name: Whole rice tissue of 21 old days plant of the genotype Nidhi fornormal versus low nitrate


title: A2Ul_Cy5_vs._A1Un_Cy3

source_name: Whole rice tissue of 21 old days plant of the genotype Nidhi for low versus normal urea


title: A3Ul_Cy3_vs._A2Un_Cy5

source_name: Whole rice tissue of 21 old days plant of the genotype Nidhi fornormal versus low urea


title: B3Ul_Cy5_vs._B1Un_Cy3

source_name: Whole rice tissue of 21 old days plant of the genotype Panvel for low versus normal urea


title: B1Ul_Cy3_vs._B2Un_Cy5

source_name: Whole rice tissue of 21 old days plant of the genotype Panvel fornormal versus low urea


title: A1Ul_Cy5_vs._A3Un_Cy3


title: Megakaryocyte Progenitor (MkP) 88

source_name: bone marrow


title: Hematopoietic stem cell (HSC) 116


title: Megakaryocyte Progenitor (MkP) 85


title: MS_grid_rep2_RNA

city: Wuhan

first: Shuhong

last: Zhao

address: No. 1 Shizishan Street, Hongshan District

institute: Huazhong Agricultural University

description:
GRID-seq
Processed data for this sample available on GSM6071454.

data_processing:
Reads of each library were trimmed by trim_galore (version: 0.4.5_dev) and kept with a minimum length of 79 bp
To precisely obtain reads and to minimize the loss of reads that did not contain the exact full linker sequence due to errors introduced in sequencing and/or PCR, we performed a tiered strategy: 1) we kept reads that contained the core 12 bp seed sequence of linkers rather than using the full linker for downstream processing, 2) MmeI motifs were used to define linker boundaries, and 3) linker orientation was used to dictate whether a read originated from RNA or genomic DNA. With this strategy, paired DNA-RNA reads that ranged from 17 bp to 23 bp were obtained. For each captured RNA read (cDNA), we used its reverse complement as the formal read, thus, this read pinpointed the exact same sequence of the RNA product sequence. All paired reads were assigned unique paired IDs. The code for processing raw reads is available on Github: https://github.com/ezioljj/scripts_for_GRID-seq
All clean read mates were aligned separately with the mouse genome (mm10) reference using Bowtie2 (version: 2.2.5) using the parameter ‘–local’. Read pairs that contained ambiguously mapped DNA or RNA reads were filtered out by SAMtools (version: 1.9) using the parameter ‘-Sbq 2 ‘.
Genomic regions with enriched GRID-seq RNA reads were detected by MACS2 (version: 2.1.2) using the broad-peak detection model.
Identifying chromatin-enriched RNAs, construction of non-specific background, and identification of specific RNA–chromatin interactions were described and carried out by standard GRID-seq pipeline.
Assembly: Sscrofa11.1
Supplementary files format and content: custom (chromatin-associated RNA and its binding loci with normalized interaction)
Library strategy: GRID-seq

organism: Sus scrofa

source_name: longissimus muscle

extract_protocol:
Skeletal muscle are collected from 2-week-old LW and MS piglets.
GRID-seq was performed as described in Li et al. Approximately 2.5×106 cells were crosslinked for 45 min at room temperature with 2mM DSG solution and further fixed in 1% formaldehyde for 10 min. Fixed cells were permeabilized in 1ml equilibrium buffer (0.2% NP-40, 5mM Tris-HCl pH 7.5, 10 mM NaCl, and 1×protease inhibitor cocktail) for 15 min on ice with brief centrifugation). To prepare nuclei, fixed cells were incubated in 300 μL of Cutsmart buffer (0.5% SDS) for 10 min at 62°C. Then, 50ul of 10% Triton X-100 was added to quench the SDS, and it was chilled on ice. To digest chromatin, nuclei were collected by brief centrifugation, washed twice with 1× Cutsmat Buffer, resuspended in 500 μl of AluI solution (1× Cutsmart Buffer, 1% Triton X-100,1 U/μL RiboLock, 0.5 U/μL AluI (NEB), and 1× protease inhibitor), and incubated at 37 °C for 4 h. After digestion, DNA ends were added with dA tailing module, and then repaired with DNA/RNA 5’phosphorylation and 3’dephosphorylation using PNK (NEB) at 37°C for 1.5h.   To ligate in situ linkers to RNA, RNA ends were ligated using 4U/ul T4 RNA Ligase 2-truncated KQ (NEB) to an oligonucleotide 'bridge' molecule that contained a 5'-adenylated ssDNA overhang and incubated at 25 °C for 3 h. To ligate in situ linkers to DNA, nuclei were collected, washed twice with 800 μL of 1× DNA Ligase Buffer (NEB) to remove free linkers, resuspended in 1 ml of DNA Ligation Solution (0.2 U/μL RiboLock, 1× DNA Ligase Buffer, 1 mg/ml BSA, 1% Triton X-100, and 1 U/μL T4 DNA Ligase (NEB)) and incubated overnight at 16 °C. Next, the pellet was washed, and the RNA strand was stabilized by first strand synthesis of the RNA through extension of the bridge by Bst 3.0 polymerase.  Reversal of crosslinking and purification of DNA/RNA. The Pellet was resuspended in 300 ul proteinase K solution (15 mM EDTA, 10 mM Tris-HCl, pH 7.5, 0.5% SDS, and 1 mg/ml proteinase K (Ambion)), and incubate at 65˚C for at least 2 h in Thermomixer. After Adding 300μL of Phenol: Chloroform: Isoamyl Alcohol (pH 8.0) to each tube, Total DNA/RNA were precipitated with 2 μL of GlycoBlue, 30μL of 3 M NaOAc (pH 5.5), and 300μL of 100% isopropanol on ice for at least 2h, followed by centrifugation for 30min at 16000g. Total DNA/RNA were dissolved in 51 μL of H2O (expect a total amount of ~10ug DNA/RNA).   Pull down biotin DNA/RNA. 50ul DNA/RNA was added to M280 streptavidin magnetic beads which had been washed three with 1×B&W Buffer (5 mM Tris-Cl pH 7.5, 0.02% Tween-20, 0.5 mM EDTA, 1 M NaCl). After incubate for 45min at RT, the beads were washed with 500 ul of 1×B&W Buffer for 5 times, and resuspended in 100 μL freshly prepared 150mM NaOH at RT for 10min. Next, the supernatant was transferred to a 1.5 mL tube and neutralized with 11 μL 10 × TE buffer and 6.5 μL of 1.25M acetic acid. Single stranded DNA (ssDNA) was precipitated with 2μL of GlycoBlue,10 μL of 3 M NaOAc (pH 5.5), and 100 μL of 100% isopropanol. With Second strand synthesis, the reaction was performed by adding 0.5 μL of 10mM dNTP, and 5 U klenow Exo-(NEB) and incubated at 37°C for 1 h. Next, Synthetic double-stranded DNA were digested with MmeI buffer (5 pmol SAM(NEB), and 4 U MmeI) for 1h at 37°C. After MmeI digestion, DNA was extracted and purified, the 84bp target band was cut and used for Illumina TrueSeq library construction.

tag: breed

value: Chinese local pig breed


title: Megakaryocyte Progenitor (MkP) 87


title: MD_H08_rep203


title: MD_G09_rep195


title: Megakaryocyte Progenitor (MkP) 83


title: Megakaryocyte Progenitor (MkP) 84


title: Megakaryocyte Progenitor (MkP) 82


title: MS_grid_rep1_DNA

description: GRID-seq


title: MS_grid_rep1_RNA

description:
GRID-seq
Processed data for this sample available on GSM6071452.


title: MD_G10_rep196


title: Megakaryocyte Progenitor (MkP) 86


title: MD_G06_rep192


title: LW_grid_rep2_RNA

description:
GRID-seq
Processed data for this sample available on GSM6071450.

value: commercial lean pig breed


title: Megakaryocyte Progenitor (MkP) 81


title: Megakaryocyte Progenitor (MkP) 80


title: Megakaryocyte Progenitor (MkP) 79


title: MD_H11_rep190


title: LW_grid_rep2_DNA

description: GRID-seq


title: Hematopoietic stem cell (HSC) 112


title: LW_grid_rep1_RNA

description:
GRID-seq
Processed data for this sample available on GSM6071448.


title: Hematopoietic stem cell (HSC) 110


title: Hematopoietic stem cell (HSC) 109


title: LW_grid_rep1_DNA

description: GRID-seq


title: MD_H10_rep189


title: Hematopoietic stem cell (HSC) 108


title: Hematopoietic stem cell (HSC) 105


title: Hematopoietic stem cell (HSC) 107


title: MD_H08_rep187


title: MD_G05_rep191


title: Hematopoietic stem cell (HSC) 106


title: MD_H09_rep188


title: MS_hichip_rep2

description: H3K27ac BL HiChIP

data_processing:
Library strategy: HiChIP-Seq
Reads of each library were trimmed by trim_galore (version: 0.4.5_dev) and kept with a minimum length of 79 bp
To precisely obtain reads and to minimize the loss of reads that did not contain the exact full linker sequence due to errors introduced in sequencing and/or PCR, we performed a tiered strategy: 1) we kept reads that contained the core 12 bp seed sequence of linkers rather than using the full linker for downstream processing, 2) MmeI motifs were used to define linker boundaries, and 3) linker orientation was used to dictate whether a read originated from RNA or genomic DNA. With this strategy, paired DNA-RNA reads that ranged from 17 bp to 23 bp were obtained. For each captured RNA read (cDNA), we used its reverse complement as the formal read, thus, this read pinpointed the exact same sequence of the RNA product sequence. All paired reads were assigned unique paired IDs. The code for processing raw reads is available on Github: https://github.com/ezioljj/scripts_for_GRID-seq
All clean read mates were aligned separately with the mouse genome (mm10) reference using Bowtie2 (version: 2.2.5) using the parameter ‘–local’. Read pairs that contained ambiguously mapped DNA or RNA reads were filtered out by SAMtools (version: 1.9) using the parameter ‘-Sbq 2 ‘.
Genomic regions with enriched GRID-seq RNA reads were detected by MACS2 (version: 2.1.2) using the broad-peak detection model.
Identifying chromatin-enriched RNAs, construction of non-specific background, and identification of specific RNA–chromatin interactions were described and carried out by standard GRID-seq pipeline.
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: mcool, bedpe and custom (chromatin-associated RNA and its binding loci with normalized interaction)
Supplementary_files_format_and_content: chromatin-associated RNA (column 1-6) and its binding loci on chromatin with normalized interaction levels (column 7-9) (binsize = 1000 bp)
Supplementary_files_format_and_content: An .mcool file is a contact map produced by Cooler and can be visualized using HiGlass or CoolBox.
Supplementary_files_format_and_content: The BEDPE format is similar to the BED format and can be used to describe pairs of genomic regions.

extract_protocol:
Skeletal muscle are collected from 2-week-old LW and MS piglets.
For BL Hi-ChIP, Approximately 0.2g of frozen muscle tissue was ground into a fine powder in liquid nitrogen and fixed with cross-linking buffer (1% formaldehyde, 0.1M NaCl, 1mM EDTA, 0.5mM EGTA and 50mM Hepes) for 15 min at room temperature. The cross-linking reaction is terminated by the addition of a final concentration of 0.2M glycine. Centrifugate at 2500rpm for 10min at 4°C to collect the fixed tissue and resuspended in tissue lysis buffer(10mM Tris-HCl pH8.0、10Mm NaCl、0.2% v/v Igepal CA630、1× protease inhibitors), incubated on ice for 30min to lyse the tissue and extract the nuclei. Filtering out impurities with a 40μl cell strainer to obtain nuclei of higher purity. The nuclei were resuspended in 1ML of SDS buffer (1×CutSmart and 0.5% SDS) and incubated for 10 min at 62°C, followed add 200µl 10% TritionX-100 and incubated at room temperature for 10 min to neutralise the SDS. Pelleting and washing with 1X Cutsmart buffer, chromatin was digested with 1U/μl AluI restriction enzyme at 37℃ for 7h. Collecting the nuclei and resuspending the nuclei in 500µl A -tailing solution and incubate for 1 hour at 37°C. Pellet again, resuspending the nuclei in 500µl ligation solution with biotinylated bridge linker and incubate over night at 16°C. Nuclear were fragmented by Covaris S220, 7.5µg antibody (H3K27ac, Abcam Cat# ab4729) and 30µl M-280 sheep anti-rabbit IgG Dynabeads (ThermoFisher, 11203D) were used to enrich the chromatin complexes mediated by H3K27ac. Purifying the ChiP-DNA and fragmenting with Tn5. Streptavidin C-1 beads were used to pull down the DNA fragement like “DNA-linker-DNA”.    GRID-seq was performed as described in Li et al. Approximately 2.5×106 cells were crosslinked for 45 min at room temperature with 2mM DSG solution and further fixed in 1% formaldehyde for 10 min. Fixed cells were permeabilized in 1ml equilibrium buffer (0.2% NP-40, 5mM Tris-HCl pH 7.5, 10 mM NaCl, and 1×protease inhibitor cocktail) for 15 min on ice with brief centrifugation). To prepare nuclei, fixed cells were incubated in 300 μL of Cutsmart buffer (0.5% SDS) for 10 min at 62°C. Then, 50ul of 10% Triton X-100 was added to quench the SDS, and it was chilled on ice. To digest chromatin, nuclei were collected by brief centrifugation, washed twice with 1× Cutsmat Buffer, resuspended in 500 μl of AluI solution (1× Cutsmart Buffer, 1% Triton X-100,1 U/μL RiboLock, 0.5 U/μL AluI (NEB), and 1× protease inhibitor), and incubated at 37 °C for 4 h. After digestion, DNA ends were added with dA tailing module, and then repaired with DNA/RNA 5’phosphorylation and 3’dephosphorylation using PNK (NEB) at 37°C for 1.5h.   To ligate in situ linkers to RNA, RNA ends were ligated using 4U/ul T4 RNA Ligase 2-truncated KQ (NEB) to an oligonucleotide 'bridge' molecule that contained a 5'-adenylated ssDNA overhang and incubated at 25 °C for 3 h. To ligate in situ linkers to DNA, nuclei were collected, washed twice with 800 μL of 1× DNA Ligase Buffer (NEB) to remove free linkers, resuspended in 1 ml of DNA Ligation Solution (0.2 U/μL RiboLock, 1× DNA Ligase Buffer, 1 mg/ml BSA, 1% Triton X-100, and 1 U/μL T4 DNA Ligase (NEB)) and incubated overnight at 16 °C. Next, the pellet was washed, and the RNA strand was stabilized by first strand synthesis of the RNA through extension of the bridge by Bst 3.0 polymerase.  Reversal of crosslinking and purification of DNA/RNA. The Pellet was resuspended in 300 ul proteinase K solution (15 mM EDTA, 10 mM Tris-HCl, pH 7.5, 0.5% SDS, and 1 mg/ml proteinase K (Ambion)), and incubate at 65˚C for at least 2 h in Thermomixer. After Adding 300μL of Phenol: Chloroform: Isoamyl Alcohol (pH 8.0) to each tube, Total DNA/RNA were precipitated with 2 μL of GlycoBlue, 30μL of 3 M NaOAc (pH 5.5), and 300μL of 100% isopropanol on ice for at least 2h, followed by centrifugation for 30min at 16000g. Total DNA/RNA were dissolved in 51 μL of H2O (expect a total amount of ~10ug DNA/RNA).   Pull down biotin DNA/RNA. 50ul DNA/RNA was added to M280 streptavidin magnetic beads which had been washed three with 1×B&W Buffer (5 mM Tris-Cl pH 7.5, 0.02% Tween-20, 0.5 mM EDTA, 1 M NaCl). After incubate for 45min at RT, the beads were washed with 500 ul of 1×B&W Buffer for 5 times, and resuspended in 100 μL freshly prepared 150mM NaOH at RT for 10min. Next, the supernatant was transferred to a 1.5 mL tube and neutralized with 11 μL 10 × TE buffer and 6.5 μL of 1.25M acetic acid. Single stranded DNA (ssDNA) was precipitated with 2μL of GlycoBlue,10 μL of 3 M NaOAc (pH 5.5), and 100 μL of 100% isopropanol. With Second strand synthesis, the reaction was performed by adding 0.5 μL of 10mM dNTP, and 5 U klenow Exo-(NEB) and incubated at 37°C for 1 h. Next, Synthetic double-stranded DNA were digested with MmeI buffer (5 pmol SAM(NEB), and 4 U MmeI) for 1h at 37°C. After MmeI digestion, DNA was extracted and purified, the 84bp target band was cut and used for Illumina TrueSeq library construction.

tag: antibody


title: MS_hichip_rep1

description: H3K27ac BL HiChIP


title: B3Nl_Cy5_vs._B1Nn_Cy3

source_name: Whole rice tissue of 21 old days plant of the genotype Panvel for low versus normal nitrate


title: A3Nl_Cy5_vs._A3Nn_Cy3


title: MD_H07_rep186


title: Hematopoietic stem cell (HSC) 104


title: Hematopoietic stem cell (HSC) 103


title: Hematopoietic stem cell (HSC) 101


title: MD_H06_rep185


title: LW_hichip_rep2

description: H3K27ac BL HiChIP


title: LW_hichip_rep1

description: H3K27ac BL HiChIP


title: Hematopoietic stem cell (HSC) 98


title: Hematopoietic stem cell (HSC) 102


title: Hematopoietic stem cell (HSC) 100


title: MD_H04_rep183


title: MD_H05_rep184


title: Hematopoietic stem cell (HSC) 111


title: Hematopoietic stem cell (HSC) 99


title: Hematopoietic stem cell (HSC) 97


title: lineage- kit+ CD150+ cell 22


title: lineage- kit+ CD150+ cell 21


title: lineage- kit+ CD150+ cell 20


title: MD_G12_rep182


title: MD_G11_rep181


title: lineage- kit+ CD150+ cell 19


title: MD_G10_rep180


title: lineage- kit+ CD150+ cell 18


title: MD_A10_rep175


title: lineage- kit+ CD150+ cell 17


title: lineage- kit+ CD41- CD150- cell 24


title: lineage- kit+ CD41- CD150- cell 23


title: MD_A05_rep172


title: MD_A03_rep174


title: lineage- kit+ CD41- CD150- cell 21


title: lineage- kit+ CD41- CD150- cell 20


title: MD_A08_rep171


title: lineage- kit+ CD41- CD150- cell 22


title: lineage- kit+ CD41- CD150- cell 19


title: lineage- kit+ CD41- CD150- cell 18


title: lineage- kit+ CD41- CD150- cell 17


title: MD_A07_rep170


title: Multipotent Progenitor (MPP) 110


title: MD_A09_rep166


title: Multipotent Progenitor (MPP) 107


title: Multipotent Progenitor (MPP) 108


title: Multipotent Progenitor (MPP) 106


title: Multipotent Progenitor (MPP) 105


title: MD_A10_rep167


title: MD_A08_rep165


title: Multipotent Progenitor (MPP) 104


title: Multipotent Progenitor (MPP) 102


title: MD_A07_rep164


title: MD_A06_rep162


title: Multipotent Progenitor (MPP) 101


title: Multipotent Progenitor (MPP) 103


title: lineage- kit+ CD150+ cell 16


title: Multipotent Progenitor (MPP) 100


title: Multipotent Progenitor (MPP) 99


title: MD_A05_rep161


title: Multipotent Progenitor (MPP) 98


title: Multipotent Progenitor (MPP) 97


title: Multipotent Progenitor (MPP) 109


title: Megakaryocyte Progenitor (MkP) 78


title: Megakaryocyte Progenitor (MkP) 77


title: Multipotent Progenitor (MPP) 96


title: MD_A03_rep159


title: MD_A02_rep158


title: MD_F05_rep156


title: Megakaryocyte Progenitor (MkP) 74


title: MD_F06_rep155


title: Megakaryocyte Progenitor (MkP) 75


title: Megakaryocyte Progenitor (MkP) 76


title: Megakaryocyte Progenitor (MkP) 71


title: Megakaryocyte Progenitor (MkP) 73


title: MD_F04_rep154


title: Megakaryocyte Progenitor (MkP) 72


title: Megakaryocyte Progenitor (MkP) 70


title: MS_grid_rep2_DNA

description: GRID-seq


title: Megakaryocyte Progenitor (MkP) 69


title: MD_F05_rep153


title: Megakaryocyte Progenitor (MkP) 68


title: Megakaryocyte Progenitor (MkP) 67


title: Megakaryocyte Progenitor (MkP) 65


title: MD_D06_rep15


title: Megakaryocyte Progenitor (MkP) 66


title: MD_F04_rep151


title: Megakaryocyte Progenitor (MkP) 64


title: MD_E12_rep148


title: Megakaryocyte Progenitor (MkP) 63


title: MD_F03_rep149


title: Megakaryocyte Progenitor (MkP) 62


title: Megakaryocyte Progenitor (MkP) 61


title: Megakaryocyte Progenitor (MkP) 60


title: MD_F04_rep146


title: Megakaryocyte Progenitor (MkP) 58


title: Megakaryocyte Progenitor (MkP) 59


title: MD_E01_rep147


title: Megakaryocyte Progenitor (MkP) 57


title: Megakaryocyte Progenitor (MkP) 55


title: MD_F07_rep144


title: Megakaryocyte Progenitor (MkP) 54


title: Megakaryocyte Progenitor (MkP) 53


title: Megakaryocyte Progenitor (MkP) 56


title: MD_F02_rep142.1


title: Megakaryocyte Progenitor (MkP) 51


title: MD_E10_rep138


title: Megakaryocyte Progenitor (MkP) 52


title: MD_D11_rep137.1


title: Megakaryocyte Progenitor (MkP) 50


title: Megakaryocyte Progenitor (MkP) 48


title: MD_D10_rep136.2


title: Multipotent Progenitor (MPP) 95


title: Megakaryocyte Progenitor (MkP) 49


title: Multipotent Progenitor (MPP) 94


title: Multipotent Progenitor (MPP) 93


title: MD_B06_rep135


title: 90 min after-deflagellation rep2 RNA-Seq

first: Jingying

last: Huang

address: Haidian  District

department: School of Life Sciences

institute: Tsinghua University

description:
mRNA
C_reinhardtii_allSamples_RNAseq_edgR_normalized_CPM.txt
C_reinhardtii_allSamples_RNAseq_genes_CDS_counts.txt

data_processing:
Tophat (v2.1.1) was used to align all reads from individual samples to Chlamydomonas v5.5 genome, parameters are the following: splice-mismatches 0; max-multihits 20; segment-mismatches 2; segment length 25; -no-novel-juncs.
HTseq-count with default setting was used to calculate exon or CDS abundance (--type) using bam files generated by Tophat with gene annotation from Chlamydomonas v5.3.1 genome.
Counts normalization and differential expession analysis by edgR.
For the riboseq data,the length range of the RPF reads and the P-site location was selected through interpretation of the metaplots drawing the distance between 5' end and start codon by RiboCode.
Chlamydomonas v5.5 genome
Tab-delimited text files include raw counts values for all sample;
Tab-delimited text files include normalized counts (CPM) for all sample;
CPM normalized bigwig converted from bam file by bamCoverage with the following setting: --binSize 5 --normalizeUsing CPM

organism: Chlamydomonas reinhardtii

extract_protocol:
Chlamydomonas cells were flash-frozen and stored in liquid nitrogen. RNA was harvested using Trizol reagent.
Libraries were performed using same strategy as Ribo-Seq
Chlamydomonas cells were flash-frozen and stored in liquid nitrogen. The sample pellets were crushed into powder in a motar filled with liquid nitrogen prior to the experiments. RPF was harvested using RNase I digestion

tag: strain


title: MD_B04_rep134


title: MD_D09_rep133.1


title: Multipotent Progenitor (MPP) 92


title: Multipotent Progenitor (MPP) 91


title: 60 min after-deflagellation rep2 RNA-Seq


title: 30 min after-deflagellation rep2 RNA-Seq


title: Multipotent Progenitor (MPP) 90


title: MD_G03_rep129.1


title: MD_D08_rep131.1


title: Multipotent Progenitor (MPP) 88


title: 60 min after-deflagellation rep1 RNA-Seq


title: 30 min after-deflagellation rep1 RNA-Seq


title: Multipotent Progenitor (MPP) 89


title: MD_E05_rep126

value: NOS


title: MD_C03_rep125

value: primary medulloblastoma


title: 15 min after-deflagellation rep2 RNA-Seq


title: Multipotent Progenitor (MPP) 87


title: Multipotent Progenitor (MPP) 86


title: MD_E11_rep122


title: 15 min after-deflagellation rep1 RNA-Seq


title: MD_D06_rep121


title: Multipotent Progenitor (MPP) 85


title: Multipotent Progenitor (MPP) 84


title: MD_E10_rep120


title: MD_E09_rep119


title: Multipotent Progenitor (MPP) 83


title: MD_E09_rep116


title: MD_C09_rep118


title: 90 min after-deflagellation rep1 Ribo-Seq

description:
Ribosome protected mRNA fragment
C_reinhardtii_allSamples_Riboseq_edgR_normalized_CPM.txt
C_reinhardtii_allSamples_Riboseq_genes_CDS_counts.txt

extract_protocol:
Chlamydomonas cells were flash-frozen and stored in liquid nitrogen. The sample pellets were crushed into powder in a motar filled with liquid nitrogen prior to the experiments. RPF was harvested using RNase I digestion
Libraries were performed as Ingolia et al. 2012 published protocol described.
Chlamydomonas cells were flash-frozen and stored in liquid nitrogen. The sample pellets were crushed into powder in a motar filled with liquid nitrogen prior to the experiments. RPF was harvested using RNase I digestion


title: 90 min after-deflagellation rep1 RNA-Seq


title: Multipotent Progenitor (MPP) 80


title: Multipotent Progenitor (MPP) 81


title: MD_D05_rep114


title: MD_C08_rep113


title: 60 min after-deflagellation rep2 Ribo-Seq


title: 60 min after-deflagellation rep1 Ribo-Seq


title: lineage- kit+ CD150+ cell 15


title: 30 min after-deflagellation rep1 Ribo-Seq


title: 30 min after-deflagellation rep2 Ribo-Seq


title: MD_E08_rep111.1


title: 15 min after-deflagellation rep2 Ribo-Seq


title: lineage- kit+ CD150+ cell 13


title: MD_F11_rep110.1


title: 15 min after-deflagellation rep1 Ribo-Seq


title: lineage- kit+ CD150+ cell 14


title: Non-treated rep2 RNA-Seq


title: MD_F11_rep11


title: lineage- kit+ CD150+ cell 12


title: Non-treated rep1 RNA-Seq


title: MD_E07_rep104


title: lineage- kit+ CD150+ cell 11


title: 90 min after-deflagellation rep2 Ribo-Seq


title: Non-treated rep1 Ribo-Seq


title: MD_E08_rep103


title: lineage- kit+ CD150+ cell 10


title: WT rep2

description: mRNA

data_processing:
Quality control using FastQC
Remove reads mapped to ribosome RNA using bowtie
Pair-end mapping was performed with STAR 2.6.1c using WBcel235 annotation, allowing a maximum of 2 mismatches and retaining only 1 alignment per read.
Expression level calculation by HTseq.
Deffirential expession analysis by DESeq2.
WormBase, WBcel235
Tab-delimited text files include raw counts values for each sample;
Tab-delimited text files include normalized counts for each sample;
CPM normalized bigwig converted from bam file by bamCoverage with the following setting: --binSize 5 --normalizeUsing CPM

organism: Caenorhabditis elegans

extract_protocol:
Worms were flash-frozen and stored in liquid nitrogen. RNA was harvested using Trizol reagent.
Library were performed using the KAPA RNA HyperPrep Kit (KAPA Biosystems, Wilmington, MA, USA).
Chlamydomonas cells were flash-frozen and stored in liquid nitrogen. The sample pellets were crushed into powder in a motar filled with liquid nitrogen prior to the experiments. RPF was harvested using RNase I digestion

value: WT


title: Multipotent Progenitor (MPP) 82


title: MD_C05_rep102


title: lineage- kit+ CD150+ cell 9


title: MD_C08_rep101


title: sptl-3 rep2

description:
mRNA
sptl_3_Expressed_gene_count_DEseq_normalized.txt

value: sptl-3 KO


title: lineage- kit+ CD150+ cell 8


title: MD_F12_rep112.1


title: lineage- kit+ CD41- CD150- cell 16


title: lineage- kit+ CD41- CD150- cell 15


title: sptl-2 rep2

description:
mRNA
sptl_2_Expressed_gene_count_DEseq_normalized.txt

value: sptl-2 KO


title: sptl-3 rep1


title: sptl-1 rep2

description:
mRNA
sptl_1_Expressed_gene_count_DEseq_normalized.txt

value: sptl-1 KO


title: lineage- kit+ CD41- CD150- cell 13

description:
raw_counts+metadata.csv
counts_filtered.csv
counts_filtered_normalized_log.csv
cell_metadata_filtered.csv


title: lineage- kit+ CD41- CD150- cell 14


title: lineage- kit+ CD41- CD150- cell 11


title: sptl-1 rep1


title: Non-treated rep2 Ribo-Seq


title: lineage- kit+ CD41- CD150- cell 10


title: lineage- kit+ CD41- CD150- cell 9


title: KKU-100 cells treatment regorafenib 10uM

city: Taipei

first: Michael

last: Hsiao

address: Academia Road, Section 2, Nankang, Taipei, 115, Ta

department: Genomics Research Center

country: Taiwan

institute: Academia Sinica

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 PLUS 2.0 . GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

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

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

growth_protocol: Cells were cultured in 5% CO2 incubator at 37℃.

extract_protocol: Qiagene RNeasy mini kit extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Cell were selected with puromycin for two weeks.  Stably transduced cells were use for this experiment.

tag: cell line

tag: cell type

tag: treatment

value: regorafenib 10uM


title: Human_Explant_FACS_Left_Targeted

city: Pittsburgh

first: Leah

last: Byrne

address: 3501 Fifth Avenue

department: Ophthalmology

institute: University of Pittsburgh

description:
10X targeted enrichment, targeting GFP and marker genes
aav_barcode_key.txt

data_processing:
scRNA-seq data was aligned and cells were demultiplexed using STARsolo (v2.7).
Empty droplets were removed using DropletUtils (v1.4.3, lower.prop=0.05). Doublets were removed using SCDS (v1.0.0), with a hybrid score cutoff of 1.3. Gene expression was normalized using Scran (v1.12.1) and imputation was achieved using ALRA (v1.0) to improve the sparsity of the scRNA-seq datasets. The analysis of scRNA-seq datasets and cell type identification was  performed with Scanpy (v1.4.4.post1). Specifically, the top 50 principal  components of the gene expression matrix were calculated and used to  compute the Euclidean distance between cells. Cells were embedded into a  neighborhood graph for visualization using the UMAP algorithm, and Leiden  clustering was performed on this graph to identify cell populations. Cell types were identified using a hypergeometric test using a list of known retinal cell type  marker genes compiled from multiple sources. P-values were corrected for multiple hypothesis testing using the Bonferroni method and the cell type for  each cluster was chosen based on the most significant marker gene intersection p-value (< 0.05). Clusters that did not meet the significance threshold for cell type identification were analyzed and annotated manually using the known gene markers.
AAV variants were identified using a unique 25 bp barcode at the end of the GFP gene for each variant. GFP was identified  from these samples using two datasets: (1) whole transcriptome scRNA-seq data and (2) 10x targeted enrichment against GFP and other marker genes.  Salmon (v0.9.1) was used for GFP transcript quantification and in-house scripts were used to identify the AAV barcode and map these reads back to  their respective cells as previously described in our scAAVengr eLife paper.
Due to ethical concerns, raw fastq files were processed with BAMboozle to remove any donor-specific genetic variants before being submitted to GEO.
Assembly: GRCh38 (GCA_000001405.15) fasta with its associated NCBI RefSeq annotation file
Supplementary files format and content: Matrix tables with raw gene expression counts for every cell; Cell-by-GFP tables with raw GFP-barcode expression counts

source_name: Retina explant all regions FACS

growth_protocol: Eyes from postmortem donors/ rhesus were dissected within 30 minutes after surgical removal. The anterior segment was removed and eye cups were flat mounted. Around 5mm wide macular (central), mid-peripheral and peripheral retina was dissected and retinal tissue was carefully separated from RPE/choroid/sclera and immediately transferred to cell culture inserts with 0.40 μm pore size, with the photoreceptor side attached to the membrane. Culture wells contained 3 retinal explants; macular (central), mid-peripheral and peripheral retina. The retinal explants were cultured in Neurobasal Plus Medium supplemented with 2% B-27, 5 μg/ml Plasmocin prophylactic and Penicillin-streptomycin at 37 °C, 5% CO2. In order to keep the retinal explant attached to the transmembrane, a volume of 1.3 mL of medium was added into each culture well, which is a sufficient volume for wetting the transmembrane but not enough to submerge the explant.

extract_protocol:
On the 8th day of AAV incubation, the 1mm edges of each explant, which had the highest level of GFP expression, were collected and underwent single-cell dissociation, FACS, and scRNA-seq. The 1mm edge of each retinal explant was placed in Hibernate solution after dissection, and was then dissociated with an enzymatic and mechanical method using a  MACS Neural Tissue Dissociation Kit for postnatal neurons according to manufacturer’s recommendations. The macular,  mid-peripheral and peripheral region from the temporal quadrant retina of  human donor#2 was dissected, and the same anatomical regions from left and  right eye were combined and immediately dissociated using the same method.  The retinal single cells were resuspended in D-PBS with 0.1% BSA and  processed immediately for scRNA-seq or FACS. The GFP-positive cells in the  retinal explant cell suspensions were enriched using a MACS Tyto sorter. GFP-positive cells were resuspended in D-PBS with 0.1% BSA and processed immediately for scRNA-seq.
Following the manufacture’s protocol, using the Chromium Single Cell 3’ v3 kit (10x Genomics), single retinal cells were partitioned into Gel Beads in Emulsion (GEMs), mRNA was reverse transcribed to cDNA and barcoded with unique molecular identifiers (UMIs). The GEM emulsions were then broken and the cDNA was purified using DynaBeads. After PCR amplification, the cDNA was cleaned and further purified with SPRIselect reagent The final indexed library was constructed following fragmentation, end repair, A-tailing, adaptor ligation, and sample index PCR steps. The libraries were sequenced on Illumina S1 flow cells at the UPMC Genome Center. GFP transcripts with unique AAV barcodes were further enriched using a custom Targeted Gene Expression kit (10x Genomics) and the resulting library was sequenced with an Illumina MiSeq reagent nano kit v2 (300 cycles).

treatment_protocol: Fresh medium was replaced at the second day of incubation and 10μl of AAV capsid library was applied dropwise onto the surface of each explant (30μl per culture well). Every second day, medium was completely replaced and AAV application was performed. A total of 120 μl of AAV suspension was applied per culture well during 8 days of AAV incubation. GFP expression in the retina was monitored using an ECHO Revolve fluorescence microscope.

value: Retina explant

tag: sorting strategy

value: FACS-sorted


title: KKU-100 cells treatment regorafenib 1uM

value: regorafenib 1uM


title: Human_Explant_Periphery_Left_Targeted

source_name: Retina explant periphery region

value: unsorted


title: Human_Explant_FACS_Right_Targeted


title: KKU-100 cells treatment solvent control

value: solvent control


title: Hematopoietic stem cell (HSC) 96

tag: col1a1 genotype

tag: rosa26 genotype

value: rtTA/rtTA

tag: doxycyclin induction

value: induced


title: HuccT1 cells treatment solvent control

value: bile duct carcinoma


title: HuccT1 cells treatment regorafenib 10uM


title: BJ-LC-13_S13

city: PITTSBURGH

first: Uma

last: Chandran

address: 5607 Baum Blvd

department: Biomedical Informatics

data_processing:
RNA-seq libraries were sequenced with single-end 50bp reads on an Illumina HiSeq4000.
FastQC (v0.11.5)
Single end Illumina reads were checked for quality using FastQC (v0.11.5) and they were trimmed for quality and adapters using Cutadapt (v1.12).
Each sample was mapped to the Mouse Ensembl reference genome GRCh38 using the fast alignment tool HISAT2 v2.1.0 with default settings and library type set to RF (1).
Genes in GRCm38 were quantified used HTSeq v0.9.0 using default settings  library type set to reverse.
edgeR, an R Bioconductor package, with R version 4.0, was used for differential gene analysis comparing various sample groups
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: liver, untreated, Tet2fl/fl vav cre+ with AIH

extract_protocol:
A piece of the left liver lobe (~3x3mm) was incubated in RNAlaterTM (Qiagen) at 4 °C for 48 h and stored at -80 °C until further analysis. For RNA extraction a Tissue-Tearor Homogenizer (Biospec) was used. RNA was extracted using the RNeasy Mini Kit (Qiagen).
RNA libraries for RNA-seq were prepared using Total RNA-seq Prep Kit following manufacturer's protocols.

value: liver

tag: genotype

value: Tet2fl/fl vav cre+

value: untreated

value: 20 weeks

tag: phenotype

value: spontaneously developing autoimmune hepatitis


title: BJ-LC-15_S15

tag: tissue


title: BJ-LC-14_S14

tag: age


title: Hematopoietic stem cell (HSC) 95


title: WT rep1

description: mRNA

value: WT


title: Hematopoietic stem cell (HSC) 94


title: Human_Explant_Periphery_Right_Targeted


title: Hematopoietic stem cell (HSC) 92


title: BJ-LC-10_S10

source_name: liver, untreated, Tet2fl/fl vav cre+ symptom free

value: asymptomatic


title: sptl-2 rep1

value: sptl-2 KO


title: lineage- kit+ CD41- CD150- cell 12


title: Human_Explant_Mid_Right_Targeted

source_name: Retina explant mid region


title: BJ-LC-09_S9


title: Hematopoietic stem cell (HSC) 91


title: Hematopoietic stem cell (HSC) 90


title: Hematopoietic stem cell (HSC) 89


title: HuccT1 cells treatment regorafenib 1uM


title: BJ-LC-07_S7

source_name: liver, untreated, Tet2fl/fl cre-

value: Tet2fl/fl cre-

value: healthy WT littermate controls


title: Hematopoietic stem cell (HSC) 88


title: Human_Explant_Mid_Left_Targeted

value: Retina explant


title: Human_Explant_Periphery_Left

description:
10x processed whole transcriptome
barcodes.tsv
genes.tsv
aav_barcode_key.txt


title: Human_Explant_FACS_Right

value: FACS-sorted


title: Human_Explant_Mid_Left

value: unsorted


title: Hematopoietic stem cell (HSC) 86


title: BJ-LC-06_S6


title: Human_Explant_Macula_Left

source_name: Retina explant macula region


title: Human_Explant_Macula_Left_Targeted


title: BJ-LC-12_S12


title: BJ-LC-03_S3


title: BJ-LC-11_S11


title: BJ-LC-01_S1


title: Hematopoietic stem cell (HSC) 85


title: BJ-LC-04_S4


title: Hematopoietic stem cell (HSC) 93


title: Human_Explant_Mid_Right


title: KO_t3

city: Changchun

first: Boqi

last: Zhang

state: Jilin

address: 5333 Xian Road

institute: Jilin University

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 mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads 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.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Genome_build: Beta_vulgaris.GCF_000511025.2_RefBeet-1.2.2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

value: testis

value: Aanat-/-