title: Nup133 KO ES cells (#19) day 3 technical replicate d

value: Nup133-/-,  likely 40 Chr, XY


title: Nup133 KO ES cells (#319) day 0 technical replicate c

status: Public on May 26 2023

type: SRA

city: PARIS

first: Stephane

last: Le Crom

address: 46 rue Ulm

department: Genomic Core Facility

country: France

institute: IBENS

library_source: transcriptomic

data_processing:
Illumina bcl2fastq 2.17.1.14 software was used for basecalling.
The analyses were performed using the Eoulsan pipeline version 2.0-alpha7, including read filtering, mapping, alignment filtering, read quantification, normalisation and differential analysis: Before mapping, poly N read tails were trimmed, reads ≤40 bases were removed, and reads with quality mean ≤30 were discarded. Reads were then aligned against the Mus musculus genome from Ensembl version 81 using STAR (version 2.4.0k). Alignments from reads matching more than once on the reference genome were removed using Java version of samtools. To compute gene expression, Mus musculus GFF genome annotation version 81 from Ensembl database was used. All overlapping regions between alignments and referenced exons were counted and aggregated by genes using the HTSeq-count algorithm.
Assembly: mm10 version Ensembl 81
Supplementary files format and content: tab-delimited text files include transcripts counting for each Sample

molecule: total RNA

organism: Mus musculus

source_name: Nup133 KO (merm #319)

growth_protocol: mESCs were grown at 37°C and 5% CO2 on Mitomycin-C inactivated feeder cells (DR4-mouse embryonic fibroblast) plated on 0.1% gelatin (Sigma-Aldrich) in serum/leukemia inhibitory factor (LIF, ESGRO, Millipore)-containing stem cell medium. Following trypsinization, feeders were removed by plating the resuspended cells in gelatin-free wells for 20 minutes. Feeder-free mESCs were  collected (day 0), or resuspended in N2B27 medium [Neurobasal, DMEM-F12, 7.5% BSA, N2 supplement, B27 supplement, Pen/Strep, L-glutamin, ß-mercaptoethanol] and plated at a density of 8500 cells/cm2 on gelatin-coated dishes. On day 2, cells were either collected (day 2 timepoint), or the medium was changed and supplemented with 1μM RA (all-trans-Retinoic acid, Sigma) for 24h before cell collection at day 3.

extract_protocol:
RNA extraction was performed using NucleoSpin RNAII isolation kit (Macherey-Nagel)
Library preparation and Illumina sequencing were performed at the Ecole normale superieure genomics core facility (Paris, France). Messenger (polyA+) RNAs were purified from 1 µg of total RNA using oligo(dT). Libraries were prepared using the strand specific RNA-Seq library preparation TruSeq Stranded mRNA kit (Illumina).

tag: cell line

value: Nup133 KO (merm #319)

tag: cell type

value: Embryonic stem cells

tag: genotype

value: Nup133merm/merm, Sox1gfp/+, 42 Chr, XX +8 +12

tag: time

value: day 0


title: Nup133 KO ES cells (#319) day 0 technical replicate d


title: Nup133 KO ES cells (#319) day 0 technical replicate b


title: leukocytes, DR group R_JS025

city: Shanghai

first: zhaoyu

last: xiang

state: Shanghai

address: No.85 Wujin Road

country: China

institute: Shanghai general hospital

description: leukocytes, DR group

data_processing:
The library construction and sequencing were performed by Sinotech Genomics Co., Ltd (Shanghai, China).
Paired-end sequence files (fastq) were mapped to the reference genome (GRCh38.100) using Hisat2 (Hierarchical Indexing for Spliced Alignment of Transcripts, version 2.0.5).
The output SAM (sequencing alignment/map) files were converted to BAM (binary alignment/map) files and sorted using SAMtools (version 1.3.1).
Gene abundance was expressed as fragments per kilobase of exon per million reads mapped (FPKM).
Stringtie software was used to count the fragment within each gene, and TMM algorithm was used for normalization.
Assembly: GRCh38.100
Supplementary files format and content: Excel file contains the FPKM value and original read count for each Sample

organism: Homo sapiens

source_name: Blood

growth_protocol: Blood samples were added with EDTA for anticoagulation, separated at 3000 RPM for 15min, and supernatant was obtained, preserved at -20°, and transported on dry ice.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1ul of total RNA was used for the construction of sequencing libraries.
Paired-end libraries were synthesized by using the TruSeq™ RNA Sample Preparation Kit (Illumina, USA) following TruSeq™ RNA Sample Preparation Guide. Briefly, The poly-A containing mRNA molecules were purified using poly-T oligo-attached magnetic beads.

tag: tissue

value: Blood

value: Leukocytes


title: Nup133 KO ES cells (#19) day 3 technical replicate b

value: day 3


title: MM-expr02-plate02-017

city: Seattle

first: Chengxiang

last: Qiu

state: WA

address: William H. Foege Hall, 3720 15th Ave NE

department: Genome Sciences

country: USA

institute: University of Washington

description: sci-RNA-seq3 library

data_processing:
Base calls were converted to fastq format using Illumina’s bcl2fastq/v2.20 and demultiplexed based on PCR i5 and i7 barcodes using maximum likelihood demultiplexing package deML (Renaud et al. 2015) with default settings. Downstream sequence processing and single cell digital expression matrix generation were similar to sci-RNA-seq (Cao et al. 2017) except that RT index was combined with hairpin adaptor index, and thus the mapped reads were split into constituent cellular indices by demultiplexing reads using both the RT index and ligation index (Levenshtein edit distance (ED) < 2, including insertions and deletions).
Briefly, demultiplexed reads were filtered based on RT index and ligation index (ED < 2, including insertions and deletions) and adaptor-clipped using trim_galore/v0.6.5 with default settings. Trimmed reads were mapped to the mouse reference genome (mm10) for mouse embryo nuclei, using STAR/v2.6.1d (Dobin et al. 2013) with default settings and gene annotations (GENCODE VM12 for mouse). Uniquely mapping reads were extracted, and duplicates were removed using the unique molecular identifier (UMI) sequence (ED < 2, including insertions and deletions), reverse transcription (RT) index, hairpin ligation adaptor index and read 2 end-coordinate (i.e. reads with UMI sequence less than 2 edit distance, RT index, ligation adaptor index and tagmentation site were considered duplicates).
Finally, mapped reads were split into constituent cellular indices by further demultiplexing reads using the RT index and ligation hairpin (ED < 2, including insertions and deletions). To generate digital expression matrices, we calculated the number of strand-specific UMIs for each cell mapping to the exonic and intronic regions of each gene with python/v2.7.13 HTseq package (Anders, Pyl, and Huber 2015). For multi-mapped reads, reads were assigned to the closest gene, except in cases where another intersected gene fell within 100 bp to the end of the closest gene, in which case the read was discarded. For most analyses we included both expected-strand intronic and exonic UMIs in per-gene single-cell expression matrices.
Assembly: mm10
Supplementary files format and content: Processed data files include a cell annotation csv  file, gene annotation csv file, and a gene count sparse matrix file

molecule: polyA RNA

source_name: mouse embryos

growth_protocol: The mutants were generated through conventional gene editing tools and breeding or tetraploid aggregation and collected at the embryonic stage E13.5, calculated from the day of vaginal plug (noon= E0.5). Collection and whole embryo dissection was performed as previously described (Kraft et al. 2015). The embryos were immediately snap-frozen in liquid nitrogen. Each wildtype and mutant was collected consistent within the background strain (either all male or half male half female).

extract_protocol:
The snap frozen embryos were processed as previously described (Cao et al. 2019). Briefly, the frozen embryos were cut into small pieces with a blade and further dissected by resuspension in 1 ml ice cold cell lysis buffer (CLB) in a 6 cm dish. adding another 3ml CLB, the sample was strained (40 µm) into a 15 ml Falcon tube and centrifuged to a pellet (500g, 5 min). Resuspending the sample with another 1 ml CLB, the isolation of nuclei was ensured. Pelleting the isolated nuclei again (500g, 5 min) was followed by a washing step by fixation in 10 ml 4% Paraformaldehyde (PFA) for 15 minutes on ice. The fixed nuclei were pelleted (500g, 3 min) and washed twice in the nuclei suspension buffer (NSB) (500g, 5 min). The nuclei finally were resuspended in 500µl NSB and split into 2 tubes, each containing 250 µl sample. The tubes were flash frozen in liquid nitrogen, until further use for library preparation. The embryo preparation was preceded randomly for nuclei isolation in order to avoid batch effects.
The library preparation proceeded as previously described (Cao et al. 2019). In short, the fixed nuclei were permeabilized, sonicated and washed. Nuclei from each mouse embryo were then distributed into several individual wells into 4 96-well plates. We split samples into four batches (~25 samples randomly selected in each batch) for sci-RNA-seq3 processing. The ID of the reverse transcription well was linked to the respective embryo for downstream analysis. In a first step the nuclei were then mixed with oligo-dT primers and dNTP mix, denatured and placed on ice, afterwards they were proceeded for reverse transcription including a grading incubation step. After reverse transcription, the Nuclei from all wells were pooled with the nuclei dilution buffer, spun down and redistributed into 96-well plates containing the reaction mix for ligation. The ligation was proceeded for 3 h at 16 °C. Afterwards, nuclei again were pooled with nuclei suspension buffer, spun down and washed and filtered. Next, the nuclei were counted and recistributed for second strand synthesis, which was was carried out at 16 °C for 3h. Afterwards tagmentation mix was added to each well and  tagmentation was carried out for 5 minutes. Stopping the reaction, DNA binding buffer was added and the sample was incubated for another 5 minutes. Following an elution step  using AMPure XP beads and elution mix, the samples were PCR amplified. Finally after PCR amplification, the nuclei were pooled and purified using AMPure XP beads. The library was analyzed by electrophoresis and the concentration was calculated using Qubit (Invitrogen). The library was sequenced on the NovaSeq platform (Illumina) (read 1: 34 cycles, read 2: 52 cycles, index 1: 10 cycles, index 2: 10 cycles).

tag: developmental stage

value: mouse embryo (E13.5)

tag: strain

value: C57BL/6, BALB/C, FVB, G4

value: multiplexed sample:WT and mutant


title: leukocytes, DR group R_JS023

description: leukocytes, DR group


title: Nup133 KO ES cells (#19) day 3 technical replicate c


title: leukocytes, DR group R_JS024

description: leukocytes, DR group


title: leukocytes, DR group R_JS027

description: leukocytes, DR group


title: MM-expr02-plate02-016

description: sci-RNA-seq3 library


title: leukocytes, DR group R_JS022

description: leukocytes, DR group


title: Nup133 KO ES cells (#19) day 2 technical replicate c

value: day 2


title: Nup133 KO ES cells (#19) day 2 technical replicate a


title: Nup133 KO ES cells (#19) day 2 technical replicate b


title: Nup133 KO ES cells (#19) day 2 technical replicate d


title: MM-expr02-plate02-015

description: sci-RNA-seq3 library


title: Nup133 KO ES cells (#19) day 0 technical replicate d


title: Nup133 KO ES cells (#19) day 3 technical replicate a


title: MM-expr02-plate02-014

description: sci-RNA-seq3 library


title: MM-expr02-plate02-013

description: sci-RNA-seq3 library


title: Nup133 KO ES cells (#19) day 0 technical replicate c


title: leukocytes, DR group R_JS020

description: leukocytes, DR group


title: leukocytes, DR group R_JS021

description: leukocytes, DR group


title: Nup133 KO ES cells (#19) day 0 technical replicate b


title: leukocytes, DR group R_JS018

description: leukocytes, DR group


title: Nup133 KO ES cells (#19) day 0 technical replicate a


title: leukocytes, DR group R_JS030

description: leukocytes, DR group


title: MM-expr02-plate02-010

description: sci-RNA-seq3 library


title: MM-expr02-plate02-011

description: sci-RNA-seq3 library


title: MM-expr02-plate02-012

description: sci-RNA-seq3 library


title: MM-expr02-plate02-009

description: sci-RNA-seq3 library


title: Nup133 KO ES cells (#14) day 3 technical replicate d


title: leukocytes, DR group R_JS019

description: leukocytes, DR group


title: indPRPL4 leaf discs, dexamethasone-induced overexpression, biol rep 5

city: Milano

first: Federico

last: Zambelli

address: Via Giovanni Celoria 26

department: Department of Biosciences

country: Italy

institute: University of Milan

data_processing:
STAR-RSEM software was employed for read mapping and quantification on Arabidopsis reference genome (TAIR10)
Differentially expressed genes have been identified through EdgeR Software.
Before DEGs calling, lowly expressed genes have been filtered by removing genes without at least 2 counts in at least 1 sample and a total number of counts lower than 10
Called DEGs were statistically filtered via Benjamini-Hochberg False Discovery Rate method (FDR < 0.05)
Assembly: TAIR10
Supplementary files format and content: Excel file (.xlsx) with RSEM expected counts matrix

organism: Arabidopsis thaliana

source_name: Young leaf material

growth_protocol: indPRPS1 and indPRPL4 inducible lines were sown on soil and placed in climate chambers for 16 days at 22 °C under long day conditions (150 μmol m−2 sec−1 16 h light/8 h dark cycles)

extract_protocol:
Total RNA extraction was performed using RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions.
Total RNA

treatment_protocol: leaf discs harvested from 16 DAS plants were vacuum infiltrated in either absence or presence of 2 µM dexamethasone and incubated for 6 hours.

value: Young leaf material

value: Col-0 trasformed with a T-DNA containing PRPL4 CDS under the control of dexamethasone-inducible promoter

tag: treatment

value: dexamethasone


title: leukocytes, DR group R_JS016

description: leukocytes, DR group


title: Nup133 KO ES cells (#14) day 3 technical replicate c


title: indPRPL4 leaf discs, dexamethasone-induced overexpression, biol rep 4


title: Nup133 KO ES cells (#14) day 3 technical replicate b


title: leukocytes, DR group R_JS014

description: leukocytes, DR group


title: indPRPL4 leaf discs, dexamethasone-induced overexpression, biol rep 2


title: leukocytes, DR group R_JS013

description: leukocytes, DR group


title: leukocytes, DR group R_JS017

description: leukocytes, DR group


title: MM-expr02-plate02-006

description: sci-RNA-seq3 library


title: MM-expr02-plate02-007

description: sci-RNA-seq3 library


title: MM-expr02-plate02-003

description: sci-RNA-seq3 library


title: MM-expr02-plate02-005

description: sci-RNA-seq3 library


title: leukocytes, DR group R_JS012

description: leukocytes, DR group


title: indPRPL4 leaf discs, no dexamethasone control, biol rep 3

value: no


title: MM-expr02-plate02-004

description: sci-RNA-seq3 library


title: indPRPL4 leaf discs, no dexamethasone control, biol rep 5


title: MM-expr02-plate02-002

description: sci-RNA-seq3 library


title: MM-expr02-plate02-008

description: sci-RNA-seq3 library


title: leukocytes, DR group R_JS011

description: leukocytes, DR group


title: indPRPL4 leaf discs, no dexamethasone control, biol rep 4


title: Nup133 KO ES cells (#14) day 2 technical replicate c


title: Nup133 KO ES cells (#14) day 2 technical replicate d


title: Nup133 KO ES cells (#14) day 3 technical replicate a


title: indPRPL4 leaf discs, no dexamethasone control, biol rep 2


title: leukocytes, DR group R_JS009

description: leukocytes, DR group


title: MM-expr02-plate02-001

description: sci-RNA-seq3 library


title: indPRPL4 leaf discs, dexamethasone-induced overexpression, biol rep 1


title: Nup133 KO ES cells (#14) day 2 technical replicate a


title: leukocytes, DR group R_JS015

description: leukocytes, DR group


title: indPRPL4 leaf discs, dexamethasone-induced overexpression, biol rep 3


title: leukocytes, DR group R_JS008

description: leukocytes, DR group


title: indPRPL4 leaf discs, no dexamethasone control, biol rep 1


title: Nup133 KO ES cells (#14) day 0 technical replicate d


title: leukocytes, DR group R_JS010

description: leukocytes, DR group


title: Nup133 KO ES cells (#14) day 0 technical replicate c


title: indPRPS1 leaf discs, dexamethasone-induced overexpression, biol rep 5

value: Col-0 trasformed with a T-DNA containing PRPS1 CDS under the control of dexamethasone-inducible promoter


title: leukocytes, DR group R_JS007

description: leukocytes, DR group


title: leukocytes, DR group R_JS006

description: leukocytes, DR group


title: MM-expr02-plate01-096

description: sci-RNA-seq3 library


title: WT ES cells (#1A4) day 3 technical replicate d

value: Nup133+/+, Sox1gfp/+, 40 Chr, XY


title: MM-expr02-plate01-094

description: sci-RNA-seq3 library


title: leukocytes, DR group R_JS005

description: leukocytes, DR group


title: WT ES cells (#1A4) day 3 technical replicate c


title: Nup133 KO ES cells (#14) day 0 technical replicate b


title: indPRPS1 leaf discs, dexamethasone-induced overexpression, biol rep 3


title: MM-expr02-plate01-092

description: sci-RNA-seq3 library


title: MM-expr02-plate01-095

description: sci-RNA-seq3 library


title: MM-expr02-plate01-093

description: sci-RNA-seq3 library


title: leukocytes, DR group R_JS004

description: leukocytes, DR group


title: leukocytes, DR group R_JS003

description: leukocytes, DR group


title: WT ES cells (#1A4) day 3 technical replicate b


title: indPRPS1 leaf discs, dexamethasone-induced overexpression, biol rep 1


title: MM-expr02-plate01-091

description: sci-RNA-seq3 library


title: WT ES cells (#1A4) day 3 technical replicate a


title: leukocytes, DR group R_JS002

description: leukocytes, DR group


title: indPRPS1 leaf discs, no dexamethasone control, biol rep 5


title: Nup133 KO ES cells (#14) day 0 technical replicate a


title: MM-expr02-plate01-090

description: sci-RNA-seq3 library


title: indPRPS1 leaf discs, dexamethasone-induced overexpression, biol rep 4


title: Nup133 KO ES cells (#14) day 2 technical replicate b


title: indPRPS1 leaf discs, no dexamethasone control, biol rep 4


title: MM-expr02-plate01-089

description: sci-RNA-seq3 library


title: indPRPS1 leaf discs, dexamethasone-induced overexpression, biol rep 2


title: indPRPS1 leaf discs, no dexamethasone control, biol rep 3


title: MM-expr02-plate01-088

description: sci-RNA-seq3 library


title: leukocytes, DM group RNA97

description: leukocytes, DM group


title: indPRPS1 leaf discs, no dexamethasone control, biol rep 2


title: leukocytes, DR group RNA98

description: leukocytes, DR group


title: WT ES cells (#1A4) day 2 technical replicate c


title: MM-expr02-plate01-087

description: sci-RNA-seq3 library


title: Fibrinogen(+)-cancer

type: RNA

city: Matsumoto

first: Sachie

last: Hiratsuka

address: 3-1-1 Asahi

department: Medicine

country: Japan

institute: Shinshu University

hyb_protocol: Five micro g of labeled cDNA was hybridized for 18h on Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in a GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned by using a GeneChip Scanner 3000 7G.

data_processing:
The data ware analyzed with AGCC (Affymetrix GeneChip Command Console Software) and further processed by Affymetrix Expression Console.
Algorithm: ExpressionStat 5.0

label: biotin

source_name: Fibrinogen(+)-cancer

label_protocol: First strand cDNAs were prepared by using Ovation Pico WTA System V2 (NuGEN technologies). Then, 2nd strand cDNAs were synthesized. After purification of the cDNAs, they were amplified by using SPIA Amplification. Then, cDNAs were further column purified, fragmentized and biotinylated by using Encore cDNA Biotin Module.

growth_protocol: A lung FFPE section was stained with anti-Fibrinogen rabbit antibody (DAKO, A0080) to spot the precise locations of fibrinogen depositions. Fibrinogen positive and negative areas were collected by using laser microdissection (Zeiss PALM Microbeam IV).

extract_protocol: FFPE RNA isolation kit was used to isolate total RNA from the four sample pools.

treatment_protocol: Dissected samples from Fibrinogen(-)-non-cancer patients, Fibrinogen(+)-non-cancer patients, Fibrinogen(-)-cancer patients, and Fibrinogen(+)-cancer patients were pooled independently.

value: Lung

tag: subject status

value: cancer patient


title: WT ES cells (#1A4) day 2 technical replicate b

value: Embryonic stem cells


title: WT ES cells (#1A4) day 2 technical replicate a


title: indPRPS1 leaf discs, no dexamethasone control, biol rep 1


title: leukocytes, DM group RNA95

description: leukocytes, DM group


title: MM-expr02-plate01-086

description: sci-RNA-seq3 library


title: Fibrinogen(+)-non-cancer

source_name: Fibrinogen(+)-non-cancer

value: non-cancer patient


title: WT ES cells (#1A4) day 0 technical replicate d

value: day 0


title: WT ES cells (#1A4) day 2 technical replicate d


title: leukocytes, DR group R_JS001

description: leukocytes, DR group

value: Blood

value: Leukocytes


title: MM-expr02-plate01-085

description: sci-RNA-seq3 library

value: mouse embryo (E13.5)


title: WT ES cells (#1A4) day 0 technical replicate c


title: leukocytes, DM group RNA89

description: leukocytes, DM group


title: Fibrinogen(-)-cancer

source_name: Fibrinogen(-)-cancer


title: WT ES cells (#1A4) day 0 technical replicate b


title: WT ES cells (#1A4) day 0 technical replicate a


title: 4xko_IgG_2_S11

first: Brian

last: Hanratty

address: 1100 Fairview Avenue

department: Division of Human Biology

institute: Fred Hutchinson Cancer Cancer

library_source: genomic

data_processing:
library strategy: CUT&RUN
Sequence reads were aligned to hg38 using bowtie2 with the options --end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700
narrowPeak files were genereated using MACS2 on .bam files with IgG as control using default settings
Assembly: h38
Supplementary files format and content: MACS2 narrowPeak file

molecule: genomic DNA

extract_protocol:
low-salt CUT&RUN protocol
MicroPlex Library Preparation Kit v2 (Diagenode, catalog C05010014)

value: Prostate Adenocarcinoma

tag: chip antibody

value: Cell Signaling Technology, #3900S


title: 4xko_IgG_3_S12


title: 4xko_IgG_1_S10


title: leukocytes, Control group RNA90

description: leukocytes, Control group


title: leukocytes, DM group RNA87

description: leukocytes, DM group


title: 4xKO_RBL2_vs_IgG_3

value: AtlasAntibodies, #HPA019703


title: leukocytes, DR group RNA86

description: leukocytes, DR group


title: 4xKO_RBL2_vs_IgG_2


title: MM-expr02-plate01-084

description: sci-RNA-seq3 library

value: C57BL/6, BALB/C, FVB, G4

value: multiplexed sample:WT and mutant


title: WT ES cells (HM1) day 3 biol rep 2 technical replicate d

value: day 3


title: MM-expr02-plate01-082

description: sci-RNA-seq3 library


title: MM-expr02-plate01-083

description: sci-RNA-seq3 library


title: MM-expr02-plate01-081

description: sci-RNA-seq3 library


title: 4xKO_RBL2_vs_IgG_1


title: WT ES cells(HM1)  day 3 biol rep 2 technical replicate c


title: leukocytes, DR group RNA94

description: leukocytes, DR group


title: leukocytes, DR group RNA78

description: leukocytes, DR group


title: WT ES cells (HM1) day 3 biol rep 2 technical replicate b


title: 4xKO_RBL1_vs_IgG_3

value: Invitrogen, #PA5-84228


title: leukocytes, DM group RNA74

description: leukocytes, DM group


title: WT ES cells (HM1) day 3 biol rep 2 technical replicate a


title: 4xKO_RBL1_vs_IgG_2


title: leukocytes, DM group RNA72

description: leukocytes, DM group


title: WT ES cells (HM1) day 2 biol rep 2  technical replicate d

value: day 2


title: MM-expr02-plate01-080

description: sci-RNA-seq3 library


title: MM-expr02-plate01-079

description: sci-RNA-seq3 library


title: MM-expr02-plate01-078

description: sci-RNA-seq3 library


title: leukocytes, DM group RNA7

description: leukocytes, DM group


title: WT ES cells (HM1) day 2 biol rep 2  technical replicate c


title: 4xKO_RBL1_vs_IgG_1


title: 4xKO_RB1_vs_IgG_3

value: Thermo Fisher Scientific, #PA5-27215


title: leukocytes, DM group RNA69

description: leukocytes, DM group


title: MM-expr02-plate01-077

description: sci-RNA-seq3 library


title: 4xKO_RB1_vs_IgG_1


title: leukocytes, DM group RNA67

description: leukocytes, DM group


title: MM-expr02-plate01-075

description: sci-RNA-seq3 library


title: MM-expr02-plate01-076

description: sci-RNA-seq3 library


title: WT ES cells (HM1) day 0 biol rep 2 technical replicate d


title: WT ES cells (HM1) day 2 biol rep 2 technical replicate a


title: leukocytes, DM group RNA75

description: leukocytes, DM group


title: L2KO_RBL1_vs_IgG_3


title: 4xKO_RB1_vs_IgG_2


title: leukocytes, DM group RNA66

description: leukocytes, DM group


title: leukocytes, DM group RNA64

description: leukocytes, DM group


title: MM-expr02-plate01-073

description: sci-RNA-seq3 library


title: MM-expr02-plate01-074

description: sci-RNA-seq3 library


title: WT ES cells (HM1) day 0 biol rep 2 technical replicate b


title: MM-expr02-plate01-072

description: sci-RNA-seq3 library


title: leukocytes, DM group RNA63

description: leukocytes, DM group


title: leukocytes, DM group RNA62

description: leukocytes, DM group


title: WT ES cells (HM1) day 0 biol rep 2 technical replicate a


title: WT ES cells (HM1) day 2 biol rep 2 technical replicate b


title: L2KO_RBL1_vs_IgG_2


title: L2KO_RBL1_vs_IgG_1


title: leukocytes, DM group RNA60

description: leukocytes, DM group


title: L1KO_RBL2_vs_IgG_3


title: WT ES cells (HM1) day 3 biol rep 1 technical replicate d


title: WT ES cells (HM1) day 0 biol rep 2 technical replicate c


title: WT ES cells(HM1)  day 3 biol rep 1 technical replicate c


title: leukocytes, DM group RNA58

description: leukocytes, DM group


title: MM-expr02-plate01-069

description: sci-RNA-seq3 library


title: MM-expr02-plate01-070

description: sci-RNA-seq3 library


title: MM-expr02-plate01-067

description: sci-RNA-seq3 library


title: WT ES cells (HM1) day 3 biol rep 1 technical replicate b


title: WT ES cells (HM1) day 3 biol rep 1 technical replicate a


title: leukocytes, DM group RNA6

description: leukocytes, DM group


title: leukocytes, Control group RNA57

description: leukocytes, Control group


title: LNCaP_RB1_vs_IgG_3

source_name: LNCaP

value: LNCaP


title: LNCaP_RB1_vs_IgG_2


title: MM-expr02-plate01-066

description: sci-RNA-seq3 library


title: L1KO_RBL2_vs_IgG_1


title: WT ES cells (HM1) day 2 biol rep 1  technical replicate d


title: leukocytes, DR group RNA535

description: leukocytes, DR group


title: MM-expr02-plate01-071

description: sci-RNA-seq3 library


title: LNCaP_RB1_vs_IgG_1


title: MM-expr02-plate01-065

description: sci-RNA-seq3 library


title: Fibrinogen(-)-non-cancer

source_name: Fibrinogen(-)-non-cancer

value: Lung


title: leukocytes, DM group RNA53

description: leukocytes, DM group


title: WT ES cells (HM1) day 2 biol rep 1  technical replicate c

value: Embryonic stem cells


title: B72_R1881_input

data_processing:
reads were trimmed and aligned with BWA , coordinate sorted, filtered to exclude low quality (<Q30) reads
Sam to bam with samtools
Sort with samtools
Mark duplicates with picard
Assembly: hg38
Supplementary files format and content: narrowPeak files were generated from .bam files using MACS2 using input controls and default settings

source_name: LNCaP-DKO B72

growth_protocol: Cell lines were cultured in RPMI-1640 containing 10% FBS

extract_protocol:
iDeal ChIP-seq Kit for Transcription Factors (Diagenode, #C01010170)
MicroPlex Library Preparation Kit v3 (Diagenode, #C05010014) and 24 Dual indexes for MicroPlex Kit v3 (Diagenode, #C05010003)

treatment_protocol: Samples labled "R1881" were treated with 10nM R1881

value: LNCaP-DKO B72

value: Prostate adenocarcinoma


title: L1KO_RBL2_vs_IgG_2


title: WT ES cells (HM1) day 2 biol rep 1 technical replicate b


title: leukocytes, DM group RNA528

description: leukocytes, DM group

value: Blood


title: MM-expr02-plate01-064

description: sci-RNA-seq3 library


title: MM-expr02-plate01-068

description: sci-RNA-seq3 library


title: MM-expr02-plate01-063

description: sci-RNA-seq3 library


title: WT ES cells (HM1) day 2 biol rep 1 technical replicate a


title: leukocytes, DM group RNA521

description: leukocytes, DM group

value: Leukocytes


title: leukocytes, DM group RNA52

description: leukocytes, DM group


title: MM-expr02-plate01-062

description: sci-RNA-seq3 library

value: mouse embryo (E13.5)


title: WT ES cells (HM1) day 0 biol rep 1 technical replicate c

value: day 0


title: leukocytes, DM group RNA519

description: leukocytes, DM group


title: LNCaP_LIN9_DF_LNCaP_R1881

value: Bethyl Laboratories, A300-BL2981


title: MM-expr02-plate01-060

description: sci-RNA-seq3 library


title: leukocytes, Control group RNA516

description: leukocytes, Control group


title: LNCaP_LIN9_LNCaP_DF_EtOH


title: MM-expr02-plate01-059

description: sci-RNA-seq3 library


title: LNCaP_LIN37_DF_LNCaP_R1881

value: Bethyl Laboratories, A300-BL298


title: LNCaP_LIN37_DF_EtOH


title: WT ES cells (HM1) day 0 biol rep 1 technical replicate a


title: leukocytes, Control group RNA511

description: leukocytes, Control group


title: WT ES cells (HM1) day 0 biol rep 1 technical replicate b


title: MM-expr02-plate01-058

description: sci-RNA-seq3 library

value: C57BL/6, BALB/C, FVB, G4


title: B72_IgG_R1881

value: Cell Signaling Technology, #3900S


title: leukocytes, Control group RNA51

description: leukocytes, Control group


title: B72_vehicle_input


title: MM-expr02-plate01-057

description: sci-RNA-seq3 library

value: multiplexed sample:WT and mutant


title: B72_IgG_vehicle


title: leukocytes, Control group RNA505

description: leukocytes, Control group


title: XBP_IRE_3_S11

city: Santiago

first: Fabiola

last: Osorio

address: Av Independencia 1027, wing I, lower floor

department: Immunology

country: Chile

institute: Universidad de Chile

data_processing:
Illumina software was used for basecalling.
Sequenced reads were inspected with FastQC v0.11.8, trimmed for adaptor sequences with Trimmomatic v0.39, then mapped to mm10 whole genome using STAR v2.7.3a and finally counted with HTSeqCount v0.11.2
Limma v3.42.2 was used to normalize the count data.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with log-CPM values for all biologically meaningfully expressed genes for each Sample

source_name: cDC1s from B16 melanoma

extract_protocol:
Cell suspensions from tumor tissue pooled from 2-4 B16 bearing mice were enriched in immune cells by positive selection with CD45+ biotin magnetic beads (MACS, Miltenyi). Intratumoral cDC1s were cell sorted directly in RLT lysis buffer (Qiagen) containing 2-mercaptoethanol. Immediately after sorting, collected cells were homogenized through vortex and frozen on dry ice before storage at -80°C. Total RNA was extracted with RNAeasy Plus Micro kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: B16 melanoma

value: XBP1 fl/fl, IRE1 fl/fl, CD11c-CRE


title: WT ES cells (HM1) day 0 biol rep 1 technical replicate d


title: B72_E2F1_R1881_3b

value: BDBiosciences, #554213


title: XBP_IRE_2_S10


title: MM-expr02-plate01-061

description: sci-RNA-seq3 library


title: XBP_IRE_1_S9


title: MM-expr02-plate01-056

description: sci-RNA-seq3 library


title: leukocytes, DM group RNA504

description: leukocytes, DM group


title: B72_E2F1_R1881_2b


title: MM-expr02-plate01-055

description: sci-RNA-seq3 library


title: XBP_4_S8

value: XBP1 fl/fl, CD11c-CRE


title: MM-expr02-plate01-054

description: sci-RNA-seq3 library


title: leukocytes, DR group RNA50

description: leukocytes, DR group


title: B72_E2F1_EtOH_3


title: XBP_3_S7


title: leukocytes, DM group RNA499

description: leukocytes, DM group


title: XBP_2_S6


title: MM-expr02-plate01-053

description: sci-RNA-seq3 library


title: B72_E2F1_EtOH_2


title: MM-expr02-plate01-052

description: sci-RNA-seq3 library


title: XBP_1_S5


title: WT_4_S4

value: XBP1 fl/fl, IRE1 fl/fl


title: leukocytes, DM group RNA488

description: leukocytes, DM group


title: R1AD1_10nM_R1881_2_48hrs

first: Ilsa

last: Coleman

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

data_processing:
Sequencing reads were mapped to the hg38 human genome using STAR.v2.7.3a.
Gene level abundance was quantitated using the GenomicAlignments summarizeOverlaps function using mode=IntersectionStrict, restricting to primary aligned reads, and counting reads mapping to the exonic regions of genes.
Assembly: hg38
Supplementary files format and content: Processed files are tab-delimited text files. Each file contains 7 columns: Entrez Gene ID, gene symbol, gene name, mRNA size, raw fragment count (by gene), FPM (fragments per million reads mapped) and FPKM (fragments per kilobase per million reads mapped).

source_name: R1AD1 human prostate tumor cell line

extract_protocol:
Total RNA was isolated from cell line samples using the RNeasy Mini Kit (Qiagen, cat#74134) with DNase digestion.
RNA-seq libraries were constructed from total RNA using the Illumina TruSeq Stranded mRNA LT Sample Prep Kit according to the manufacturer’s protocol.

treatment_protocol: Cells were cultured for 48 hours in their normal growth media (10% FBS) with 10nM R1881. After 48 hours, RNA was harvested.

tag: Sex

value: male

value: prostate cancer

tag: growth media

value: Cells were cultured in RPMI-1640, no phenol red (GIBCO, cat#11835030) with 10% FBS (GIBCO, cat#10437-02).

tag: timepoint

value: 48 hours


title: WT_3_S3

value: XBP1 fl/fl


title: MM-expr02-plate01-050

description: sci-RNA-seq3 library

value: mouse embryo (E13.5)


title: MM-expr02-plate01-049

description: sci-RNA-seq3 library


title: leukocytes, Control group RNA500

description: leukocytes, Control group

value: Blood

value: Leukocytes


title: leukocytes, Control group RNA484

description: leukocytes, Control group


title: WT_2_S2


title: WT_1_S1


title: B72_E2F1_R1881_1b

value: LNCaP-DKO B72

value: Prostate adenocarcinoma


title: MM-expr02-plate01-048

description: sci-RNA-seq3 library

value: C57BL/6, BALB/C, FVB, G4


title: R1AD1_10uM_ENZA_2_48hrs

treatment_protocol: Cells were cultured for 48 hours in their normal growth media (10% FBS) with 10uM enzalutamide. After 48 hours, RNA was harvested.


title: R1AD1_10uM_ENZA_1_48hrs


title: leukocytes, Control group RNA482

description: leukocytes, Control group


title: leukocytes, Control group RNA48

description: leukocytes, Control group


title: B72_E2F1_EtOH_1


title: R1AD1_DMSO_Veh_2_48hrs

treatment_protocol: Cells were cultured for 48 hours in their normal growth media (10% FBS) with vehicle (DMSO). After 48 hours, RNA was harvested.


title: leukocytes, Control group RNA49

description: leukocytes, Control group


title: MM-expr02-plate01-051

description: sci-RNA-seq3 library

value: multiplexed sample:WT and mutant


title: leukocytes, Control group RNA479

description: leukocytes, Control group


title: R1AD1_DMSO_Veh_1_48hrs


title: 22PC-EP_10nM_R1881_2_48hrs

source_name: 22PC-EP human prostate tumor cell line


title: leukocytes, DM group RNA476

description: leukocytes, DM group


title: leukocytes, DM group RNA483

description: leukocytes, DM group


title: R1AD1_10nM_R1881_1_48hrs


title: MM-expr02-plate01-047

description: sci-RNA-seq3 library


title: MM-expr02-plate01-046

description: sci-RNA-seq3 library


title: MM-expr02-plate01-045

description: sci-RNA-seq3 library


title: 22PC-EP_10uM_ENZA_2_48hrs


title: leukocytes, Control group RNA47

description: leukocytes, Control group


title: 22PC-EP_10nM_R1881_1_48hrs


title: leukocytes, Control group RNA469

description: leukocytes, Control group


title: 22PC-EP_10uM_ENZA_1_48hrs


title: leukocytes, DM group RNA471

description: leukocytes, DM group


title: MM-expr02-plate01-043

description: sci-RNA-seq3 library


title: MM-expr02-plate01-041

description: sci-RNA-seq3 library


title: MM-expr02-plate01-044

description: sci-RNA-seq3 library


title: leukocytes, DM group RNA466

description: leukocytes, DM group


title: MM-expr02-plate01-042

description: sci-RNA-seq3 library


title: leukocytes, DM group RNA457

description: leukocytes, DM group


title: 22PC-EP_DMSO_Veh_2_48hrs


title: 22PC-EP_DMSO_Veh_1_48hrs


title: MM-expr02-plate01-040

description: sci-RNA-seq3 library


title: MM-expr02-plate01-039

description: sci-RNA-seq3 library


title: leukocytes, Control group RNA456

description: leukocytes, Control group


title: LAPC4_10nM_R1881_2_48hrs

source_name: LAPC4 human prostate tumor cell line

value: Cells were cultured in IMDM, no phenol red (Thermo Fisher Scientific, cat#21056023) with 10% FBS (GIBCO, cat#10437-02).


title: U2OS, Screen, Rep1 [ISG]

city: Dallas

first: John

last: Schoggins

state: TX

address: 6000 Harry Hines Blvd

department: Microbiology

institute: UT Southwestern Medical Center

description:
S1_A07_S4_R1_001
PCR amplicon

data_processing:
Bcl files were demultiplexed using bcl2fastq (v2.20).
sgRNA sequences were trimmed using an inhouse script.
Enriched genes and normalized read counts were identified via MAGeCK, Model-based Analysis of Genome-wide CRISPR/Cas9 Knockout (MAGeCK) method for prioritizing single-guide RNAs, genes and pathways in genome-scale CRISPR/Cas9 knockout screens.
Assembly: Human Interferon-Stimulated Gene CRISPR Knockout Library (Addgene Pooled Library #125753).
Supplementary files format and content: JS.count.txt: Tab-delimited text file that includes the raw counts for each sgRNA.

source_name: U-2 OS

growth_protocol: U-2 OS cells were treated with CRISPR-library lentivirus for 2 days, then selected with media containing 1 ug/mL puromycin for 3 days. Cells were then maintained in 0.5 ug/mL puromycin before being plated into 15cm dishes. Cells were treated with IFNβ 20U/mL for 24 hours and then infected with VEEV (TC-83 strain) for 5hrs. The infected cells were harvested and prepared for flow cytometry. By FACS, GFP-positive gated cells were collected, pelleted, and lysed for genomic DNA extraction.

extract_protocol:
Genomic DNA was extracted by phenol:chloroform:isoamyl alcohol and purified by ethanol precipitation.
Three micrograms of total genomic DNA were used per PCR reaction with barcoded primers to produce a CRISPR amplicon library for each sample. Amplicon library samples were purified with AmpureXP beads and tested for purity by Agilent Bioanalyzer and qPCR with sequencing specific primers. Samples were quantified by Qubit, pooled, then sequenced on an Illumina NextSeq 500.

value: U-2 OS

value: osteosarcoma epithelial cells

tag: condition

value: Screen

value: IFNbeta

tag: infection

value: Venezuelan equine encephalitis virus


title: U2OS, Input, Rep 1 [ISG]

description:
In1_A01_S1_R1_001
PCR amplicon

value: Control


title: leukocytes, Control group RNA455

description: leukocytes, Control group


title: U2OS, Screen, Rep2 [ISG]

description:
S2_B05_S5_R1_001
PCR amplicon


title: U2OS, Screen, Rep1 [GW]

description:
S1_B01_S2_R1_001
PCR amplicon

data_processing:
Bcl files were demultiplexed using bcl2fastq (v2.20).
sgRNA sequences were trimmed using an inhouse script.
Enriched genes and normalized read counts were identified via MAGeCK, Model-based Analysis of Genome-wide CRISPR/Cas9 Knockout (MAGeCK) method for prioritizing single-guide RNAs, genes and pathways in genome-scale CRISPR/Cas9 knockout screens.
Assembly: Human CRISPR Knockout Pooled Library (Brunello).
Supplementary files format and content: JSMO.count.txt: Tab-delimited text file that includes the raw counts for each sgRNA.

extract_protocol:
Genomic DNA was extracted by phenol:chloroform:isoamyl alcohol and purified by ethanol precipitation.
Six micrograms of total genomic DNA were used per PCR reaction with barcoded primers to produce a CRISPR amplicon library for each sample. Amplicon library samples were purified with AmpureXP beads and tested for purity by Agilent Bioanalyzer and qPCR with sequencing specific primers. Samples were quantified by Qubit, pooled, then sequenced on an Illumina NextSeq 500.


title: U2OS, Input, Rep 3 [ISG]

description:
In3_A06_S3_R1_001
PCR amplicon


title: U2OS, Input, Rep 2 [ISG]

description:
In2_A02_S2_R1_001
PCR amplicon


title: U2OS, Input, Rep 1 [GW]

description:
In1_A01_S1_R1_001
PCR amplicon


title: U2OS, Input, Rep 2 [GW]

description:
In2_A02_S3_R1_001
PCR amplicon


title: U2OS, Screen, Rep3 [ISG]

description:
S3_B06_S6_R1_001
PCR amplicon


title: MM-expr02-plate01-038

description: sci-RNA-seq3 library


title: LAPC4_10nM_R1881_1_48hrs

value: male

value: prostate cancer


title: leukocytes, DM group RNA454

description: leukocytes, DM group


title: MM-expr02-plate01-037

description: sci-RNA-seq3 library


title: LAPC4_10uM_ENZA_2_48hrs

value: 48 hours


title: U2OS, Screen, Rep2 [GW]

description:
S2_B02_S4_R1_001
PCR amplicon


title: MM-expr02-plate01-036

description: sci-RNA-seq3 library

value: mouse embryo (E13.5)


title: leukocytes, Control group RNA449

description: leukocytes, Control group

value: Blood


title: LAPC4_10uM_ENZA_1_48hrs


title: LAPC4_DMSO_Veh_2_48hrs


title: MM-expr02-plate01-035

description: sci-RNA-seq3 library


title: leukocytes, DM group RNA442

description: leukocytes, DM group

value: Leukocytes


title: MM-expr02-plate01-034

description: sci-RNA-seq3 library


title: MM-expr02-plate01-033

description: sci-RNA-seq3 library


title: VCAP_10nM_R1881_2_48hrs

source_name: VCaP (ATCC, CRL-2876) human prostate tumor cell line

value: Cells were cultured in DMEM/F12, no phenol red (Thermo Fisher Scientific, cat#11039021) with 10% FBS (GIBCO, cat#10437-02).


title: leukocytes, Control group RNA441

description: leukocytes, Control group


title: leukocytes, DR group RNA44

description: leukocytes, DR group


title: leukocytes, Control group RNA437

description: leukocytes, Control group


title: LAPC4_DMSO_Veh_1_48hrs


title: VCAP_10nM_R1881_1_48hrs


title: VCAP_10uM_ENZA_2_48hrs


title: leukocytes, DR group RNA431

description: leukocytes, DR group


title: leukocytes, Control group RNA425

description: leukocytes, Control group


title: VCAP_10uM_ENZA_1_48hrs


title: VCAP_DMSO_Veh_2_48hrs


title: MM-expr02-plate01-031

description: sci-RNA-seq3 library


title: MM-expr02-plate01-032

description: sci-RNA-seq3 library


title: VCAP_DMSO_Veh_1_48hrs


title: MM-expr02-plate01-028

description: sci-RNA-seq3 library


title: ID10v6, SCI, 6mpi

city: Manhasset

first: Ona

last: Bloom

state: New York

address: 350 Community Dr

department: Molecular Medicine

institute: Feinstein Institute

data_processing:
Partek Genomics Flow software
trimmed reads aligned to hg38 genome assembly using STAR
filtered for expression >50
normalized using the Trimmed Mean of M-values (TMM) method using the edgeR package
log2 transformed
Assembly: hg38

source_name: Whole blood

extract_protocol:
Total RNA was isolated using the PAXgene total RNA kit and the Qiagen QIAcube, acccording to manufacturer's protocol
RNA seq libraries were prepared using Illumina TruSeq Stranded Total RNA according to manufacturer's instructions.

value: Whole blood

tag: group

value: SCI


title: MM-expr02-plate01-027

description: sci-RNA-seq3 library

value: C57BL/6, BALB/C, FVB, G4

value: multiplexed sample:WT and mutant


title: ID10v12, SCI, 12mpi


title: leukocytes, Control group RNA419

description: leukocytes, Control group


title: MM-expr02-plate01-030

description: sci-RNA-seq3 library


title: LNCaP_10uM_ENZA_2_48hrs

source_name: LNCaP (ATCC, CRL-1740) human prostate tumor cell line

value: Cells were cultured in RPMI-1640, no phenol red (GIBCO, cat#11835030) with 10% FBS (GIBCO, cat#10437-02).


title: MM-expr02-plate01-026

description: sci-RNA-seq3 library


title: leukocytes, DM group RNA409

description: leukocytes, DM group

source_name: Blood


title: ID10v3, SCI, 3mpi


title: LNCaP_10uM_ENZA_1_48hrs


title: leukocytes, Control group RNA400

description: leukocytes, Control group


title: MM-expr02-plate01-025

description: sci-RNA-seq3 library

source_name: mouse embryos


title: LNCaP_48h_R1881_1nM_2

treatment_protocol: Cells were cultured for 48 hours in their normal growth media (10% FBS) with 1nM R1881. After 48 hours, RNA was harvested.


title: ID9v6, SCI,  6mpi


title: MM-expr02-plate01-029

description: sci-RNA-seq3 library


title: leukocytes, Control group RNA396

description: leukocytes, Control group


title: leukocytes, DM group RNA418

description: leukocytes, DM group


title: leukocytes, DR group RNA39

description: leukocytes, DR group


title: ID9v3, SCI,  3mpi


title: MM-expr02-plate01-022

description: sci-RNA-seq3 library


title: LNCaP_48h_R1881_10pM_2

treatment_protocol: Cells were cultured for 48 hours in their normal growth media (10% FBS) with 10pM R1881. After 48 hours, RNA was harvested.


title: MM-expr02-plate01-021

description: sci-RNA-seq3 library


title: LNCaP_48h_R1881_100pM_1

treatment_protocol: Cells were cultured for 48 hours in their normal growth media (10% FBS) with 100pM R1881. After 48 hours, RNA was harvested.


title: leukocytes, DR group RNA385

description: leukocytes, DR group


title: MM-expr02-plate01-020

description: sci-RNA-seq3 library


title: ID8v12, SCI, 12mpi


title: leukocytes, DM group RNA41

description: leukocytes, DM group


title: LNCaP_48h_R1881_10pM_1


title: leukocytes, DM group RNA392

description: leukocytes, DM group


title: LNCaP_48h_R1881_100pM_2


title: ID8v3, SCI, 3mpi


title: ID8v6, SCI, 6mpi


title: leukocytes, DM group RNA383

description: leukocytes, DM group


title: LNCaP_48h_DMSO_2


title: MM-expr02-plate01-019

description: sci-RNA-seq3 library


title: MM-expr02-plate01-024

description: sci-RNA-seq3 library


title: MM-expr02-plate01-018

description: sci-RNA-seq3 library


title: LNCaP_48h_DMSO_1


title: LNCaP_48h_R1881_1nM_1


title: leukocytes, DM group RNA38

description: leukocytes, DM group


title: ID7v6, SCI,  6mpi


title: leukocytes, DR group RNA379

description: leukocytes, DR group


title: leukocytes, DM group RNA386

description: leukocytes, DM group


title: LNCaP_RB1KOTP53KO_A18A40_R1881

source_name: LNCaP-RB1/TP53 double knockout human prostate tumor cell line


title: MM-expr02-plate01-017

description: sci-RNA-seq3 library


title: MM-expr02-plate01-023

description: sci-RNA-seq3 library


title: MM-expr02-plate01-016

description: sci-RNA-seq3 library


title: ID7v3, SCI,  3mpi


title: leukocytes, DM group RNA37

description: leukocytes, DM group


title: LNCaP_RB1KO_TP53KO_A18_A40_Veh

treatment_protocol: Cells were cultured for 48 hours in their normal growth media (10% FBS) with vehicle (EtOH). After 48 hours, RNA was harvested.


title: MM-expr02-plate01-015

description: sci-RNA-seq3 library


title: LNCaP_RB1KOTP53KO_A15B72_R1881


title: leukocytes, DM group RNA368

description: leukocytes, DM group


title: LNCaP_RB1KO_TP53KO_A15_B72_Veh


title: MM-expr02-plate01-014

description: sci-RNA-seq3 library


title: ID6v6, SCI, 6mpi


title: ID6v12, SCI, 12mpi


title: leukocytes, DM group RNA365

description: leukocytes, DM group


title: MM-expr02-plate01-013

description: sci-RNA-seq3 library


title: ID5v6, SCI,  6mpi


title: leukocytes, DM group RNA35

description: leukocytes, DM group


title: MM-expr02-plate01-010

description: sci-RNA-seq3 library


title: leukocytes, Control group RNA364

description: leukocytes, Control group


title: LNCaP_TP53KO_A58_10nM_R1881

source_name: LNCaP-TP53 knockout human prostate tumor cell line


title: leukocytes, Control group RNA345

description: leukocytes, Control group


title: ID6v3, SCI, 3mpi


title: leukocytes, DM group RNA358

description: leukocytes, DM group


title: ID5v3, SCI,  3mpi


title: LNCAP_TP53_A1_veh


title: MM-expr02-plate01-009

description: sci-RNA-seq3 library


title: MM-expr02-plate01-011

description: sci-RNA-seq3 library


title: leukocytes, Control group RNA338

description: leukocytes, Control group


title: LNCAP_TP53_A5_veh


title: leukocytes, DM group RNA336

description: leukocytes, DM group


title: MM-expr02-plate01-012

description: sci-RNA-seq3 library


title: LNCAP_RB1KO_A18_veh

source_name: LNCaP-RB1 knockout human prostate tumor cell line


title: LNCaP_RB1KO_A15_10nM_R1881


title: LNCaP_RB1KO_A18_10nM_R1881


title: leukocytes, Control group RNA339

description: leukocytes, Control group


title: MM-expr02-plate01-006

description: sci-RNA-seq3 library


title: ID4v12, SCI, 12mpi


title: MM-expr02-plate01-008

description: sci-RNA-seq3 library


title: LNCaP_TP53KO_A1_10nM_R1881


title: ID4v6, SCI, 6mpi


title: MM-expr02-plate01-007

description: sci-RNA-seq3 library


title: leukocytes, DM group RNA334

description: leukocytes, DM group


title: LNCAP_RB1KO_A15_veh


title: MM-expr02-plate01-005

description: sci-RNA-seq3 library


title: ID4v3, SCI, 3mpi


title: LNCaP_10nM_R1881_2_48hrs


title: ID3v6, SCI,  6mpi


title: LNCaP_10nM_R1881_1_48hrs


title: leukocytes, DM group RNA331

description: leukocytes, DM group


title: LNCaP_DMSO_Veh_2_48hrs


title: leukocytes, Control group RNA330

description: leukocytes, Control group


title: leukocytes, DM group RNA328

description: leukocytes, DM group


title: ID3v3, SCI,  3mpi


title: Normal-Cancer-freeP73

city: Santa Monica

first: Dave

last: Hoon

state: CA

address: 2200 Santa Monica Boulevard

department: Translational Molecular Medicine

institute: Saint John's Cancer Institute

data_processing:
FASTQ files were generated from raw sequencing data using Illumina BaseSpace and Illumina Local Run Manager Software.
FASTQ files were analyzed with HTG EdgeSeq parser software to generate raw counts for 2,083 miRs per sample.
Supplementary_files_format_and_content: Raw counts obtained by using HTG EdgeSeq parser software

source_name: Plasma

extract_protocol:
Blood samples from NHD and cancer patients were obtained. All blood samples were collected in Streck tubes (Streck, La Vista, NE, USA) or EDTA tubes (BD vacutainers®, USA). Blood samples were processed and cryopreserved at -80°C. All plasma samples were analyzed by the HTG miR WTA.
Libraries were prepared according to Illumina instrument sequencing protocols. Probe-captured miR samples were amplified and indexed via polymerase chain reaction (PCR) using master mix (dNTP 10 mM, 5X Hemo Klentaq® Reaction buffer, Hemo Klentaq® DNA polymerase (New England Biolabs Inc., Ipswich, MA), forward, and reverse primers (HTG Molecular Diagnostics Inc., Tucson, AZ).  Following PCR, library cleanup was performed using Ampure® XP beads (Beckman Coulter Inc., Brea, CA, USA). The samples were mixed  and incubated with the beads at room temperature  for 5 min. The bead-bound libraries were then  washed twice with 80% ethanol. After washing, the samples were dried at RT for 2 min. The libraries were then  eluted off the beads with 10 mM Tris hydrochloride, pH 8.0.

treatment_protocol: Plasma samples were thawed, mixed, and analyzed using the HTG miRNA WTA following the manufactures’ recommendations.

tag: sample type

value: Normal - Cancer-free


title: ID3v12, SCI, 12mpi


title: leukocytes, DM group RNA319

description: leukocytes, DM group


title: leukocytes, Control group RNA325

description: leukocytes, Control group


title: leukocytes, DR group RNA32

description: leukocytes, DR group


title: leukocytes, DR group RNA335

description: leukocytes, DR group


title: Normal-Cancer-freeP71


title: ID2v6, SCI, 6mpi


title: Normal-Cancer-freeP72


title: Normal-Cancer-freeP69


title: leukocytes, Control group RNA318

description: leukocytes, Control group


title: MM-expr02-plate01-002

description: sci-RNA-seq3 library


title: MM-expr01-plate01-096

description: sci-RNA-seq3 library


title: MM-expr02-plate01-004

description: sci-RNA-seq3 library


title: MM-expr02-plate01-003

description: sci-RNA-seq3 library


title: MM-expr02-plate01-001

description: sci-RNA-seq3 library


title: LNCaP_DMSO_Veh_1_48hrs


title: MM-expr01-plate01-095

description: sci-RNA-seq3 library


title: MM-expr01-plate01-094

description: sci-RNA-seq3 library


title: MM-expr01-plate01-093

description: sci-RNA-seq3 library


title: Normal-Cancer-freeP68


title: Normal-Cancer-freeP70


title: ID2v3, SCI, 3mpi


title: leukocytes, Control group RNA315

description: leukocytes, Control group


title: leukocytes, DR group RNA314

description: leukocytes, DR group


title: ID1v12, SCI, 12mpi


title: ID2v12, SCI, 12mpi


title: MM-expr01-plate01-091

description: sci-RNA-seq3 library


title: MM-expr01-plate01-092

description: sci-RNA-seq3 library


title: leukocytes, Control group RNA310

description: leukocytes, Control group


title: Normal-Cancer-freeP67


title: MM-expr01-plate01-090

description: sci-RNA-seq3 library


title: ID1v6, SCI, 6mpi


title: leukocytes, DR group RNA31

description: leukocytes, DR group


title: Normal-Cancer-freeP66


title: leukocytes, DR group RNA303

description: leukocytes, DR group


title: Normal-Cancer-freeP65


title: ID1v3, SCI, 3mpi


title: Normal-Cancer-freeP63


title: Normal-Cancer-freeP64


title: MM-expr01-plate01-087

description: sci-RNA-seq3 library


title: MM-expr01-plate01-089

description: sci-RNA-seq3 library


title: MM-expr01-plate01-088

description: sci-RNA-seq3 library


title: leukocytes, Control group RNA298

description: leukocytes, Control group


title: Normal-Cancer-freeP62


title: leukocytes, DM group RNA3

description: leukocytes, DM group


title: leukocytes, DM group RNA295

description: leukocytes, DM group


title: MM-expr01-plate01-085

description: sci-RNA-seq3 library


title: MM-expr01-plate01-086

description: sci-RNA-seq3 library


title: Sample_P199L---2

city: Petah Tikva

first: Eitan

last: Kugler

state: Please make your selection

address: Zeev Jabutinsky Rd 39

department: Hematology

country: Israel

institute: Rabin medical center

description: Lineage negative fetal liver cells were enriched through negative selection by using magnetic beads

data_processing:
Illumina adapters and polyA/T stretches were trimmed using cutadap, reads that were less then 40 bp long were removed. Sequenced reads were mapped to the Mus Musculus genome version GRCm38 using STAR.
Genes were identified using a .gtf obtained from ensembl release 82. Per gene reads were counted using HTSeq.
Normalization of read counts and p-values for differential expression genes were computed using Deseq2, with the design formula counts ~ replicate + mutation.
Assembly: GRCm38
Supplementary files format and content: count matrix with raw reads per sample

source_name: Murine fetal liver derived HSPC

extract_protocol:
Murine fetal liver derived HSPC were transduced with human WT and P199L ERG. All samples were sorted for GFP positive cells (5x105 cells/sample), centrifuged (10min, 1200rpm), fluidized in TRIzol reagent, and purified using the TRIzolTM Plus RNA Purification Kit (Invitrogen).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: transfection

value: P199L ERG

value: Lineage negative primary cells


title: Sample_P199L---4

tag: cell type


title: Sample_P199L---1


title: MM-expr01-plate01-084

description: sci-RNA-seq3 library

tag: genotype


title: leukocytes, Control group RNA292

description: leukocytes, Control group


title: Normal-Cancer-freeP60


title: MM-expr01-plate01-083

description: sci-RNA-seq3 library


title: Sample_WT-2

value: WT ERG


title: Sample_WT-4


title: leukocytes, DM group RNA29

description: leukocytes, DM group


title: Normal-Cancer-freeP59


title: leukocytes, DM group RNA302

description: leukocytes, DM group


title: leukocytes, DM group RNA288

description: leukocytes, DM group


title: Normal-Cancer-freeP58


title: Sample_WT-1


title: MM-expr01-plate01-082

description: sci-RNA-seq3 library


title: leukocytes, Control group RNA278

description: leukocytes, Control group


title: Sample_Empty---4

value: empty


title: Normal-Cancer-freeP57


title: leukocytes, DM group RNA277

description: leukocytes, DM group


title: Sample_Empty---2


title: Normal-Cancer-freeP56


title: MM-expr01-plate01-079

description: sci-RNA-seq3 library


title: Sample_Empty---1


title: Normal-Cancer-freeP61


title: Normal-Cancer-freeP55


title: P199L-ERG_HDAC rep4

description: ER-Hoxb8 cells transduced with human P199L-ERG treated with HDAC3 inhibitor

data_processing:
Poly-A/T stretches and Illumina adapters were trimmed from the reads using cutadapt; resulting reads shorter than 30bp were discarded.
Reads were mapped to the M. musculus reference genome GRCm38 using STAR, supplied with gene annotations downloaded from Ensembl (and with EndToEnd option and outFilterMismatchNoverLmax was set to 0.04).
Expression levels for each gene were quantified using htseq-count, using the gtf above.
Differentially expressed genes were identified using DESeq2 with the betaPrior, cooksCutoff and independentFiltering parameters set to False. Raw P values were adjusted for multiple testing using the procedure of Benjamini and Hochberg.
Assembly: GRCm38
Supplementary files format and content: count matrix with raw reads per sample

source_name: Hoxb8-ER cells

extract_protocol:
Hoxb8-ER cells were transduced with ERG variants and treated with either DMSO or BRD3308. Cells were fluidized in TRIzol reagent, and RNA was purified using the TRIzolTM Plus RNA Purification Kit (Invitrogen).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: myeloid progenitors

value: BRD3308 (HDAC3 inhibitor)


title: MM-expr01-plate01-078

description: sci-RNA-seq3 library


title: leukocytes, DM group RNA26

description: leukocytes, DM group


title: Normal-Cancer-freeP53


title: leukocytes, Control group RNA267

description: leukocytes, Control group


title: P199L-ERG_HDAC rep3


title: P199L-ERG_HDAC rep2


title: MM-expr01-plate01-077

description: sci-RNA-seq3 library


title: leukocytes, Control group RNA259

description: leukocytes, Control group


title: MM-expr01-plate01-081

description: sci-RNA-seq3 library


title: Normal-Cancer-freeP52


title: MM-expr01-plate01-076

description: sci-RNA-seq3 library


title: P199L-ERG_HDAC rep1


title: P199L-ERG_DMSO rep4

description: ER-Hoxb8 cells transduced with human P199L-ERG  treated with DMSO

value: DMSO


title: MM-expr01-plate01-080

description: sci-RNA-seq3 library

value: mouse embryo (E13.5)


title: leukocytes, Control group RNA257

description: leukocytes, Control group

value: Blood


title: Normal-Cancer-freeP51


title: leukocytes, DR group RNA253

description: leukocytes, DR group

value: Leukocytes


title: leukocytes, Control group RNA275

description: leukocytes, Control group


title: Normal-Cancer-freeP50


title: Normal-Cancer-freeP54


title: P199L-ERG_DMSO rep2


title: leukocytes, DR group RNA246

description: leukocytes, DR group


title: P199L-ERG_DMSO rep3


title: Normal-Cancer-freeP48


title: MM-expr01-plate01-075

description: sci-RNA-seq3 library


title: MM-expr01-plate01-072

description: sci-RNA-seq3 library


title: MM-expr01-plate01-074

description: sci-RNA-seq3 library


title: MM-expr01-plate01-073

description: sci-RNA-seq3 library


title: P199L-ERG_DMSO rep1


title: leukocytes, Control group RNA242

description: leukocytes, Control group


title: MM-expr01-plate01-070

description: sci-RNA-seq3 library


title: Normal-Cancer-freeP47


title: MM-expr01-plate01-071

description: sci-RNA-seq3 library


title: WT_ERG_HDAC rep4

description: ER-Hoxb8 cells transduced with human WT-ERG treated with HDAC3 inhibitor


title: leukocytes, DR group RNA23

description: leukocytes, DR group


title: Normal-Cancer-freeP46


title: MM-expr01-plate01-069

description: sci-RNA-seq3 library


title: WT_ERG_HDAC rep3


title: leukocytes, Control group RNA252

description: leukocytes, Control group


title: WT_ERG_HDAC rep2


title: leukocytes, Control group RNA220

description: leukocytes, Control group


title: Normal-Cancer-freeP45


title: Normal-Cancer-freeP44


title: Normal-Cancer-freeP49


title: leukocytes, DM group RNA219

description: leukocytes, DM group


title: MM-expr01-plate01-068

description: sci-RNA-seq3 library


title: MM-expr01-plate01-067

description: sci-RNA-seq3 library


title: Normal-Cancer-freeP43


title: WT_ERG_HDAC rep1


title: Normal-Cancer-freeP42


title: MM-expr01-plate01-066

description: sci-RNA-seq3 library


title: leukocytes, Control group RNA218

description: leukocytes, Control group


title: MM-expr01-plate01-065

description: sci-RNA-seq3 library


title: leukocytes, DM group RNA209

description: leukocytes, DM group


title: WT_ERG_DMSO rep3

description: ER-Hoxb8 cells transduced with human WT-ERG treated with DMSO


title: leukocytes, DM group RNA213

description: leukocytes, DM group


title: Normal-Cancer-freeP40


title: Normal-Cancer-freeP41


title: WT_ERG_DMSO rep1


title: leukocytes, Control group RNA224

description: leukocytes, Control group


title: leukocytes, DM group RNA205

description: leukocytes, DM group


title: Normal-Cancer-freeP38


title: BB_HDAC rep4

description: ER-Hoxb8 cells transduced with an empty lenti-viral vector treated with HDAC3 inhibitor


title: BB_HDAC rep3


title: leukocytes, DR group RNA201

description: leukocytes, DR group


title: leukocytes, DM group RNA2

description: leukocytes, DM group


title: Normal-Cancer-freeP37


title: MM-expr01-plate01-063

description: sci-RNA-seq3 library


title: MM-expr01-plate01-062

description: sci-RNA-seq3 library


title: WT_ERG_DMSO rep4


title: MM-expr01-plate01-059

description: sci-RNA-seq3 library


title: Normal-Cancer-freeP36


title: leukocytes, DR group RNA185

description: leukocytes, DR group


title: MM-expr01-plate01-060

description: sci-RNA-seq3 library


title: BB_HDAC rep1


title: leukocytes, DR group RNA18

description: leukocytes, DR group


title: MM-expr01-plate01-064

description: sci-RNA-seq3 library


title: WT_ERG_DMSO rep2


title: Normal-Cancer-freeP39


title: Normal-Cancer-freeP35


title: BB_DMSO rep4

description: ER-Hoxb8 cells transduced with an empty lenti-viral vector treated with DMSO


title: MM-expr01-plate01-058

description: sci-RNA-seq3 library


title: Normal-Cancer-freeP34


title: MM-expr01-plate01-057

description: sci-RNA-seq3 library


title: BB_DMSO rep3


title: leukocytes, DR group RNA174

description: leukocytes, DR group


title: Normal-Cancer-freeP33


title: MM-expr01-plate01-061

description: sci-RNA-seq3 library


title: BB_DMSO rep2


title: leukocytes, Control group RNA167

description: leukocytes, Control group


title: MM-expr01-plate01-055

description: sci-RNA-seq3 library


title: Normal-Cancer-freeP32


title: MM-expr01-plate01-056

description: sci-RNA-seq3 library


title: BB_HDAC rep2


title: BB_DMSO rep1


title: Normal-Cancer-freeP31


title: IgG_pool

data_processing:
Adapters were trimmed using the cutadapt tool. Following adapter removal, reads that were shorter than 30 nucleotides were discarded (cutadapt option –m 30).
The reads were aligned uniquely to the mouse genome (mm10) using bowtie.
Bound regions were detected using MACS2.
Bedtool commands were used for merging and intersections between peak files.
Assembly: mm10
Supplementary files format and content: Merged peaks for each Histon mark from all conditions in excel file
Supplementary files format and content: bigwig files were generated using MACS2

growth_protocol: ChIP material was prepared from ER-Hoxb8 cells stably expressing ERG variants and an empty vector for control. 10^7 cells were used per sample

extract_protocol:
Cells were crosslinked with 1% paraformaldehyde for 15 minutes and were quenched with glycine for 5 minutes at room temperature. Lysis buffer with protease inhibitor was gently added to cell pellet. Fixed chromatin was sonicated with the Bioruptor Pico using pre-optimised conditions and immunoprecipitated with the indicated antibody. Immunoprecipitation was preform using polyclonal antibody raised against H3K27ac, H3K4me1, H3K4me3, H3K9ac (Abcam). As a control, nonspecific rabbit IgG (I5006; Sigma Aldrich) was used.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.

value: control

value: IgG


title: leukocytes, Control group RNA160

description: leukocytes, Control group


title: MM-expr01-plate01-054

description: sci-RNA-seq3 library


title: ERG_P199L_H3K27Ac

value: H3K27Ac (Abcam)


title: MM-expr01-plate01-053

description: sci-RNA-seq3 library

value: C57BL/6, BALB/C, FVB, G4


title: leukocytes, DM group RNA165

description: leukocytes, DM group


title: Normal-Cancer-freeP30


title: Normal-Cancer-freeP29


title: leukocytes, DM group RNA179

description: leukocytes, DM group


title: leukocytes, DM group RNA152

description: leukocytes, DM group


title: Normal-Cancer-freeP28


title: leukocytes, DR group RNA155

description: leukocytes, DR group


title: ERG_P199L_H3K27me3

value: H3K27me3 (Abcam)


title: leukocytes, DM group RNA151

description: leukocytes, DM group


title: Normal-Cancer-freeP27


title: leukocytes, DR group RNA150

description: leukocytes, DR group


title: MM-expr01-plate01-052

description: sci-RNA-seq3 library

value: multiplexed sample:WT and mutant


title: MM-expr01-plate01-051

description: sci-RNA-seq3 library


title: Normal-Cancer-freeP26

value: Normal - Cancer-free


title: ERG_P199L_H3K4me3

value: H3K4me3 (Abcam)


title: leukocytes, DM group RNA145

description: leukocytes, DM group


title: ERG_P199L_H3K9Ac

value: H3K9Ac (Abcam)


title: ERG_P199L_H3K4me1

value: H3K4me1 (Abcam)


title: Normal-Cancer-freeP25


title: leukocytes, DR group RNA140

description: leukocytes, DR group


title: ERG_wt_H3K27Ac


title: Normal-Cancer-freeP24


title: leukocytes, Control group RNA133

description: leukocytes, Control group


title: Normal-Cancer-freeP23


title: ERG_wt_H3K27me3


title: ERG_wt_H3K9Ac


title: leukocytes, DM group RNA132

description: leukocytes, DM group


title: Normal-Cancer-freeP22


title: Normal-Cancer-freeP21


title: ERG_wt_H3K4me3


title: ERG_wt_H3K4me1


title: leukocytes, Control group RNA124

description: leukocytes, Control group


title: Normal-Cancer-freeP20


title: empty_H3K27Ac

value: empty


title: leukocytes, Control group RNA117

description: leukocytes, Control group


title: Normal-Cancer-freeP19


title: leukocytes, DR group RNA116

description: leukocytes, DR group


title: MM-expr01-plate01-047

description: sci-RNA-seq3 library


title: MM-expr01-plate01-050

description: sci-RNA-seq3 library


title: MM-expr01-plate01-046

description: sci-RNA-seq3 library


title: MM-expr01-plate01-044

description: sci-RNA-seq3 library


title: MM-expr01-plate01-045

description: sci-RNA-seq3 library


title: MM-expr01-plate01-049

description: sci-RNA-seq3 library


title: MM-expr01-plate01-048

description: sci-RNA-seq3 library


title: MM-expr01-plate01-043

description: sci-RNA-seq3 library


title: empty_H3K27me3

value: myeloid progenitors


title: Normal-Cancer-freeP18


title: MM-expr01-plate01-042

description: sci-RNA-seq3 library


title: leukocytes, DM group RNA115

description: leukocytes, DM group


title: Normal-Cancer-freeP17


title: MM-expr01-plate01-041

description: sci-RNA-seq3 library


title: empty_H3K9Ac


title: empty_H3K4me3


title: leukocytes, DM group RNA114

description: leukocytes, DM group


title: Normal-Cancer-freeP16


title: leukocytes, DM group RNA110

description: leukocytes, DM group


title: leukocytes, Control group RNA109

description: leukocytes, Control group


title: WT 4 6h [6hWT4]

city: Derio

first: Ana

middle: Maria

last: Aransay

state: BIZKAIA

address: Parque tecnologico de Bizkaia, Building 801-A

department: Genome Analysis Platform

country: Spain

institute: CIC bioGUNE

data_processing:
FASTQ files were aligned to Genome data base using STAR software [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3530905/],and read counts obtained for each gene
Differential Expression was estimated using DESeq2 [https://www.ncbi.nlm.nih.gov/pubmed/25516281] and edgeR [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2796818/]
Genome_build: Mus_musculus.GRCm38.94.gtf
Supplementary_files_format_and_content: A matrix is generated as a plain text file (*.txt), in which each column is a sample, each row is a gene (ensembl_ID), and in each cell indicates the number of raw counts obtained by STAR per sample and gene.

source_name: CD4+ T cells from spleen of WT #4 6h stimulation

growth_protocol: Culture in RP10 between 0 and 24 h

extract_protocol:
The CD4+ T cells were washed with PBS and pelleted. Then the cells were resuspended in RLT buffer from the RNeasy Mini kit (Qiagen) and from there we followed the protocol of the kit.
Sequencing libraries were prepared following the protocol "TruSeqStrandedmRNASamplePreparationGuide(Part#15031047Rev.E)" with the "TruSeq stranded mRNAseq library preparation kit” (Illumina Inc., Cat.#RS-122-2101orRS-122-2102(SetAorB,respectively))
mRNA stranded library sequencing

treatment_protocol: Stimulation with anti-CD3/CD28 between 0 h and 24 h

tag: strain background

tag: genotype/variation

value: WT

value: 6h stimulation with anti-CD3/CD28

value: spleen

value: CD4+ T cells


title: Normal-Cancer-freeP14


title: MM-expr01-plate01-038

description: sci-RNA-seq3 library

tag: developmental stage

value: mouse embryo (E13.5)


title: leukocytes, DM group RNA108

description: leukocytes, DM group

tag: tissue

value: Blood

value: Leukocytes


title: leukocytes, DR group RNA102

description: leukocytes, DR group


title: Normal-Cancer-freeP13


title: leukocytes, DM group RNA104

description: leukocytes, DM group


title: MM-expr01-plate01-040

description: sci-RNA-seq3 library

tag: strain


title: AIM2-/- 4 6h [6hKO4]

source_name: CD4+ T cells from spleen of Aim2 KO #4 6h stimulation

tag: treatment


title: leukocytes, DM group RNA1

description: leukocytes, DM group


title: WT 1 6h [6hWT1]

source_name: CD4+ T cells from spleen of WT #1 6h stimulation


title: AIM2-/- 2 6h [6hKO2]

source_name: CD4+ T cells from spleen of Aim2 KO #2 6h stimulation


title: Normal-Cancer-freeP12


title: WT 3 6h [6hWT3]

source_name: CD4+ T cells from spleen of WT #3 6h stimulation


title: AIM2-/- 1 6h [6hKO1]

source_name: CD4+ T cells from spleen of Aim2 KO #1 6h stimulation


title: Normal-Cancer-freeP10


title: Normal-Cancer-freeP09


title: leukocytes, DM group RNA126

description: leukocytes, DM group


title: Normal-Cancer-freeP15


title: empty_H3K4me1

tag: chip antibody


title: MM-expr01-plate01-036

description: sci-RNA-seq3 library


title: MM-expr01-plate01-035

description: sci-RNA-seq3 library


title: MM-expr01-plate01-033

description: sci-RNA-seq3 library


title: MM-expr01-plate01-034

description: sci-RNA-seq3 library


title: EasySci-RNA, human brain

city: New York

first: Junyue

last: Cao

state: NY

address: 1230 York Avenue

institute: The Rockefeller University

description: EasySci-RNA library

library_source: transcriptomic single cell

data_processing:
EasySci-RNA data processing: A custom computational pipeline was developed to process the raw fastq files from the EasySci libraries. Similar to our previous studies10,11, the barcodes of each read pair were extracted. Both adaptor and barcode sequences were trimmed from the reads. Second, an extra trimming step is implemented using Trim Galore 60 with default settings to remove the poly(A) sequences and the low-quality base calls from the cDNA. Afterward, the paired-end sequences were aligned to the genome with the STAR aligner 61, and the PCR duplicates removed based on the UMI sequence and the alignment location. Finally, the reads are split into SAM files per cell, and the gene expression is counted using a custom script. At this level, the reads from the same cell originating from the short dT and the random hexamer RT primers were counted as independent cells. During the gene counting step, we assigned reads to genes if the aligned coordinates overlapped with the gene locations on the genome. If a read was ambiguous between genes and derived from the short dT RT primer, we assigned the read to the gene with the closest 3’ end; otherwise, the reads were labeled as ambiguous and not counted. If no gene was found during this step, we then searched for candidate genes 1000 bp upstream of the read or genes on the opposite strand. Reads without any overlapped genes were discarded. We used a similar strategy to generate an exon count matrix across cells. Specifically, we counted the number of expressed exons based on the number of reads overlapping each exon. If one read overlapped with multiple exons, this read was split between the exons. Read overlapped with multiple genes were discarded, except if we can determine the exact gene based on the other paired-end read. For reads without overlapped genes, we checked if there are any overlapped exons on the opposite strand. Reads without any overlapped exons were discarded.
Assembly: human reference genome (hg38)
Supplementary files format and content: Processed data files include a cell annotation csv file, a gene annotation csv file, and a gene count sparse matrix file for RNA data.
Supplementary files format and content: cell_annotation.csv: Cell annotation file: sample is cell id of each single cell with the ligation and reverse transcription barcode attached; UMAP_1 and UMAP_2 are cell coordinates after UMAP dimension reduction; Cell_type contains the cell type annotation.
Supplementary files format and content: gene_annotation.csv: Gene annotation file including gene id, gene type and gene short name.
Supplementary files format and content: gene_count.txt: A sparse matrix file: each row corresponds to gene id (with gene information in the gene_annotation.csv); each column corresponds to each cell (with cell source information in the cell_annotation.csv); each value in the matrix corresponds to UMI count.

source_name: Human brain

extract_protocol:
EasySci-RNA: Twenty-four post-mortem human brain samples across two regions (hippocampus and superior and middle temporal gyrus) and twelve individuals, including six controls and six Alzheimer's disease patients ranging from 70 to 94 in age, were collected from the University of Kentucky Alzheimer's Disease Center Tissue Bank. Each surveyed sample underwent rigorous quality control, including short PMI, and was subjected to EasySci-RNA profiling. For nuclei extraction, thawed samples were minced in 1 mL PBS (Genesee, 25-507) with 1% Diethyl Pyrocarbonate (DEPC) (VWR, 97062-652) using a blade on a 6 cm dish (Genesee, 25-260) on ice. After centrifuging for 5 minutes at 200g (4 °C), 1mL ice-cold EZ lysis buffer (Millipore Sigma, NUC101-1KT) +1% DEPC was added to the tissue (0.1g-0.5g) for nuclei extraction and kept on ice for 5 minutes. The nuclei suspension was homogenized through 40 µm cell strainers (VWR, 470236-276) with the rubber tips of syringes inside a 6-cm dish, centrifuged for 5 minutes at 500g, re-suspended in 500ul EZ lysis buffer + 0.1% SuperRnase Inhibitor (Thermo Fisher Scientific, AM2696). After repeated centrifugation for 5 minutes at 500g, the nuclei are fixed using 1mL ice-cold 0.1% Formaldehyde (Thermofisher, 28906) on ice for 10 minutes. The fixed nuclei are centrifuged for 3 minutes at 500g, resuspended in 500ul EZ buffer + 0.1% SuperRnase Inhibitor, centrifuged again for 5 minutes at 500g, and re-suspended in 500mL EZ buffer + 0.1% SuperRnase Inhibitor. After checking the nuclei morphology, the nuclei are re-suspended in 100uL nuclei suspension buffer (NSB) [Nuclei Buffer (10mM Tris-HCl, pH 7.5 (Thermo Fisher Scientific, 15567027); 10mM NaCl (Thermo Fisher Scientific, AM9759); 3mM MgCl2 (Thermo Fisher Scientific, AM9530G) in nuclease-free water (Ambion, AM 9937)) with 1% SuperRnase Inhibitor and 1% BSA (NEB, B9000S)] + 10% Dimethyl Sulfoxide (DMSO) (VWR, 97063-136) and slow frozen to -80C for storage.
EasySci-RNA: On the day of the library preparation, nuclei were thawed in a 37°C water bath and placed on ice immediately. After thawing, 500 μL NSB + Triton X-100 (Sigma Aldrich, 93443-100ML) is added, and the nuclei are sonicated for 12 seconds at low power. After filtering the nuclei through a 20 μm filter (PluriSelect 43-10020-70) the sample is pelletized for 5 minutes, 500 g at 4°C and resuspended in 100 μL of NSB. After nuclei counting the concentration is set to 20,000 nuclei/μL. For the reverse transcription reaction nuclei in 4 μL of NSB, 0.5 μL of 10 mM dNTP (Thermo Fisher Scientific, R0192), 1 μL 50 μM short-dT primer (100 μM, 5′-/5Phos/ACGACGCTCTTCCGATCTNNNNNNNN[10bp barcode]TTTTTTTTTTTTTTTT-3′, where “N” is any base; IDT) and 1μL 50 μM randomN primer (100 μM, 5'-/5Phos/ACGACGCTCTTCCGATCTNNNNNNNN[10bp barcode]NNNNNN-3', where "N" is any base; IDT) are distributed on every well of a 96-well plate and incubated at 55°C for 5 minutes. 3.5 μL of reverse transcription reaction mix [Maxima H Minus Reverse Transcriptase (105 μL) with Buffer (420 μL) (ThermoFisher, EP0753); 105 μL SuperRnase Inhibitor; 105 μL nuclease-free water] is added to each well and the following thermocycler program is used for the reaction: 4°C for 2 minutes, 10°C for 2 minutes, 20°C for 2 minutes, 30°C for 2 minutes, 40°C for 2 minutes, 50°C for 2 minutes, 55°C for 15 minutes. After the reverse transcription reaction, 10 μL NBB (Nuclear Buffer + 1% BSA + 0.1% Triton-X-100) is added to each well, the wells are pooled and moved into a 15 mL tube and centrifuged for 3 minutes, 1000 g at 4°C. Then the nuclei is resuspended in 1 mL NBB, moved into a 1.5 mL microcentrifuge tube, and centrifuged again for 3 minutes, 1000 g at 4°C. For the ligation reaction, the cells are resuspended in 950 μL NBB, and distributed into four PCR plates with 2.5 μL of the solution going into each well. Then 1 μL of the DNA ligation primer(100 μM, 5’-AATGATACGGCGACCACCGAGATCTACAC[10bp barcode]ACACTCTTTCCCTAC-3’, IDT) + adaptor (100 μM,5'-A*G*A*T*C*G*G*A*A*G*A*G*C*G*T*C*G*T*G*T*A*G*G*G*A*A*A*G*A*G*T*G*T*/3ddC/, IDT) complex (3.125 μM) is added with 1.5 μL of the ligation reaction mix [210 μL 10x T4 Ligation Buffer with 210 μL T4 DNA Ligase (NEB, M0202L); 21 μL SuperRnase Inhibitor; 189 μL nuclease free water] and the mixture is incubated for 30 minutes at room temperature with gentle shaking (300 rpm with Thermomixer, 50 rpm on Fisherbrand Nutating Mixer). After 30 minutes, 1 μL EDTA (18 mM) (VWR, 97062-656) is added to each well, and the wells are pooled into a 15 mL tube. After centrifuging the tube for 3 minutes, 1000 g at 4°C, the nuclei are resuspended in 1 mL NBB, centrifuged again for 3 minutes, 1000 g at 4°C, resuspended in 500 μL NBB and filtered through a 40 μM filter and centrifuged again for 3 minutes, 1000 g at 44°C and resuspended in 500 μL NBB for nuclei counting. After counting, 10,000 nuclei per well is distributed in 4 μL / well volume on a 96 well plate. The second-strand synthesis is performed by adding 1 μL enzyme-buffer mix [⅔ μL Second-Strand Synthesis buffer + ⅓ μL Second-Strand Synthesis Enzyme Mix (NEB, E7550S)] and incubating at 16°C for one hour, followed by 0.8X AMPure beads (Beckman Coulter, A63882) purification. For the tagmentation step, 6.6 μL of the tagmentase-buffer mix (Nextera N7 adaptor loaded Tn5 (provided by Illumina) or custom Tn5) is added and the solution is incubated at 55°C for 5 minutes. Next, 0.4 µL 1% SDS (ThermoFisher AM9820) and 0.4 µL BSA is added and incubated at 55°C for 15 minutes to stop the tagmentation reaction. Then, 2 μL 10% Tween-20 (Millipore Sigma, P9416-100ML) was added to quench the SDS. Following on, 1 μL of 10 μM universal P5 primer (5′-AATGATACGGCGACCACCGAGATCTACAC-3′, IDT), 1 μL of 10 μM indexed P7 primer (5′-CAAGCAGAAGACGGCATACGAGAT[i7]GTCTCGTGGGCTCGG-3′, IDT) and 10 μL NEBNext High-Fidelity 2X PCR Master Mix (NEB, M0541L) were added into each well. Amplification was carried out using the following program: 72°C for 5 minutes, 98°C for 30 seconds, 12-15 cycles of (98°C for 10 seconds, 66°C for 30 seconds, 72°C for 30 seconds) and a final 72°C for 5 minutes. Final PCR products were pooled and purified with 0.8X AMPure beads and the second round of 0.9X AMPure beads to remove primer dimers. Library concentrations were determined by Qubit and the libraries were visualized by electrophoresis on a 2% E-Gel™ EX Agarose Gels (ThermoFisher, G402002).

value: brain

tag: brain region

value: mixed sample (non-demultiplexed)

tag: diagnosis


title: WT 4 3h [3hWT4]

source_name: CD4+ T cells from spleen of WT #4 3h stimulation

value: 3h stimulation with anti-CD3/CD28


title: MM-expr01-plate01-037

description: sci-RNA-seq3 library

value: C57BL/6, BALB/C, FVB, G4

value: multiplexed sample:WT and mutant


title: Normal-Cancer-freeP11

value: Normal - Cancer-free


title: Normal-Cancer-freeP08


title: MM-expr01-plate01-039

description: sci-RNA-seq3 library


title: WT 3 3h [3hWT3]

source_name: CD4+ T cells from spleen of WT #3 3h stimulation


title: WT 1 3h [3hWT1]

source_name: CD4+ T cells from spleen of WT #1 3h stimulation


title: AIM2-/- 4 3h [3hKO4]

source_name: CD4+ T cells from spleen of Aim2 KO #4 3h stimulation


title: MM-expr01-plate01-032

description: sci-RNA-seq3 library

source_name: mouse embryos


title: MM-expr01-plate01-030

description: sci-RNA-seq3 library


title: MM-expr01-plate01-029

description: sci-RNA-seq3 library


title: spermidine-plus-rna-seq1

city: Bethesda

first: Philip

last: Adams

state: MD

address: 9000 Rockville Pike

department: NICHD

institute: National Institutes of Health

data_processing:
Raw sequence reads were processed using lcdb-wf (lcdb.github.io/lcdb-wf/) according to the following steps, as previously performed (Adams et al., 2021). Raw sequence reads were trimmed with cutadapt 2.3 (Martin, 2011) to remove any adapters while performing light quality trimming with parameters “-a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -q 20 –minimum-length=25.” Sequencing library quality was assessed with fastqc v0.11.8 with default parameters. The presence of common sequencing contaminants was evaluated with fastq_screen v0.13.0 with parameters “–subset 100000 –aligner bowtie2.” Trimmed reads were mapped to the B. burgdorferi reference genome (GCF_000008685.2_ASM868v2
Supplementary files format and content: TSV containing raw counts from featurecounts with and without the parameter "--allowMultiOverlap") using BWA-MEM. Multimapping reads were filtered using samtools (Li et al., 2009). Uniquely aligned reads were then mapped using subread featureCounts v1.6.4 with default parameters to gene features made from the union of NCBI B. burgdorferi B31 gene annotations GCF_000008685.2 and updated sRNA annotations. BedGraph files were generated using deepTools (Ramírez et al., 2016) on reads from each strand separately. Raw counts were quantified using featurecounts from the subread package v.2.0.1. Numerous gene features overlap other features in B. burgdorferi; to estimate the expression of such overlapping genes, the quantification was performed two ways, one which included reads overlapping 2 or more features (parameter “--allowMultiOverlap”), one performed with standard quantification parameters that included only reads overlapping a single feature. Differential expression was performed using raw counts provided to DESeq2 v1.30.0 with the following modifications from lfcShrink default parameters: type="normal". A gene was considered differentially expressed if the false discovery rate (FDR) was <0.1 (default for DESeq2) for the statistical test that magnitude of the log2-fold change is greater than 0 (lfcThreshold=0, default for DESeq2).
Assembly: GCF_000008685.2_ASM868v2
Supplementary files format and content: TSV containing raw counts from featurecounts with and without the parameter "--allowMultiOverlap"

organism: Borreliella burgdorferi

source_name: B. burgdorferi B31 (lab strain number: PA003)

growth_protocol: B. burgdorferi were cultivated in liquid Barbour-Stoenner-Kelly (BSK) II medium supplemented with gelatin and 6% rabbit serum. Three cultures of B. burgdorferi B31 (lab strain number:PA003) spirochetes were diluted into BSK-II or BSK-II +10mM spermidine, adjusted to pH 7.8. Cells were collected in stationary phase (~1e8 – 2e8 cells/ml), after ~80 h of growth in BSK-II alone or ~96 h of growth in BSK-II +10mM spermidine.

extract_protocol:
RNA was isolated using TRIzol.
Total RNA-seq library construction was carried out based on the RNAtag-seq methodology (Shishkin et al., 2015), which was adapted to capture bacterial sRNAs (Melamed et al., 2018).

tag: growth phase

value: stationary

value: 10 mM spermidine


title: spermidine-minus-rna-seq2

value: B. burgdorferi B31 (lab strain number:PA003)

value: control


title: spermidine-plus-rna-seq3


title: spermidine-plus-rna-seq2


title: MM-expr01-plate01-028

description: sci-RNA-seq3 library

data_processing:
Base calls were converted to fastq format using Illumina’s bcl2fastq/v2.20 and demultiplexed based on PCR i5 and i7 barcodes using maximum likelihood demultiplexing package deML (Renaud et al. 2015) with default settings. Downstream sequence processing and single cell digital expression matrix generation were similar to sci-RNA-seq (Cao et al. 2017) except that RT index was combined with hairpin adaptor index, and thus the mapped reads were split into constituent cellular indices by demultiplexing reads using both the RT index and ligation index (Levenshtein edit distance (ED) < 2, including insertions and deletions).
Briefly, demultiplexed reads were filtered based on RT index and ligation index (ED < 2, including insertions and deletions) and adaptor-clipped using trim_galore/v0.6.5 with default settings. Trimmed reads were mapped to the mouse reference genome (mm10) for mouse embryo nuclei, using STAR/v2.6.1d (Dobin et al. 2013) with default settings and gene annotations (GENCODE VM12 for mouse). Uniquely mapping reads were extracted, and duplicates were removed using the unique molecular identifier (UMI) sequence (ED < 2, including insertions and deletions), reverse transcription (RT) index, hairpin ligation adaptor index and read 2 end-coordinate (i.e. reads with UMI sequence less than 2 edit distance, RT index, ligation adaptor index and tagmentation site were considered duplicates).
Finally, mapped reads were split into constituent cellular indices by further demultiplexing reads using the RT index and ligation hairpin (ED < 2, including insertions and deletions). To generate digital expression matrices, we calculated the number of strand-specific UMIs for each cell mapping to the exonic and intronic regions of each gene with python/v2.7.13 HTseq package (Anders, Pyl, and Huber 2015). For multi-mapped reads, reads were assigned to the closest gene, except in cases where another intersected gene fell within 100 bp to the end of the closest gene, in which case the read was discarded. For most analyses we included both expected-strand intronic and exonic UMIs in per-gene single-cell expression matrices.
Assembly: mm10
Supplementary files format and content: Processed data files include a cell annotation csv  file, gene annotation csv file, and a gene count sparse matrix file

extract_protocol:
The snap frozen embryos were processed as previously described (Cao et al. 2019). Briefly, the frozen embryos were cut into small pieces with a blade and further dissected by resuspension in 1 ml ice cold cell lysis buffer (CLB) in a 6 cm dish. adding another 3ml CLB, the sample was strained (40 µm) into a 15 ml Falcon tube and centrifuged to a pellet (500g, 5 min). Resuspending the sample with another 1 ml CLB, the isolation of nuclei was ensured. Pelleting the isolated nuclei again (500g, 5 min) was followed by a washing step by fixation in 10 ml 4% Paraformaldehyde (PFA) for 15 minutes on ice. The fixed nuclei were pelleted (500g, 3 min) and washed twice in the nuclei suspension buffer (NSB) (500g, 5 min). The nuclei finally were resuspended in 500µl NSB and split into 2 tubes, each containing 250 µl sample. The tubes were flash frozen in liquid nitrogen, until further use for library preparation. The embryo preparation was preceded randomly for nuclei isolation in order to avoid batch effects.
The library preparation proceeded as previously described (Cao et al. 2019). In short, the fixed nuclei were permeabilized, sonicated and washed. Nuclei from each mouse embryo were then distributed into several individual wells into 4 96-well plates. We split samples into four batches (~25 samples randomly selected in each batch) for sci-RNA-seq3 processing. The ID of the reverse transcription well was linked to the respective embryo for downstream analysis. In a first step the nuclei were then mixed with oligo-dT primers and dNTP mix, denatured and placed on ice, afterwards they were proceeded for reverse transcription including a grading incubation step. After reverse transcription, the Nuclei from all wells were pooled with the nuclei dilution buffer, spun down and redistributed into 96-well plates containing the reaction mix for ligation. The ligation was proceeded for 3 h at 16 °C. Afterwards, nuclei again were pooled with nuclei suspension buffer, spun down and washed and filtered. Next, the nuclei were counted and recistributed for second strand synthesis, which was was carried out at 16 °C for 3h. Afterwards tagmentation mix was added to each well and  tagmentation was carried out for 5 minutes. Stopping the reaction, DNA binding buffer was added and the sample was incubated for another 5 minutes. Following an elution step  using AMPure XP beads and elution mix, the samples were PCR amplified. Finally after PCR amplification, the nuclei were pooled and purified using AMPure XP beads. The library was analyzed by electrophoresis and the concentration was calculated using Qubit (Invitrogen). The library was sequenced on the NovaSeq platform (Illumina) (read 1: 34 cycles, read 2: 52 cycles, index 1: 10 cycles, index 2: 10 cycles).


title: AIM2-/- 1 3h [3hKO1]

source_name: CD4+ T cells from spleen of Aim2 KO #1 3h stimulation


title: Normal-Cancer-freeP04

source_name: Plasma


title: Normal-Cancer-freeP05


title: spermidine-minus-rna-seq1


title: Normal-Cancer-freeP03


title: WT 4 24h [24hWT4]

source_name: CD4+ T cells from spleen of WT #4 24h stimulation

value: WT

value: 24h stimulation with anti-CD3/CD28


title: MM-expr01-plate01-027

description: sci-RNA-seq3 library


title: Normal-Cancer-freeP06


title: MM-expr01-plate01-031

description: sci-RNA-seq3 library


title: Normal-Cancer-freeP02


title: Normal-Cancer-freeP07


title: MM-expr01-plate01-026

description: sci-RNA-seq3 library


title: MM-expr01-plate01-025

description: sci-RNA-seq3 library


title: WT 3 24h [24hWT3]

source_name: CD4+ T cells from spleen of WT #3 24h stimulation

value: spleen


title: Normal-Cancer-freeP01


title: Tre3

city: Belfast

first: Andrew

last: Marshall

state: Select...

address: 19 Chlorine Gardens

country: United Kingdom

institute: Queen's University Belfast

data_processing:
Differential gene expression analysis was carried out by mapping the sequenced reads to the C. difficile R20291 reference genome (https://www.ncbi.nlm.nih.gov/nuccore/FN545816.1). Reads were filtered by using the trimming pipeline, which filtered low sequencing score and reads aligned to adapter sequences. Raw reads were trimmed against adaptors and then reads were quality trimmed by skewer. Reads that passed the filter were then mapped onto the reference genome by the hisat2 mapping tool. Mapped reads were then counted by using the “featurecounts” tool (http://subread.sourceforge.net/) to determine the number of uniquely and correctly aligned reads per gene. Normalised read counts (RPKM) for a given gene were determined by normalising the exon space of a gene against the total number of mapped reads (excluding rRNA and reads not uniquely mapped according to their mapping quality score [MAPQ] using MAPQ20) in an alignment file and against the total length of the gene’s exon space. Differentially expressed genes were then determined using the DESeq package, which analyses the variance between biological replicates within the RNA-seq analysis in order to better model the expression values of individual genes within the group of replicates. DESeq then determines differentially expressed genes for each comparison by using, p value= ≤ 0.05.
Assembly: FN545816.1
Supplementary files format and content: Excel file shows transcripts per million (TPM) which is equivalent to RPKM

organism: Clostridioides difficile R20291

growth_protocol: BHIS overnight R20291 cultures of each were sub-cultured to an OD600 of 0.05 in 25 mL of DMM supplemented with either 20 mM glucose, 10 mM trehalose or 20 mM glucose and 10 mM trehalose. These were grown to mid-logarithmic phase (strain dependent 4-6 h), mixed with an equal volume of ice-cold 1:1 ethanol: acetone mix and stored at -80oC.

extract_protocol:
The cell suspension was thawed on ice, centrifuged at 5 000 x g for 10 min at 4oC, supernatant decanted and the pellet resuspended in 5 mL 1% beta-mercaptoethanol. The suspension was then centrifuged once more at 10 000 x g for 5 min at 4oC. RNA isolation was carried out using a Qiagen RNeasy Mini Kit (Qiagen, Manchester, UK ). Cells were resuspended in 200 µL TE buffer (10 mM Tris-HCl, 1 mM EDTA pH 8.0) containing 15 mg/mL lysozyme and 1.5 mg/ml Proteinase K (Qiagen, Manchester, UK) and incubated for 10 min at room temperature followed by the addition of 700 µL buffer RLT with 1% beta-mercaptoethanol. Cells were then transferred to a 2 mL Lysing Matrix B tube (MP Biomedicals, Cambridge, UK) and treated in a FastPrep-24 instrument (MP Biomedicals, Cambridge, UK) at a setting of 6.0 m/s for 45 s. The lysate was then centrifuged at 13 000 x g for 10 min and the supernatant added to 500 µL of 98% ethanol before RNA isolation and clean-up using a RNeasy column by following the manufacturer’s instructions. The protocol was modified to include an initial on-column DNA digestion step using the RNase-free DNase set (Qiagen, Manchester, UK) according to the manufacturer’s instructions.
RNA integrity was assessed using the Agilent 4200 TapeStation and the Agilent RNA ScreenTape Assay (Agilent, SantaClara, USA) with RNA samples of RIN > 8.0 being used for subsequent procedures. Ribodepletion was performed on 500 ng of total RNA, using the Qiagen FastSelect-5S/16S/23S ribodepletion kit (Qiagen, Manchester, UK) using the protocol: FastSelect-5S/16S/23S with NEBNext Ultra II Directional Library Prep Kit. Indexed sequencing libraries were then prepared using the NEBNext Ultra II Directional RNA Library Preparation Kit for Illumina (New England BioLabs, Ipswich, UK) and NEBNextMultiplex Oligos for Illumina (96 Unique Dual Index Primer Pairs) (New England Bio Labs, Ipswich, UK). Libraries were quantified using the Qubit Fluorometer and the Qubit dsDNA HS Kit (Thermo Fisher Scientific, Massachusetts, USA). Library fragment-length distributions were analysed using the Agilent TapeStation 4200 and the Agilent High Sensitivity D1000 ScreenTape Assay (Agilent, Santa Clara, USA). Libraries were pooled in equimolar amounts and final library quantification performed using the KAPA Library Quantification Kit for Illumina (Roche; Diagnostics, UK). The library pool was sequenced on the Illumina NextSeq 500 on a NextSeq500 High Output 300 cycle kit (Illumina, San Diego, USA), to generate over 10 million pairs of 150-bp paired-end reads per sample.

value: mid-logarithmic phase

value: Trehalose grown


title: Tre2


title: MM-expr01-plate01-024

description: sci-RNA-seq3 library

value: mouse embryo (E13.5)


title: AIM2-/- 2 3h [3hKO2]

source_name: CD4+ T cells from spleen of Aim2 KO #2 3h stimulation

value: CD4+ T cells


title: WT 1 24h [24hWT1]

source_name: CD4+ T cells from spleen of WT #1 24h stimulation


title: Tre1


title: spermidine-minus-rna-seq3


title: tcf21+, development, scRNAseq

city: ATLANTA

first: Jinhu

last: Wang

state: Georgia

address: 101 WOODRUFF CIRCLE WMB 2304

institute: Emory University

description: 10x Genomics

data_processing:
All processing was performed in 10X Genomics CellRanger v3.1.0 using default parameters
Assembly: Danio_rerio_GRCz11
Supplementary files format and content: Cell Ranger outputs a .mtx file with the feature-barcode matrix. This matrix contains the counts of molecules per cell (UMI/cell) as determined after filtering and counting by Cell Ranger. The matrix is in market exchange format while the row (gene or feature) and columns (cell barcodes) are provided as TSV files. File formats are documented in the Cell Ranger software manual

organism: Danio rerio

source_name: heart

extract_protocol:
Hearts were dissected from juvenile zebrafish, and ventricles were digested with Liberase TM (0.26 U/ml ). Dissociated cells were spun down and live EGFP+ cells were sorted by flow cytometry.
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics )

value: EK

value: heart

value: epicardial cells

tag: cell type (sorted)

tag: age

value: 7 weeks


title: AIM2-/- 4 24h [24hKO4]

source_name: CD4+ T cells from spleen of Aim2 KO #4 24h stimulation


title: MM-expr01-plate01-022

description: sci-RNA-seq3 library

value: C57BL/6, BALB/C, FVB, G4

value: multiplexed sample:WT and mutant


title: hapln1a+, regeneration, scRNAseq

description: 10x Genomics

extract_protocol:
Adult hearts were extracted at 7 days post amputation and the wounded apex region was collected and digested with Liberase TM (0.26 U/ml ). Dissociated cells were spun down and live EGFP+ cells were sorted by flow cytometry.
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics )

value: adult


title: MM-expr01-plate01-021

description: sci-RNA-seq3 library


title: AIM2-/- 2 24h [24hKO2]

source_name: CD4+ T cells from spleen of Aim2 KO #2 24h stimulation


title: hapln1a+, development, scRNAseq

description: 10x Genomics