title: RBG26162_Plate_4_WT [SLX.14258.i726_i506]


title: RBG26165_Plate_4_WT [SLX.14258.i729_i506]

status: Public on Jul 05 2022

type: SRA

city: Cambridge

first: Hugo

middle: P.

last: Bastos

address: Jeffrey Cheah Biomedical Centre, Puddicombe Way

department: Haematology

country: United Kingdom

institute: Wellcome - MRC Cambridge Stem Cell Institute

library_source: transcriptomic

data_processing:
RNA-seq reads were aligned to mm10 + ERCC92 using GSNAP (version 2018-03-25) with parameters (-B 5 -t 24 -n 1 -Q -N 1).
Reads in features were counted with htseq-count (HTSeq version 0.9.1) with the parameter (-s no).
Genome_build: GRCm38.81
Supplementary_files_format_and_content: Processed files are cell gene count matrices, both raw and filtered and normalized and associated cell metadata

molecule: total RNA

organism: Mus musculus

source_name: bone marrow

extract_protocol:
Bone marrow cells were harvested from STAT1KO and WT control mice, single ESLAM HSCs was FACS sorted into 2.3ul 0.2% Triton-100 containg RNAse inhibitor
Tagmentation is carried out using the Illumina Nextera XT DNA sample preparation kit. The protocol is based on the Tagmentation protocol from Fluidigm.

tag: cell type

value: ESLAM

tag: genotype

value: WT

tag: tissue

value: bone marrow


title: RBG26164_Plate_4_WT [SLX.14258.i728_i506]


title: RBG26167_Plate_4_KO [SLX.14258.i718_i507]

value: KO


title: RBG26161_Plate_4_WT [SLX.14258.i724_i506]


title: RBG26189_Plate_4_WT [SLX.14258.i729_i508]


title: RBG26187_Plate_4_WT [SLX.14258.i727_i508]


title: RBG26188_Plate_4_WT [SLX.14258.i728_i508]


title: RBG26190_Plate_4_KO [SLX.14258.i716_i510]


title: RBG26191_Plate_4_KO [SLX.14258.i718_i510]


title: RBG26178_Plate_4_KO [SLX.14258.i716_i508]


title: RBG26180_Plate_4_KO [SLX.14258.i719_i508]


title: RBG26181_Plate_4_KO [SLX.14258.i720_i508]


title: RBG26182_Plate_4_KO [SLX.14258.i721_i508]


title: RBG26177_Plate_4_WT [SLX.14258.i729_i507]


title: RBG26186_Plate_4_WT [SLX.14258.i726_i508]


title: RBG26141_Plate_4_WT [SLX.14258.i729_i503]


title: RBG26183_Plate_4_KO [SLX.14258.i722_i508]


title: RBG26140_Plate_4_WT [SLX.14258.i728_i503]


title: RBG26142_Plate_4_KO [SLX.14258.i716_i505]


title: RBG26143_Plate_4_KO [SLX.14258.i718_i505]


title: RBG26185_Plate_4_WT [SLX.14258.i724_i508]


title: RBG26166_Plate_4_KO [SLX.14258.i716_i507]


title: RBG26138_Plate_4_WT [SLX.14258.i726_i503]


title: RBG26184_Plate_4_WT [SLX.14258.i723_i508]


title: RBG26139_Plate_4_WT [SLX.14258.i727_i503]


title: RBG26136_Plate_4_WT [SLX.14258.i723_i503]


title: RBG26137_Plate_4_WT [SLX.14258.i724_i503]


title: RBG26176_Plate_4_WT [SLX.14258.i728_i507]


title: RBG26179_Plate_4_KO [SLX.14258.i718_i508]


title: RBG26134_Plate_4_KO [SLX.14258.i721_i503]


title: RBG26129_Plate_4_WT [SLX.14258.i729_i502]


title: RBG26128_Plate_4_WT [SLX.14258.i728_i502]


title: RBG26158_Plate_4_KO [SLX.14258.i721_i506]


title: RBG26130_Plate_4_KO [SLX.14258.i716_i503]


title: RBG26132_Plate_4_KO [SLX.14258.i719_i503]


title: RBG26156_Plate_4_KO [SLX.14258.i719_i506]


title: RBG26152_Plate_4_WT [SLX.14258.i728_i505]


title: RBG26157_Plate_4_KO [SLX.14258.i720_i506]


title: RBG26149_Plate_4_WT [SLX.14258.i724_i505]


title: RBG26153_Plate_4_WT [SLX.14258.i729_i505]


title: RBG26148_Plate_4_WT [SLX.14258.i723_i505]


title: RBG26159_Plate_4_KO [SLX.14258.i722_i506]


title: RBG26146_Plate_4_KO [SLX.14258.i721_i505]


title: RBG26155_Plate_4_KO [SLX.14258.i718_i506]


title: RBG26150_Plate_4_WT [SLX.14258.i726_i505]


title: RBG26154_Plate_4_KO [SLX.14258.i716_i506]


title: RBG26135_Plate_4_KO [SLX.14258.i722_i503]


title: RBG26147_Plate_4_KO [SLX.14258.i722_i505]


title: RBG26151_Plate_4_WT [SLX.14258.i727_i505]


title: RBG26133_Plate_4_KO [SLX.14258.i720_i503]


title: RBG26145_Plate_4_KO [SLX.14258.i720_i505]


title: RBG26144_Plate_4_KO [SLX.14258.i719_i505]


title: RBG26109_Plate_3_KO [SLX.14258.i720_i522]


title: RBG26131_Plate_4_KO [SLX.14258.i718_i503]


title: RBG26108_Plate_3_KO [SLX.14258.i719_i522]


title: RBG26111_Plate_3_KO [SLX.14258.i722_i522]


title: RBG26110_Plate_3_KO [SLX.14258.i721_i522]


title: RBG26105_Plate_3_WT [SLX.14258.i729_i521]


title: RBG26104_Plate_3_WT [SLX.14258.i728_i521]


title: RBG26107_Plate_3_KO [SLX.14258.i718_i522]


title: RBG26101_Plate_3_WT [SLX.14258.i724_i521]


title: RBG26106_Plate_3_KO [SLX.14258.i716_i522]


title: RBG26100_Plate_3_WT [SLX.14258.i723_i521]


title: RBG26103_Plate_3_WT [SLX.14258.i727_i521]


title: RBG26097_Plate_3_KO [SLX.14258.i720_i521]


title: RBG26099_Plate_3_KO [SLX.14258.i722_i521]


title: RBG26096_Plate_3_KO [SLX.14258.i719_i521]


title: RBG26124_Plate_4_WT [SLX.14258.i723_i502]


title: RBG26125_Plate_4_WT [SLX.14258.i724_i502]


title: RBG26120_Plate_4_KO [SLX.14258.i719_i502]


title: RBG26127_Plate_4_WT [SLX.14258.i727_i502]


title: RBG26121_Plate_4_KO [SLX.14258.i720_i502]


title: RBG26122_Plate_4_KO [SLX.14258.i721_i502]


title: RBG26116_Plate_3_WT [SLX.14258.i728_i522]


title: RBG26123_Plate_4_KO [SLX.14258.i722_i502]


title: RBG26117_Plate_3_WT [SLX.14258.i729_i522]


title: RBG26112_Plate_3_WT [SLX.14258.i723_i522]


title: RBG26113_Plate_3_WT [SLX.14258.i724_i522]


title: RBG25971_Plate_2_WT [SLX.14258.i712_i517]


title: RBG26119_Plate_4_KO [SLX.14258.i718_i502]


title: RBG26118_Plate_4_KO [SLX.14258.i716_i502]


title: RBG26114_Plate_3_WT [SLX.14258.i726_i522]


title: RBG26098_Plate_3_KO [SLX.14258.i721_i521]


title: RBG26102_Plate_3_WT [SLX.14258.i726_i521]


title: RBG26115_Plate_3_WT [SLX.14258.i727_i522]


title: RBG26126_Plate_4_WT [SLX.14258.i726_i502]


title: RBG25829_Plate_1_KO [SLX.14258.i702_i502]


title: RBG25828_Plate_1_KO [SLX.14258.i701_i502]


title: RBG25838_Plate_1_WT [SLX.14258.i711_i502]


title: RBG25834_Plate_1_KO [SLX.14258.i705_i502]


title: RBG25835_Plate_1_KO [SLX.14258.i706_i502]


title: RBG25833_Plate_1_KO [SLX.14258.i704_i502]


title: RBG25934_Plate_2_WT [SLX.14258.i711_i513]


title: RBG25837_Plate_1_WT [SLX.14258.i710_i502]


title: RBG25930_Plate_2_KO [SLX.14258.i705_i513]


title: RBG25929_Plate_2_KO [SLX.14258.i704_i513]


title: RBG25836_Plate_1_WT [SLX.14258.i707_i502]


title: RBG25839_Plate_1_WT [SLX.14258.i712_i502]


title: RBG25925_Plate_1_WT [SLX.14258.i715_i511]


title: RBG25935_Plate_2_WT [SLX.14258.i712_i513]


title: RBG25832_Plate_1_KO [SLX.14258.i703_i502]


title: RBG25927_Plate_2_KO [SLX.14258.i702_i513]


title: RBG25931_Plate_2_KO [SLX.14258.i706_i513]


title: RBG25924_Plate_1_WT [SLX.14258.i714_i511]


title: RBG25928_Plate_2_KO [SLX.14258.i703_i513]


title: RBG25923_Plate_1_WT [SLX.14258.i712_i511]


title: RBG25920_Plate_1_WT [SLX.14258.i707_i511]


title: RBG25919_Plate_1_KO [SLX.14258.i706_i511]


title: RBG25921_Plate_1_WT [SLX.14258.i710_i511]


title: RBG25917_Plate_1_KO [SLX.14258.i704_i511]


title: RBG25918_Plate_1_KO [SLX.14258.i705_i511]


title: RBG25914_Plate_1_KO [SLX.14258.i701_i511]


title: RBG25933_Plate_2_WT [SLX.14258.i710_i513]


title: RBG25932_Plate_2_WT [SLX.14258.i707_i513]


title: RBG25916_Plate_1_KO [SLX.14258.i703_i511]


title: RBG25915_Plate_1_KO [SLX.14258.i702_i511]


title: RBG25926_Plate_2_KO [SLX.14258.i701_i513]


title: RBG25912_Plate_1_WT [SLX.14258.i714_i510]


title: RBG25911_Plate_1_WT [SLX.14258.i712_i510]


title: RBG25908_Plate_1_WT [SLX.14258.i707_i510]


title: RBG25922_Plate_1_WT [SLX.14258.i711_i511]


title: RBG25905_Plate_1_KO [SLX.14258.i704_i510]


title: RBG25910_Plate_1_WT [SLX.14258.i711_i510]


title: RBG25907_Plate_1_KO [SLX.14258.i706_i510]


title: RBG25961_Plate_2_WT [SLX.14258.i715_i516]


title: RBG25909_Plate_1_WT [SLX.14258.i710_i510]


title: RBG25960_Plate_2_WT [SLX.14258.i714_i516]


title: RBG25906_Plate_1_KO [SLX.14258.i705_i510]


title: RBG25904_Plate_1_KO [SLX.14258.i703_i510]


title: RBG25964_Plate_2_KO [SLX.14258.i703_i517]


title: RBG25965_Plate_2_KO [SLX.14258.i704_i517]


title: RBG25962_Plate_2_KO [SLX.14258.i701_i517]


title: RBG25963_Plate_2_KO [SLX.14258.i702_i517]


title: RBG25967_Plate_2_KO [SLX.14258.i706_i517]


title: RBG25957_Plate_2_WT [SLX.14258.i710_i516]


title: RBG25956_Plate_2_WT [SLX.14258.i707_i516]


title: RBG25959_Plate_2_WT [SLX.14258.i712_i516]


title: RBG25958_Plate_2_WT [SLX.14258.i711_i516]


title: RBG25966_Plate_2_KO [SLX.14258.i705_i517]


title: RBG25913_Plate_1_WT [SLX.14258.i715_i510]


title: RBG25955_Plate_2_KO [SLX.14258.i706_i516]


title: RBG25952_Plate_2_KO [SLX.14258.i703_i516]


title: RBG25954_Plate_2_KO [SLX.14258.i705_i516]


title: RBG25948_Plate_2_WT [SLX.14258.i714_i515]


title: RBG25949_Plate_2_WT [SLX.14258.i715_i515]


title: RBG25953_Plate_2_KO [SLX.14258.i704_i516]


title: RBG25944_Plate_2_WT [SLX.14258.i707_i515]


title: RBG25945_Plate_2_WT [SLX.14258.i710_i515]


title: RBG25947_Plate_2_WT [SLX.14258.i712_i515]


title: RBG25951_Plate_2_KO [SLX.14258.i702_i516]


title: RBG25941_Plate_2_KO [SLX.14258.i704_i515]


title: RBG25938_Plate_2_KO [SLX.14258.i701_i515]


title: RBG25936_Plate_2_WT [SLX.14258.i714_i513]


title: RBG25946_Plate_2_WT [SLX.14258.i711_i515]


title: RBG25937_Plate_2_WT [SLX.14258.i715_i513]


title: RBG25943_Plate_2_KO [SLX.14258.i706_i515]


title: RBG25942_Plate_2_KO [SLX.14258.i705_i515]


title: RBG25940_Plate_2_KO [SLX.14258.i703_i515]


title: RBG25870_Plate_1_KO [SLX.14258.i705_i506]


title: RBG25864_Plate_1_WT [SLX.14258.i714_i505]


title: RBG25867_Plate_1_KO [SLX.14258.i702_i506]


title: RBG25865_Plate_1_WT [SLX.14258.i715_i505]


title: RBG25868_Plate_1_KO [SLX.14258.i703_i506]


title: RBG25950_Plate_2_KO [SLX.14258.i701_i516]


title: RBG25856_Plate_1_KO [SLX.14258.i703_i505]


title: RBG25858_Plate_1_KO [SLX.14258.i705_i505]


title: RBG25863_Plate_1_WT [SLX.14258.i712_i505]


title: RBG25860_Plate_1_WT [SLX.14258.i707_i505]


title: RBG25862_Plate_1_WT [SLX.14258.i711_i505]


title: RBG25859_Plate_1_KO [SLX.14258.i706_i505]


title: RBG25861_Plate_1_WT [SLX.14258.i710_i505]


title: RBG25857_Plate_1_KO [SLX.14258.i704_i505]


title: RBG25851_Plate_1_WT [SLX.14258.i712_i503]


title: RBG25850_Plate_1_WT [SLX.14258.i711_i503]


title: RBG25939_Plate_2_KO [SLX.14258.i702_i515]


title: RBG25866_Plate_1_KO [SLX.14258.i701_i506]


title: RBG25849_Plate_1_WT [SLX.14258.i710_i503]


title: RBG25848_Plate_1_WT [SLX.14258.i707_i503]


title: RBG25842_Plate_1_KO [SLX.14258.i701_i503]


title: RBG25853_Plate_1_WT [SLX.14258.i715_i503]


title: RBG25855_Plate_1_KO [SLX.14258.i702_i505]


title: RBG25852_Plate_1_WT [SLX.14258.i714_i503]


title: RBG25854_Plate_1_KO [SLX.14258.i701_i505]


title: RBG25841_Plate_1_WT [SLX.14258.i715_i502]


title: RBG25871_Plate_1_KO [SLX.14258.i706_i506]


title: RBG25846_Plate_1_KO [SLX.14258.i705_i503]


title: RBG25845_Plate_1_KO [SLX.14258.i704_i503]


title: RBG25869_Plate_1_KO [SLX.14258.i704_i506]


title: RBG25843_Plate_1_KO [SLX.14258.i702_i503]


title: RBG25900_Plate_1_WT [SLX.14258.i714_i508]


title: RBG25901_Plate_1_WT [SLX.14258.i715_i508]


title: RBG25896_Plate_1_WT [SLX.14258.i707_i508]


title: RBG25897_Plate_1_WT [SLX.14258.i710_i508]


title: RBG25844_Plate_1_KO [SLX.14258.i703_i503]


title: RBG25840_Plate_1_WT [SLX.14258.i714_i502]


title: RBG25847_Plate_1_KO [SLX.14258.i706_i503]


title: RBG25899_Plate_1_WT [SLX.14258.i712_i508]


title: RBG25902_Plate_1_KO [SLX.14258.i701_i510]


title: RBG25888_Plate_1_WT [SLX.14258.i714_i507]


title: RBG25898_Plate_1_WT [SLX.14258.i711_i508]


title: RBG25890_Plate_1_KO [SLX.14258.i701_i508]


title: RBG25889_Plate_1_WT [SLX.14258.i715_i507]


title: RBG25903_Plate_1_KO [SLX.14258.i702_i510]


title: RBG25892_Plate_1_KO [SLX.14258.i703_i508]


title: RBG25883_Plate_1_KO [SLX.14258.i706_i507]


title: RBG25893_Plate_1_KO [SLX.14258.i704_i508]


title: RBG25891_Plate_1_KO [SLX.14258.i702_i508]


title: RBG25885_Plate_1_WT [SLX.14258.i710_i507]


title: RBG25884_Plate_1_WT [SLX.14258.i707_i507]


title: RBG25881_Plate_1_KO [SLX.14258.i704_i507]


title: RBG25895_Plate_1_KO [SLX.14258.i706_i508]


title: RBG25894_Plate_1_KO [SLX.14258.i705_i508]


title: RBG25887_Plate_1_WT [SLX.14258.i712_i507]


title: GAM1GAM2.2.1

city: Villaviciosa

first: Natalia

last: Molinero Garcia

state: Asturias

address: IPLA-CSIC, Paseo Rio Linares S/N

department: DEPARTMENT OF MICROBIOLOGY AND BIOCHEMISTRY OF DAIRY PRODUCTS

country: Spain

institute: Dairy Products Institute of Asturias (IPLA-CSIC)

description:
Coculture of R.gauvreauii IPLA60001 and R. biliarensis IPLA60002 in M2 medium supplemented to Starch from Rice in 8hours Replicate 1
countscomparacion2Name.txt and countscomparacion5Name.txt
diffexpr-results-mrs_vs_pH2.csvt and diffexpr-results-mrs_vs_pH5.csv

data_processing:
Alignment with their reference genomes using Bowtie2 v.2.2.6 (.sam files)
SAMtools v.1.4 was used to generate the ".bam" files and "sorted.bam" files
Read counts were generated using FeatureCounts
Differential gene expression analysis was performed using the Bioconductor package DESeq2
Genome_build: Accessions number: for R.gauvreauii IPLA60001 is SRR10273262 and for R. bilirensis IPLA60002 is SRR9209608

organism:
Ruminococcus gauvreauii
Ruminococcoides bili

source_name: Coculture of Ruminococcus gauvreauii IPLA60001 and Ruminocoides biliarensis IPLA60002

growth_protocol: To study the interaction between Rc. biliarensis IPLA60002 and R. gauvreauii IPLA60001 we made co-cultures combinations in M2 broth medium supplemented with 30%CBRF (clarified bovine rumen fluid) and 0.2% Starch from Rice (Sigma-Aldrich) as only carbon source. The co-culture conditions were as follows: 10ml of initial exponential phase co-cultures of R. biliarensis IPLA60002 and R. gauvreauii IPLA60001 (6 h), and 10ml co-cultures for middle exponential phase (8 h). The strains were grown in monoculture to have control conditions: R. gauvreauii was growth in M2 medium supplemented with 30% CBRF and 0,2% D-glucose, and R. biliarensis was growth in M2 medium supplemented with 30%CBRF and 0.2% starch from rice. Three technical replicates were performed for each condition. The tubes were centrifuged 10 min and the pellet was immediately resuspended in 1ml of RNAlaterTM (Qiagen) and frozen at -80ᵒC.

extract_protocol:
Total RNA was extracted from the pellets that were resuspended in 200 μl of lysozyme (concentración) and mutanolysin (concentración) solution and incubated at 37°C for 1 h. Then, 800 μl of QIAzol (Qiagen) were added and placed in a tube containing 0.8 g of glass beads (106 μm diameter; Sigma). The cells were lysed by shaking the mix on a BioSpec homogenizer (BioSpec Products, Inc., USA) for 2 min followed by 2 min in ice. This step was repeated three times. Samples were further treated with chloroform and then centrifuged at 12,000 rpm for 15 min at 4°C. The upper phase containing the RNA was recovered. Samples were further purified using the RNeasy Mini Kit (Qiagen) following the manufacturer’s protocol. Quality and integrity of the RNA was checked by an Agilent 2200 Tape Station Nucleic Acid System (Agilent Technologies, Palo Alto, Calif., USA). The amount of RNA was quantified in a Qubit™ 4 fluorometer with Qubit RNA assay kits (Thermo Fisher Scientific, Inc., Waltham, MA, USA). One to 2.5 μg of total RNA was depleted using Ribo-Zero rRNA removal kit (Illumina) to remove rRNA according to the supplier’s instructions. The yield of rRNA depletion was checked in the Agilent Tape Station and rRNA-depleted RNA samples were treated with the TruSeq Stranded mRNA sample preparation kit (Illumina). Size evaluation and quantification of RNA samples was performed as above described.
Whole transcriptome library was sequenced by means of a NextSeq 550 Sequencing System (Illumina) using a High Output kit v2.5 (75 cycles) flow cell

tag: strain

tag: treaatment


title: GAM1GAM2.2.3

description:
Coculture of R.gauvreauii IPLA60001 and R. biliarensis IPLA60002 in M2 medium supplemented to Starch from Rice in 8hours Replicate 3
countscomparacion2Name.txt and countscomparacion5Name.txt
diffexpr-results-mrs_vs_pH2.csvt and diffexpr-results-mrs_vs_pH5.csv


title: GAM1GAM2.2.2

description:
Coculture of R.gauvreauii IPLA60001 and R. biliarensis IPLA60002 in M2 medium supplemented to Starch from Rice in 8hours Replicate 2
countscomparacion2Name.txt and countscomparacion5Name.txt
diffexpr-results-mrs_vs_pH2.csvt and diffexpr-results-mrs_vs_pH5.csv


title: RBG25873_Plate_1_WT [SLX.14258.i710_i506]


title: GAM1GAM2.1.2

description:
Coculture of R.gauvreauii IPLA60001 and R. biliarensis IPLA60002 in M2 medium supplemented to Starch from Rice in 6hours Replicate 2
countscomparacion1Name.txt and countscomparacion5Name.txt
diffexpr-results-mrs_vs_pH1.csv and diffexpr-results-mrs_vs_pH5.csv


title: RBG25875_Plate_1_WT [SLX.14258.i712_i506]


title: RBG25872_Plate_1_WT [SLX.14258.i707_i506]


title: GAM1GAM2.1.3

description:
Coculture of R.gauvreauii IPLA60001 and R. biliarensis IPLA60002 in M2 medium supplemented to Starch from Rice in 6hours Replicate 3
countscomparacion1Name.txt and countscomparacion5Name.txt
diffexpr-results-mrs_vs_pH1.csv and diffexpr-results-mrs_vs_pH5.csv


title: GAM1GAM2.1.1

description:
Coculture of R.gauvreauii IPLA60001 and R. biliarensis IPLA60002 in M2 medium supplemented to Starch from Rice in 6hours Replicate 1
countscomparacion1Name.txt and countscomparacion5Name.txt
diffexpr-results-mrs_vs_pH1.csv and diffexpr-results-mrs_vs_pH5.csv


title: RBG25874_Plate_1_WT [SLX.14258.i711_i506]


title: RBG25877_Plate_1_WT [SLX.14258.i715_i506]


title: RBG25879_Plate_1_KO [SLX.14258.i702_i507]


title: HS766T cells, Talazoparib treated, replicate 2

city: San Diego

first: Xia

last: Ding

address: 10724 Science Center Dr

country: USA

institute: Pfizer, Inc.

data_processing:
Sequencing was performed using an Illumina systems following Illumina-provided protocols for 2×150 paired-end sequencing in Mingma Technologies at Shanghai, China.
Assembly: hg38
Supplementary files format and content: excel files include RPKM values for each Sample

organism: Homo sapiens

growth_protocol: Cells were maintained in RPMI1640+10%FBS

extract_protocol:
Approximately Two million cells in triplicate were harvested, rinsed with PBS and stored in RNAlater RNA stabilization solution
RNA purification, reverse transcription, library construction and sequencing were performed at Mingma Technologies at Shanghai according to the manufacturer's instructions (Illumina). The mRNA-focused sequencing libraries from total RNA were prepared using Illumina TruSeq Stranded mRNA Library Prep kit. PolyA mRNA was purified from total RNA using oligo-dT-attached magnetic beads and then fragmented by fragmentation buffer. Taking these short fragments as templates, first strand cDNA was synthesized using reverse transcriptase and random primers. Then in the process of second strand cDNA synthesis, RNA template was removed and a replacement strand, incorporating dUTP in place of dTTP to generate ds cDNA, was synthesized. The incorporation of dUTP quenches the second strand during amplification, because the polymerase does not incorporate past this nucleotide. AMPure XP (Beckmen) beads were then used to purify the ds cDNA from the reaction mix. Next, the ds cDNA was subjected to end-repair, phosphorylation and 'A' base addition according to Illumina's library construction protocol. In the following process, Illumina sequencing adapters were added to both size of the dscDNA fragments. After PCR amplification for DNA enrichment, the AMPure XP Beads were used to clean up the target fragments of 200-300 bp. After library construction, Qubit 2.0 fluorometer dsDNA HS Assay (ThermoFisher Scientific) was used to quantify concentration of the resulting sequencing libraries, while the size distribution was analyzed using Agilent BioAnalyzer 2100 (Agilent).

tag: cell line

value: Pancreatic cancer cells

tag: treatment

value: Talazoparib, 100 nM

tag: time

value: Day 3


title: HS766T cells, Talazoparib treated, replicate 3


title: HS766T cells, DMSO treated, replicate 3

value: DMSO


title: RBG25880_Plate_1_KO [SLX.14258.i703_i507]


title: HS766T cells, Talazoparib treated, replicate 1


title: RBG25882_Plate_1_KO [SLX.14258.i705_i507]


title: RBG25878_Plate_1_KO [SLX.14258.i701_i507]


title: RBG25886_Plate_1_WT [SLX.14258.i711_i507]


title: HS766T cells, DMSO treated, replicate 1


title: SW1990 cells, Talazoparib treated, replicate 3


title: SW1990 cells, Talazoparib treated, replicate 1


title: SW1990 cells, Talazoparib treated, replicate 2


title: SW1990 cells, DMSO treated, replicate 3


title: NAAC124_Alone

first: April

middle: Elizabeth

last: Williams

state: California

address: 10010 N Torrey Pines Rd

department: IGC

institute: Salk Institute for Biological Studies

data_processing:
Sequenced reads were quality-tested using FASTQC v0.11.8
The genome index was constructed using the gene annotation supplied with the mm10 Illumina iGenomes collection and sjdbOverhang value of 100.
Reads were aligned to the mm10 mouse genome using the STAR aligner version 2.5.3a. Mapping was carried out using default parameters, filtering non-canonical introns and allowing up to 10 mismatches per read and only keeping uniquely mapped reads.
Raw or FPKM (fragments per kilobase per million mapped reads) gene expression was quantified across all gene exons with HOMER v4.10.4 analyzeRepeats.pl with mm10 annotation v5.10 and parameters -strand + -count exons -condenseGenes (top-expressed isoform as proxy for gene expression)
Differential gene expression was carried out on the raw counts with HOMER getDiffExpression.pl that runs DESeq2 v1.14.1 using replicates to compute within-group dispersion. BMP6 samples were adjusted for mouse-specific batch effects using the -batch flag. Differentially expressed genes were defined as having FDR<0.05, FC>1.5, and FPKM>1, when comparing two experimental conditions.
Genome_build: mm10
Supplementary_files_format_and_content: Excel table of FPKM values

source_name: P7 mouse cortex

extract_protocol:
RNA was extracted using the RNEasy Micro Plus kit (Qiagen 74034).
For RNA sequencing RNA libraries were prepared with TrueSeq Stranded mRNA Library Prep Kit (Illumina), from on average 0.8ug total RNA. Poly(A) mRNA was isolated from total RNA samples, followed by mRNA fragmentation, first strand cDNA synthesis, second cDNA synthesis and adaptor ligation, and isolation and amplification of cDNA fragments. Illumina HiSeq 2500 instrument was used for sequencing, with a read length of 50bp single-end, and an average of 36 million reads per sample.

treatment_protocol: Astrocytes isolated from the P7 mouse cortex of WT, FXS, RTT, DS mice using immunopanning. Maintained in vitro in defined serum free media for 12 days before RNA collection. Biological replicates for NDs: WT=6, FXS=6, RTT=6, DS=4. For comparing gene expression in WT astrocytes treated with BMP6, WT astrocytes were treated for the last 5 days of the culture period with BMP6 or left untreated (Alone condition). Biological replicates for BMP6: Alone=6, BMP6=6.

tag: disease state

value: Alone

value: astrocyte in vitro

tag: batch


title: NAAC124_BMP6


title: NAAC120_BMP6


title: NAAC122_BMP6


title: NAAC122_Alone


title: NAAC120_Alone


title: RBG25876_Plate_1_WT [SLX.14258.i714_i506]


title: SW1990 cells, DMSO treated, replicate 1


title: NAAC91_Alone


title: NAAC91_BMP6


title: PANC1 cells, Talazoparib treated, replicate 2


title: PANC1 cells, Talazoparib treated, replicate 1


title: PANC1 cells, Talazoparib treated, replicate 3


title: HS766T cells, DMSO treated, replicate 2


title: NAAC81_Alone


title: GAM2.2

description:
Pure culture of R.biliarensis IPLA60002 in M2 medium supplemented to Starch from Rice in 8hours Replicate 2
countscomparacion3Name.txt and countscomparacion4Name.txt
diffexpr-results-mrs_vs_pH3.csv and diffexpr-results-mrs_vs_pH4.csv

organism: Ruminococcoides bili

source_name: Culture of Ruminocoides biliarensis IPLA60002


title: GAM2.3

description:
Pure culture of R.biliarensis IPLA60002 in M2 medium supplemented to Starch from Rice in 8hours Replicate 3
countscomparacion3Name.txt and countscomparacion4Name.txt
diffexpr-results-mrs_vs_pH3.csv and diffexpr-results-mrs_vs_pH4.csv


title: PANC1 cells, DMSO treated, replicate 3


title: NAAC81_BMP6


title: NAAC76_Alone


title: PANC1 cells, DMSO treated, replicate 1


title: GAM2.1

description:
Pure culture of R.biliarensis IPLA60002 in M2 medium supplemented to Starch from Rice in 8hours Replicate 1
countscomparacion3Name.txt and countscomparacion4Name.txt
diffexpr-results-mrs_vs_pH3.csv and diffexpr-results-mrs_vs_pH4.csv


title: PANC1 cells, DMSO treated, replicate 2


title: Sample 1474_LIRKO_2

city: St. Louis

first: Paul

last: Cliften

address: 4320 Forest Park Parkway

department: Genetics

institute: Washington University

description: Homozygous_all.gene_moderated_log2cpm.xls

data_processing:
Basecalls performed using RTA Version 2.7.3
Sequence reads were aligned to the GRCm38 genome assembly using STAR version 2.0.4b
Gene counts were computed from uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5
Genome_build: Ensembl release 76 top-level assembly (GRCm38)
Supplementary_files_format_and_content: gene counts

growth_protocol: 4-5 month old male mice were studied

extract_protocol: Described in Kulkarni et al., PPAR Research, 2021

value: C57BL6/J x FVBN

tag: gender

value: male

tag: age

value: 4-5 months

value: Liver

value: LIRKO


title: SW1990 cells, DMSO treated, replicate 2


title: Sample 1483_LIRKO_2


title: NAAC76_BMP6


title: NAAC44_RTT

value: Rett's syndrome


title: PANC1 cells, TalaR, replicate 3

value: TalaR

value: Talazoparib, 50 nM

value: 4 months


title: Sample 1468_LIRKO_2


title: PANC1 cells, TalaR, replicate 2


title: NAAC43_RTT


title: Sample 1586_WT_2

value: WT


title: Sample 1601_WT_2


title: PANC1 cells, TalaR, replicate 1


title: Sample 1564_WT_2


title: Sample 1877_PiZ x LIRKO (ZZ)

value: PiZ x LIRKO (ZZ)


title: Sample 1855_PiZ x LIRKO (ZZ)


title: Sample 1858_PiZ x LIRKO (ZZ)


title: NAAC40_RTT


title: Sample 1813_PiZ x LIRKO (ZZ)


title: PANC1 cells, parental replicate 2

value: Pancreatic cancer cells

value: Day 0


title: Sample 1810_PiZ x LIRKO (ZZ)


title: PANC1 cells, parental replicate 3


title: NAAC35_WT


title: NAAC39_DS

value: Down's syndrome


title: Sample 1600_LIRKO_2


title: Sample 1809_PiZ (ZZ)

value: PiZ (ZZ)


title: NAAC38_FXS

value: Fragile X syndrome


title: Sample 1682_PiZ (ZZ)


title: Sample 1783_PiZ x LIRKO (ZZ)


title: PSN1 cells, Talazoparib treated, replicate 2

value: Day 3


title: PANC1 cells, parental replicate 1


title: Sample 1846_PiZ (ZZ)

value: C57BL6/J x FVBN


title: NAAC31_FXS

value: astrocyte in vitro


title: NAAC34_WT


title: NAAC30_WT


title: Sample 182_PiZ (Z*)

description: Hemizygous_all.gene_moderated_log2cpm.xls

value: male

value: 4-5 months

value: PiZ (Z*)


title: PSN1 cells, DMSO treated, replicate 1

value: DMSO


title: Sample 1876_PiZ x LIRKO (ZZ)

value: Liver


title: NAAC28_FXS


title: Sample 1586_WT

source_name: IRZZ


title: NAAC32_DS


title: Sample 1601_WT


title: Sample 251_PiZ (Z*)


title: PSN1 cells, Talazoparib treated, replicate 1

value: Talazoparib, 50 nM


title: PSN1 cells, Talazoparib treated, replicate 3


title: Sample 249_PiZ (Z*)


title: PSN1 cells, DMSO treated, replicate 2


title: NAAC33_WT


title: Sample 1564_WT


title: NAAC27_RTT

value: Rett's syndrome


title: Sample 1410_PiZ (Z)

value: liver

value: PiZ (Z)


title: PSN1 cells, DMSO treated, replicate 3

value: Pancreatic cancer cells

value: WT


title: Sample 285_PiZ (Z*)


title: Sample 120_PiZ (Z*)


title: NAAC29_FXS


title: Sample 1445_PiZ (Z)


title: Sample 1450_PiZ x LIRKO (Z)

value: PiZ x LIRKO (Z)


title: Sample 1443_PiZ (Z)


title: Sample 1427_PiZ x LIRKO (Z)


title: Sample 1442_PiZ (Z)


title: Sample 1428_PiZ x LIRKO (Z)


title: HCC1806 cells, TalaR-maintained in drug media, replicate 3

value: Breast cancer cells

value: TalaR-M

value: 4 months


title: Sample 1411_PiZ (Z)

value: C57BL6/J x FVBN


title: HCC1806 cells, TalaR-maintained in drug media, replicate 2


title: HCC1806 cells, TalaR-cultured in drug free media, replicate 3

value: TalaR-DF

value: Day 0


title: NAAC24_FXS

value: Fragile X syndrome

value: astrocyte in vitro


title: Sample 207_PiZ x LIRKO x F1KO (Z)

value: male

value: 4-5 months

value: PiZ x LIRKO x F1KO (Z)


title: Sample 1412_PiZ x LIRKO (Z)


title: Sample 201_PiZ x LIRKO x F1KO (Z)

value: Liver


title: HCC1806 cells, TalaR-cultured in drug free media, replicate 2


title: NAAC21_DS

value: Down's syndrome


title: Sample 206_PiZ x LIRKO x F1KO (Z)


title: NAAC22_WT


title: HCC1806 cells, TalaR-cultured in drug free media, replicate 1


title: Sample 169_PiZ x LIRKO x F1KO (Z)


title: Sample 170_PiZ x LIRKO x F1KO (Z)


title: Sample 1483_LIRKO

value: LIRKO


title: NAAC20_RTT

value: Rett's syndrome


title: NAAC19_DS


title: HCC1806 cells, parental, replicate 3

value: WT


title: NAAC18_RTT


title: Sample 1600_LIRKO


title: HCC1806 cells, TalaR-maintained in drug media, replicate 1

value: Talazoparib, 50 nM


title: Sample 1474_LIRKO


title: HCC1806 cells, parental, replicate 2

value: Breast cancer cells


title: NAAC26_WT


title: Sample 1468_LIRKO


title: HCC1806 cells, parental, replicate 1


title: Txnrd1 KO Tom.2

city: Charleston

first: Jennifer

middle: S

last: Stancill

state: South Carolina

address: 173 Ashley Avenue, CR513

department: Biochemistry and Molecular Biology

institute: Medical University of South Carolina

data_processing:
Data was trimmed and quality assessed with FastQC and RSeQC
Reads were aligned to the mouse reference Gencode vM23 (based on Ensembl v98) using the STAR aligner and MAPR-Seq workflow v3.0
Differential gene expression was processed through EdgeR utilizing both the pairwise and generalized linear model statistics with the cutoffs set at an FDR <0.05 and log 2 fold change ≥1 or ≤-1.
Assembly: Gencode vM23 (GRCm38.p6)
Supplementary files format and content: excel tables with gene counts (GeneCount.xlsx) and differential analysis results (DEAnalyses_pairwise.xlsx)

source_name: Panctreatic islets

extract_protocol:
Pancreatic islets were isolated from experimental mice (age 10-20 weeks) and cultured overnight at 37 degrees C, 5% CO2, in CMRL supplemented with 10% heat-inactivated FBS and containing 5.5 mM glucose. The next day, islets were dispersed into single cells using trypsin. Populations of live GFP+ (beta cells) and Tom+ (non-beta cells) were collected by fluorescence-activated cell sorting (FACS). DAPI was used to exclude dead cells. Total RNA was isolated using an RNeasy kit (Qiagen). Genomic DNA was removed using a TURBO DNA-free Kit (ThermoFisher Scientific).
RNA was quantifed by fluorimetric methods (Qubit, Invitrogen) and quality assessed by Fragment Analysis (Agilent).  cDNA was synthesized using 5-10ng of input RNA with with libraries prepared following manufacturer's recommendations in the SMARTseq Ultra Low Input workflow (Takara Bio Inc.).  Libraries were completed, indexed and amplified with the Nextera DNA Library kit (Illumina).  Final libraries were quantified by qPCR (Kapa Library Quantification Kit, Kapa Biosystems) and fragment size observed with high sensitivity DNA fragment analysis (Agilent).  Paired end sequencing was completed on the NovaSeq 6000 at 2x100bp reads, targeting 50 million reads per sample.

value: non-beta-cells


title: NAAC17_FXS


title: Txnrd1 KO Tom.3


title: PSN1 cells, TalaR-cultured in drug free media, replicate 3

value: Pancreatic cancer cells


title: Txnrd1 KO GFP.2

value: beta-cells


title: HCC1806, TalaR, scRNAseq

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
For Single Cell RNA sequencing Normalization and Analysis, raw sequencing reads were aligned to the human genome (hg38) using CellRanger V3.0.2. CellRanger filtered reads were imported into R V3.6.0 using Seurat V3.2.0 (Stuart et al., 2019). Low quality cells were filtered from the analysis if the mitochondrial content was >20% of reads, if the ribosomal content was >40% of reads or if total UMI <1500. Doublets were filtered from the analysis based on total UMI content > 30000. Comparisons corresponding to samples which were sequenced across different batches were batch corrected with Harmony (Korsunsky et al., 2019) using the parameters theta=3 and lambda=1. To mitigate the effects of cell cycle heterogeneity in data, we followed a previously published approach by assigning each cell a score based on its expression of canonical cell phase markers and then regressing these out using Seurat. We also regressed out effects associated with the number of UMIs, mitochondrial content and ribosomal gene content using the SCTransform (Hafemeister and Satija, 2019) function in Seurat. Principal component analysis (PCA) using the top 14 principal components was performed on the top variable genes determined in Seurat. Dimensionality was reduced and data was visualized using both tSNE and UMAP representations. Phenograph clustering as a part of the Seurat package was used to discretely segregate cells into clusters. To choose an optimal resolution value, clusters were generated for resolutions spanning r=.1 to r=2. The optimal resolution value was chosen ad hoc by calculating differential expression and comparing visual separation between clusters for each resolution value. After selection of a resolution value, differential gene expression was calculated using the FindAllMarkers function in Seurat using a likelihood-ratio test for single cell gene expression, selecting genes expressed in at least 20% of cells within a cluster with a fold-change > .2. Pathway enrichment for genes positively associated with a cluster was calculated using a hypergeometric test.
Assembly: hg38
Supplementary files format and content: normalized count matrix

source_name: cell line

extract_protocol:
Cells were detached using trypsinization and washed with 10x wash buffer (PBS plus 0.04% BSA) twice using 300g centrifugation. After last wash, the cell numbers were counted, and viability was assessed. The final sample were at the cell density of 0.7-1.2 million/mL.
About 5000 cells per sample were mixed with 10x Single Cell 3’ v2 RT reagents and loaded onto one channel of 10X Chromium Controller (10x Genomics, PN-1000202). After GEM generation, the RNA-seq libraries were processed following 10x Single Cell 3’ Library Construction protocol (10X Genomics, Chromium™ Single Cell 3’ Library Construction Kit v2, PN-120237). Final libraries were sequenced by SeqMatic (44846 Osgood Rd, Fremont, CA 94539) using Illumina NavoSeq 6000 system, with 2x75 paired-end kits.

treatment_protocol: HCC1806 cells were cultured in media containing 50 nM Talazoparib for 4 months to allow resistance development

value: cell line


title: PSN1 cells, TalaR-cultured in drug free media, replicate 2

value: TalaR-DF

value: Day 0


title: HCC1806, parental, scRNAseq

description: 10x Genomics


title: Txnrd1 KO GFP.1


title: PSN1 cells, TalaR-cultured in drug free media, replicate 1


title: Txnrd1 WT Tom.2


title: PSN1 cells, TalaR-maintained in drug media, replicate 3

value: TalaR-M

value: 4 months


title: Txnrd1 WT Tom.4


title: Txnrd1 WT GFP.2


title: Txnrd1 WT GFP.3


title: PSN1 cells, TalaR-maintained in drug media, replicate 1


title: Zygote.Lsm1FLAG.RIPseq.rep2

city: Shanghai

first: Jiang

last: Zhu

address: 1239 Siping Road

country: China

institute: Tongji University

description: RNA after IP

data_processing:
Adapter trimming using Trimmomatic with default parameters, followed by a quality control step using FastQC.
FASTQ reads were aligned to the transcriptome (RefSeq transcriptome assembly, and Repbase transposon sequences) using salmon.
TPM values from the salmon results were used for further analysis.
Genome_build: mm10
Supplementary_files_format_and_content: salmon output .sf file per sample

source_name: Zygotes

growth_protocol: B6D2F1 female mice (8–10 weeks old) were super-ovulated by injection with 7 IU each of pregnant mare serum gonadotropin (PMSG), followed by injection of 5 IU of human chorionic gonadotropin (hCG) 48 hr later. The super-ovulated female mice were mated with male mice. The zygote were collected at 18-20 hr post-hCG injection, and micro-injected with different RNAs.

extract_protocol:
For Lsm1 knockdown zyogtes, RNA was harvested using Trizol reagent. For RIP-seq zygotes, Protein-RNA complex were isolated by ANTI-FLAG® M2 Affinity Gel, then RNA was harvested using Trizol reagent.
For Lsm1 knockdown zyogtes, RNA libraries were prepared for sequencing using KAPA Stranded RNA-Seq Kit with RiboErase (HMR) (KapaBiosystems, Cat. Nos.KK8483);  For RIP-seq zygotes, RNA libraries were prepared for sequencing using SMARTer Stranded Total RNA-Seq Kit v2 (Takara, Cat. Nos. 635005)

treatment_protocol: Lsm1KD group were injected with Lsm1 siRNA; WT group were injected with Lsm1 scramble siRNA; LLsm1FLAGRIP group were injected with Lsm1_3XFlag mRNA; CtrlRIP group were injected with Lsm1 mRNA

value: Zygotes collected after Lsm1_3XFlag mRNA injection

tag: rip antibody

value: ANTI-FLAG® M2 Affinity Gel (Merk, A2220)


title: PSN1 cells, parental, replicate 3


title: Txnrd1 WT Tom.3


title: Txnrd1 WT GFP.4


title: Zygote.Lsm1FLAG.RIPseq.rep1

description: RNA after IP


title: Txnrd1 KO Tom.1


title: Zygote.Lsm1FLAG.Input.RNAseq.rep2

description: total RNA


title: Txnrd1 KO GFP.3


title: PSN1 cells, TalaR-maintained in drug media, replicate 2


title: Txnrd1 WT GFP.1


title: Zygote.Lsm1FLAG.Input.RNAseq.rep1

description: total RNA


title: NHDF-1

city: Los Angeles

first: Melanie

last: Galano

address: 1985 Zonal Ave

institute: University of Southern California

data_processing:
Raw sequencing reads were trimmed first by quality score (minimum base quality 20, trimmed reads shorter than 20-bp were discarded) and then the first 16bp from the 5'-end.
Trimmed reads were aligned to the human genome hg38 using STAR 2.7.3 with Gencode v36 as guidance.
Aligned reads were quantified to Gencode v36 genes with Partek E/M method.
Annotated features with less than 10 counts in all samples were removed from further analysis.  The remaining features were normalized using the Upper Quatile method with an offset of 1.
Differential expression analysis was done using Partek's Gene Specific Analysis (GSA) method
Assembly: hg38
Supplementary files format and content: Raw read count in txt format

source_name: Human dermal fiboblasts

growth_protocol: NHDF and WESP cells were grown normally

extract_protocol:
Total RNA was extracted using the Qiagen Allprep RNA/DNA isolation kit, according to the manufacturer's recommendations
For library prep, the Clontech Takara SMARTer Total RNA Stranded Pico V2 Library prep kit was used, according to the manufacturer's recommendations

treatment_protocol: NHDF and WESP cells were untreated

value: NHDF

value: human fibroblast

value: wild type


title: NHDF-3


title: NHDF-2


title: WESP-1

value: WESP

value: SCP2 mutant


title: WESP-2


title: Zygote.IgG.RIPseq.rep2

description: RNA after IP

value: Zygotes collected after Lsm1 mRNA injection


title: Zygote.IgG.RIPseq.rep1

description: RNA after IP


title: Zygote.WT.RNAseq.rep2

description: total RNA

value: Zygotes collected after Lsm1 scramble siRNA injection


title: Zygote.IgG.Input.RNAseq.rep2

description: total RNA


title: WESP-3


title: Zygote.IgG.Input.RNAseq.rep1

description: total RNA


title: 6-day-old Arabidopsis plants (Col-0) treated 6h with 15 µM DMMTA, biological replicate 3

city: Bayreuth

first: Fabrizio

last: Barozzi

address: Universitätsstraße 30

department: Lehrstuhl Pflanzenphysiologie

country: Germany

institute: Universität Bayreuth

data_processing:
Paired reads were created, trimmed and mapped to the reference genome using GENEIOUS-Prime software (version 2021.2.2). This software was also used to calculate and compare expression levels.
Paired reads were created using the single paired-end. Adapters were trimmed in this step.
Raw sequence reads were trimmed using BBDuk. Settings for Trim Low Quality; Trim = Both Ends, Minimum Quality = 6. Settings for Discard Short Reads; Minumum Lenght = 80bp.
Map to Reference was performed using like reference A. thaliana genome (TAIR 11). Mapper = Geneious RNA, Sensitivity: Medium-Low.
Each contigs were used to calculate the expression level of each gene.
DESeq2 algoritm was used to compare the expression levels between control and treated condition.
Log2fold change equal or higher than 1 or equal or lower than -1 were used to define DEGs. Only DEGs with a p-value equal or lover than 0,05 were take in consideration.
Assembly: TAIR 11
Supplementary files format and content: semicolon-delimited CSV files include Name, gene, TPM, RPKM, FPKM and  locus_tag values for each Sample.

organism: Arabidopsis thaliana

source_name: seedling

growth_protocol: Plants were grown in petri dishes containing 20 mL of medium with shaking at 75 rpm under long day condition (16h light/8h dark). Medium was changed at day 5.

extract_protocol:
RNA was extracted using TriSURE™ (Bioline) and was cleaned using the RNeasy® Mini Kit (QIAGEN). RNA quantity was measured using a Qubit-Photometer (Invitrogen) and the quality was checked using Fragment Analyzer (Agilent 2100 Bioanalyzer).
Strand-specific libraries were prepared from total RNA (NEBNext Ultra II Directional library preparation kit) after PolyA-selection (NEBNext® Poly(A) mRNA Magnetic Isolation Module).

treatment_protocol: At day 6 DMMTA was or wasn't added to the samples at the final concentration of 15 µm for 6h.

value: seedling

tag: ecotype

value: DMMTA 15 µM


title: Zygote.WT.RNAseq.rep1

description: total RNA


title: PSN1 cells, parental, replicate 1

value: Pancreatic cancer cells

value: WT


title: 6-day-old Arabidopsis plants (Col-0) treated 6h with 15 µM DMMTA, biological replicate 2


title: Zygote.Lsm1KD.RNAseq.rep1

description: total RNA

value: Zygotes collected after Lsm1 siRNA injection


title: DMS53

city: NASHVILLE

first: Marisol

last: Ramirez

state: TENNESSEE

address: 2220 Pierce Avenue, 571 Preston Research Building

department: Center for Quantitative Sciences, Department of Biostatisticss

institute: Vanderbilt University Medical Center

data_processing:
Single cell RNA-seq counts matrices were primarily analyzed using the Python packages Scanpy and scVelo (Bergen et al., 2020; Wolf et al., 2018). First, the scRNAseq read counts, including both spliced and unspliced counts, for each of the 8 cell line samples were generated using the command line interface (run_dropest) from velocyto on the BAM files generated from DropEst, as described above. This tool generates loom files that can be used with Scanpy and scVelo for preprocessing and velocity calculations. We then used Scanpy to read in the loom files as an AnnData object (anndata.readthedocs.io).
We initially filter out cells with < 100 genes using scanpy.pp.filter_cells with min_genes = 100. This reduces the total number of cells (in all 8 samples) from 86,492 to 86,349. We remove genes found in < 3 total spliced counts across all samples with scanpy.pp.filter_genes with min_counts < 3. This reduces the number of genes from 63,677 to 22,475. These filtering steps ensure we remove any cells or genes with low or no reads, to prepare for further filtering steps below.
We then use Dropkick v1.2.6 (https://github.com/KenLauLab/dropkick) to label and filter out low quality cells from each sample. Once each sample has dropkick scores and labels (using dropkick score > 0.5 to identify high quality cells), we then concatenate the datasets with a batch key for each cell line. In downstream analyses, we can analyze the dataset as a whole (such as in the PCA reduction) or we can analyze each batch independently (such as in calculating RNA velocity by batch).
We normalize the data using scanpy.pp.normalize_total, which removes any biases due to varying total counts per cell. We used default arguments for this normalization (as described in the Scanpy API v 1.8), such that after normalization, each cell has a total count equal to the median of total counts for cells before normalization. Next, numpy.log1p is used to log transform the data (+1, which keeps zeroes from being transformed to negative infinity). Finally, the log-transformed, normalized counts are then scaled using scapy.pp.scale, which rescales the data to unit variance and mean-centers each gene. We then use scanpy.tl.pca to compute a 50-component PCA embedding of the data, using all genes, and use scvelo.pp.neighbors and scvelo.tl.umap to generate a UMAP dimensionality reduction.
Imputation of single cell data with a tool such as MAGIC has been shown to improve archetype detection (Dijk et al., 2018). We therefore use MAGIC to build a model with the default parameters (knn =5, decay = 1, t= 3). We fit this operator with solver = ‘approximate’ and genes = ‘all_genes’ and transform the preprocessed data after the filtering and normalization described above (16,108 cells and 20,446 genes).
Genome_build: Hg38
Supplementary_files_format_and_content: 2637-SM-1-GCCAAT_S1.loom, 2637-SM-2-CTTGTA_S2.loom, 2637-SM-3-ACAGTG_S3.loom, 2638-SM-1-GCCAAT_S1.loom, 2638-SM-2-CTTGTA_S2.loom, 2638-SM-4-GTGAAA_S4.loom, 2639-SM-1-GCCAAT_S1.loom, 2639-SM-2-CTTGTA_S2.loom. Loom format containing spliced, unspliced, ambiguous and spanning matrices.

source_name: human SCLC cell line

growth_protocol: Cell lines were grown in the preferred media by ATCC in incubators at 37 degrees Celsius and 5% CO2 in media suggested by ATCC.

extract_protocol:
Cells were dissociated with TrypLE, washed with PBS three times, and then the cells were counted, and concentration was adjusted to 100 cells/μL.
Droplet-based single cell encapsulation and barcoding was performed using the inDrop platform (1CellBio), with an in vitro transcription library preparation protocol (Klein et al., 2015).

value: SCLC cell line

tag: canonical subtype


title: Zygote.Lsm1KD.RNAseq.rep2

description: total RNA


title: H69

value: A


title: liver, PO3

city: Qingdao

first: xiufei

last: cao

address: Wenhai Road

institute: ocean university of china

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2) by Removing reads containing sequencing adapter
Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The clean reads were mapped to the reference genome using HISAT2 (v2.0.4).
Bowtie2 (v2.2.5) was applied to align the clean reads to the gene set, a database built by BGI (Beijing Genomic Institute in ShenZhen), in which known and novel, coding and noncoding transcripts were included, then expression level of gene was calculated by RSEM (v1.2.12).
Genome_build: L_crocea_2.0
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each Sample

organism: Larimichthys crocea

source_name: Liver

extract_protocol:
Total RNAs were extracted using TRIzol reagent (Invitrogen, United States USA) according to the manufacturer’s protocol. The quantity and quality of total RNA were determined by using the NanoDrop 2000 (Thermo Fisher Scientific, USA) and the Agilent 2100 Bioanaylzer (Agilent Technologies, USA, respectively. Ribosomal RNA of the 12 RNA samples was removed using the Ribo-Zero™ rRNA Removal Kit (Epicentre, USA).
RNA libraries were prepared for sequencing using BGISEQ500

value: Liver

value: PO


title: 6-day-old Arabidopsis plants (Col-0) treated 6h with 0 µM DMMTA, biological replicate 3

value: control


title: PSN1 cells, parental, replicate 2

value: Day 0


title: liver, PO2


title: H82

value: N


title: liver, PO1


title: liver, OO3

value: OO


title: liver, OO2


title: H841

value: Y


title: 6-day-old Arabidopsis plants (Col-0) treated 6h with 0 µM DMMTA, biological replicate 2


title: liver, SO3

value: SO


title: 6-day-old Arabidopsis plants (Col-0) treated 6h with 0 µM DMMTA, biological replicate 1


title: CORL279

value: A/N


title: liver, OO1


title: H524


title: 6-day-old Arabidopsis plants (Col-0) treated 6h with 15 µM DMMTA, biological replicate 1


title: Sample 6_mRNA Arabidopsis prp8a-14 mutant

city: Houston

first: Bonnie

last: Bartel

state: TX

address: 6100 Main St

department: Biosciences

institute: Rice University

description: 6.AGGACTGAAC-AGTGAGCAAC.HVVFKDSXY_AGGACTGAAC-AGTGAGCAAC_L004

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read.  RNA-seq reads were then aligned to the Ensembl release 76 primary assembly with STAR version 2.5.1a.  Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.6-p5. Isoform expression of known Ensembl transcripts were estimated with Salmon version 0.8.2.  Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected.  The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 2.6.2.
All gene counts were then imported into the R/Bioconductor package EdgeR and TMM normalization size factors were calculated to adjust for samples for differences in library size.  Ribosomal genes and genes not expressed in the smallest group size minus one samples greater than one count-per-million were excluded from further analysis.  The TMM size factors and the matrix of counts were then imported into the R/Bioconductor package Limma. Weighted likelihoods based on the observed mean-variance relationship of every gene and sample were then calculated for all samples with the voomWithQualityWeights.  The performance of all genes was assessed with plots of the residual standard deviation of every gene to their average log-count with a robustly fitted trend line of the residuals. Differential expression analysis was then performed to analyze for differences between conditions and the results were filtered for only those genes with Benjamini-Hochberg false-discovery rate adjusted p-values less than or equal to 0.05.
Genome_build: Ensembl release 76 primary assembly
Supplementary_files_format_and_content: Differential_Expression

source_name: Arabidopsis whole-plant extract

growth_protocol: 8 day-old continuous light-grown

extract_protocol:
whole seedlings were collected and flash frozen in liquid nitrogen. Tissue was ground with mortar and pestel. RNA was extracted with Qaigen Rneasy plant kit
Total RNA integrity was determined using Agilent Bioanalyzer or 4200 Tapestation.  Library preparation was performed with 5 to 10ug of total RNA with a Bioanalyzer RIN score greater than 8.0. Ribosomal RNA was removed by poly-A selection using Oligo-dT beads (mRNA Direct kit, Life Technologies). mRNA was then fragmented in reverse transcriptase buffer and heating to 94 degrees for 8 minutes. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies, per manufacturer’s instructions) and random hexamers. A second strand reaction was performed to yield ds-cDNA. cDNA was blunt ended, had an A base added to the 3’ ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq 6000 using paired end reads extending 150 bases

treatment_protocol: grown in  plant nutrient media (Haughn and Somerville, 1986)

value: whole plant


title: liver, SO2


title: DMS454


title: Sample 5_mRNA Arabidopsis prp8a-14 mutant

description: 5.AGCACCAGTC-ATCATGCTAC.HVVFKDSXY_AGCACCAGTC-ATCATGCTAC_L004


title: liver, FO2

value: FO


title: liver, FO3


title: liver, SO1


title: liver, FO1


title: Sample 4_mRNA Arabidopsis prp8a-14 mutant

description: 4.AGAAGGCCAG-GACGTCGATA.HVVFKDSXY_AGAAGGCCAG-GACGTCGATA_L004


title: Pietrobon_mix3

city: Ottawa

first: William

last: Stanford

state: Ontario

address: 501 Smyth Road

country: Canada

institute: Ottawa Hospital Research Institute

description:
polyA mRNA capture
_SC fastq files
_BC fastq files
filtered_counts_all_samples_processed.rds
metadata_all_samples_processed.csv

data_processing:
Raw sequencing data were processed using the CellRanger (v5.0.0, 10X Genomics) software with default paramters for the refdata-gex-GRCh38-2020-A reference.
FASTQ files were generated using the Cell Ranger mkfastq function, and cells were counted using Cell Ranger count.
MULTIseq barcodes were processed using the deMULTIplex pipeline to associate cells with their sample of origin
Filtered count matrices (filtered_feature_bc_matrix) were loaded into R as a sparse matrix with the Seurat::Read10X() function, and exported in RDS format. Sample barcodes were demultipliexed using the standard deMULTIplex workflow (https://github.com/chris-mcginnis-ucsf/MULTI-seq).
To generate a filtered matrix of all samples, mixes were combined and subjected to QC thresholds, removing cells with UMI counts < 500, number of uniquely detected genes < 250, and/or fraction of mitochondrial reads > 15%. We also removed samples labelled as “doublets” or “negatives” by the MULTI-seq analysis pipeline. A subset of cells that were later identified as dying, despite passing QC metrics, were also removed. Finally, we removed the gene SST, as this gene was aberrantly high in a limited number of cells and believed to be a technical artifact. This generated the "filtered_counts_all_samples_processed.rds" file.
Metadata matrices include annotations for individual cells, including genotype, cell line, and day differentiation. Metadata of all samples after processing includes additional variables such as cluster annotation, cell cycle phase, and so forth.
Fastq files from three separate NextSeq 500 runs were concatenated into a single file for each read for each library. Fastq files are included for both single cell GEX data (_SC files) and MULTI-seq barcodes (_BC files)
Genome_build: GRCh38
Supplementary_files_format_and_content: RDS (serialized R object) containing a sparse matrix of filtered counts.
Supplementary_files_format_and_content: CSV (comma-separated values) containing cell annotation metadata.
filtered_counts_all_samples_processed.rds (Sparse matrix of raw counts for cells of all samples after processing)
filtered_counts_mix1.rds (Sparse matrix of raw counts for cells of samples in mix 1)
filtered_counts_mix2.rds (Sparse matrix of raw counts for cells of samples in mix 2)
filtered_counts_mix3.rds (Sparse matrix of raw counts for cells of samples in mix 3)
metadata_all_samples_processed.csv (Metadata for cells of all samples after processing)
metadata_mix1.csv (Metadata for cells of samples in mix 1)
metadata_mix2.csv (Metadata for cells of samples in mix 2)
metadata_mix3.csv (Metadata for cells of samples in mix 3)

molecule: polyA RNA

source_name: Mix of genotypes (WT, TSC1-/-, TSC2-/-), cell lines (H9, 1681d2), and day diff (9, 13)

extract_protocol:
Sample were dissociated with Accutase and individual cells were encapsulated and lysed using a Chromium Controller (10X Genomics)
GEX library construction (10X Genomics)
scRNA-seq

value: mixed sample (non-demultiplexed) representing WT, TSC1-/- and TSC2-/-

value: mixed sample (non-demultiplexed) representing H9 and 168 1d2

value: mixed sample (non-demultiplexed) representing 9, 13 days of differentiation

value: pluripotent stem cell-derived renal organoid cells


title: Pietrobon_mix1

source_name: Mix of genotypes (WT, TSC1-/-, TSC2-/-), cell lines (H9, 1681d2), and day diff (17, 21)

value: mixed sample (non-demultiplexed) representing 17, 21 days of differentiation


title: Sample 3_mRNA Arabidopsis wild type Col-0

description: 3.AGACATATGG-ATCAACATCG.HVVFKDSXY_AGACATATGG-ATCAACATCG_L004

value: wild type


title: Pietrobon_mix2


title: Aortic Neurospheres, 100ng/mL Activin A

type: RNA

city: Toronto

first: Sarah

middle: Katherina

last: Steinbach

address: 200 Elizabeth Street

department: Experimental Therapeutics

institute: University Health Network

description:
Treated with 100ng/mL Activin A
SAMPLE 3

hyb_protocol: N/Ap

scan_protocol: N/Ap

data_processing: Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]

label: SYBR Green

organism: Rattus

source_name: Neonatal Aorta

label_protocol: PCR assays were performed using primers designed by the experimenter.  Reverse transcription was performed from 2 ug total RNA using Superscript III (Invitrogen). Quantitative real-time PCR were performed (Light Cycler 480, Roche) with 45 cycles at 94 oC for 15 seconds and 63 oC for 60 seconds.

growth_protocol: DMEM/F12 3:1 with 2% B27, 20ng/mL EGF, 40ng/mL bFGF, 1ug/mL Fungizone, 1% penicillin streptomycin.

extract_protocol: Total RNA was extracted with Trizol followed by DNase I treatment.

treatment_protocol: Untreated and treated with 50ng/mL Activin A and 100 ng/mL Activin A.

tag: developmental stage

value: neonate

value: aorta

tag: cells

value: Aortic Neurospheres (ANS)

value: 100ng/mL Activin A

value: 24 hours


title: Aortic Neurospheres, untreated

description:
Untreated
SAMPLE 1

value: Untreated


title: Sample 2_mRNA Arabidopsis wild type Col-0

description: 2.AAGCATCCTG-GACCGATACA.HVVFKDSXY_AAGCATCCTG-GACCGATACA_L004


title: H1048

tag: cell type

value: SCLC cell line

value: P


title: Aortic Neurospheres, 50ng/mL Activin A

description:
Treated with 50ng/mL Activin A
SAMPLE 2

value: 50ng/mL Activin A


title: Cancer rep2

city: Warsaw

first: Klaudia

last: Brodaczewska

address: Szaserow 128

country: Poland

institute: Military Institute of Medicine

description:
raw_counts_HN_CaN.txt
3_1CaN

data_processing:
Single-end reads were aligned to Ensembl GRCh38 himan genome with STAR (v2.7)
Counts were obtained using featureCounts v1.6.3
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file include table with raw gene counts for every gene and every sample

source_name: breast

growth_protocol: The samples of healthy tissue and primary breast tumor were obtained from the same patient and were seeded at density 5x10^4 cells/10cm^2. Both endothelial cell lines were cultured on Primaria Tissue Culture Flask (Corning #353808) in the presence of Opti-MEM I Reduced Serum Medium (Gibco #31985070) supplemented with 2% (vol/vol) fetal bovine serum (Gibco #A3840402). All cells were maintained at 37°C and 5% CO2 in humidified atmosphere. Lastly, to experiments cells were detached with enzyme cell detachment medium: Accutase supplied in Dulbecco's PBS containing 0.5 mM EDTA and phenol red (Invitrogen #E136579). The cell lines were mycoplasma free (PromoKine #PK-CA91-1096).

extract_protocol:
Total RNA was isolated from the cell cultured upon normoxia for 48h, accordingly to manufacturer’s protocol with RNeasy Plus Mini Kit (Qiagen #74136)
Libraries were prepared with the NEBNext Library Prep Kit (BioLabs #E7770S)

value: endothelial cells

value: primary tumor


title: SKPs

description:
Test
SAMPLE 1

source_name: Neonatal Whisker Pads

treatment_protocol: N/Ap

value: Whisker Pad

value: Skin-derived Precursors (SKPs)


title: ANS from neonatal rat aortas

description: SAMPLE 1

source_name: neonatal aorta

value: Progenitor Cell


title: D1 [WTCHG_823226_70145086]

city: Oxford

first: Marco

last: Fernandes

address: Department of Psychiatry, Warneford Ln, Headington

institute: University of Oxford

description: adult, neurotypical

data_processing:
QC using FastQC v0.11.5.
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Cutadapt v1.13.
Trimmed sequence reads were aligned to GRCh37 using BWA-MEM v0.7.15.
Read count extraction and normalization were summarised to the gene-level using the summarizeOverlaps function of the GenomicAlignments R package. Normalised counts using the median of ratios method (estimateSizeFactors function) implemented in DESeq2 v1.28.1.
Assembly: GRCh37.EBVB95-8wt.ERCC
Supplementary files format and content: tab-delimited text files include normalised counts using the median of ratios.

source_name: CTR M3 36S

extract_protocol:
RNA was harvested using Qiagen RNeasy Mini PLUS Kit (Qiagen). 100 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq RNA Library Preparation Kit (Illumina) following manufacturer's protocols.

value: CTR M3 36S

value: keratinocytes iPSCs

tag: genotype

value: exon2 -/-

value: untreated

tag: Sex

value: male


title: Normal rep2

description:
raw_counts_HN_CaN.txt
7_2HN

tag: tissue

value: healthy tissue


title: Cancer rep1

description:
raw_counts_HN_CaN.txt
9_2CaN


title: D1 [WTCHG_823226_70035075]

department: Department of Psychiatry, Warneford Ln, Headington

description: adult, neurotypical

value: abeta


title: Normal rep1

description:
raw_counts_HN_CaN.txt
1_1HN


title: CTR [WTCHG_823226_70115083]

description: adult, neurotypical

value: wt


title: CTR [WTCHG_823226_70055077]

description: adult, neurotypical


title: D1 [WTCHG_823226_70025074]

description: adult, neurotypical


title: CTR [WTCHG_823226_70105082]

description: adult, neurotypical


title: CTR [WTCHG_823226_70045076]

description: adult, neurotypical


title: Sample 1_mRNA Arabidopsis wild type Col-0

description: 1.TGCATATAGG-GAACTGTCGC.HVVFKDSXY_TGCATATAGG-GAACTGTCGC_L004

value: whole plant

value: wild type


title: D1 [WTCHG_823226_70155087]

description: adult, neurotypical


title: D1 [WTCHG_823226_70085080]

description: adult, neurotypical


title: Day7.360min_D2

city: York

first: Matthew

middle: Anthony

last: Care

state: North Yorkshire

address: Wentworth Way

department: Department of Biology

institute: The University of York

data_processing:
The fastq files were assessed for initial quality using FastQC v0.11.8, trimmed for adapter sequences using TrimGalore v0.6.0  and aligned to GRCh38.p12 (Gencode release 28) with STAR aligner (v2.6.0c) using twopassMode.
Transcript abundance was estimated using RSEM v1.3.0 and imported into R v3.5.1 using txImport v1.10.1 and then processed using DESeq2 v1.22.2, generating VST transformed data.
Genome_build: GRCh38.p12/hg38 (Gencode release 28)
Supplementary_files_format_and_content: Tab separated sheets containing DESeq2 rLog transformed data

source_name: Peripheral blood

growth_protocol: Cells were maintained in Iscove’s Modified Dulbecco Medium (IMDM) supplemented with Glutamax and 10% heat-inactivated fetal bovine serum (HIFBS, Invitrogen); Lipid Mixture 1, chemically defined and MEM Amino Acids solution (both at 1x final concentration) were added from day 3 onwards.  Day 0 to day 3 – B cells were cultured in 24 well plates at 2.5 X 10^5/ml with IL2 (20 U/ml), IL21 (50 ng/ml), F(ab’)2 goat anti-human IgM & IgG (10 µg/ml) on γ-irradiated CD40L expressing L-cells (6.25 X 10^4/well).  Day 3 to day 6 – At day 3, cells were detached from the CD40L L-cell layer and reseeded at 1 X 10^5/ml in media supplemented with IL2 (20 U/ml) and IL21 (50 ng/ml).  At day 6, PBs were seeded at 1 X 10^6/ml in phenol red free IMDM supplemented with 0.5% HIFBS, IL6 (10 ng/ml), IL21 (10 ng/ml) and GSI (100nM), and incubated for 20 hours. Multimeric-APRIL (100ng/ml) was then added. Gene expression data sets were generated from differentiating PBs (day 7). A pre-treatment sample (0min) and post treatment samples were removed at +30min, +60min, +120min and +360min.

extract_protocol:
Peripheral blood was obtained from healthy donors after informed consent. Mononuclear cells were isolated by Lymphoprep (Axis Shield) density gradient centrifugation. Total B-cells were isolated by negative selection with the Memory B cell Isolation Kit (Miltenyi).
RNA was extracted with TRIzol (Invitrogen) then subjected to DNAseI treatment (DNAfree, Ambion).
RNA samples were quantified with a Qubit HS RNA assay kit (Thermo Fisher Scientific) and the quality was assessed by RNA HS assay using the TapeStation system (Agilent). Sequencing libraries were generated by using a TruSeq Stranded Total RNA Human/Mouse/Rat kit (Illumina) according to the manufacturer’s protocol. Library performance was checked on the TapeStation followed by picogreen quantification. Equimolar pooling was performed across all the libraries and the final pool was sequenced on a NextSeq 500 platform (Illumina) using 76-bp single-end sequencing.

tag: treatment time

value: Plasmablast


title: CTR [WTCHG_823226_70955071]

description: adult, neurotypical

tag: cell line


title: Day7.360min_D3


title: CTR [WTCHG_823226_70945070]

description: adult, neurotypical

tag: treatment


title: A4 [WTCHG_823226_70135085]

description: adult, neurotypical


title: D1 [WTCHG_823226_70095081]

description: adult, neurotypical


title: A4 [WTCHG_823226_70015073]

description: adult, neurotypical


title: short4

city: Fukuoka City

first: Mariko

last: Minami

address: 3-1-1, Maidashi

department: Medicine and Biosystemic Science

country: Japan

institute: Kyushu University Graduate School of Medical Science

description: Gene expression of CD33+ short type APL Pt 4

hyb_protocol: cRNA (1ug) was hybridized to the microarray chip (SurePrint G3 Human Gene Expression 8x60K v3, Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the SureScan Microarray Scanner (G4900DA) using one color scan setting for 8x60k array slides (Scan resolution 3um, Dye channel is set to Green and Green PMT sensitivity is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction software (Agilent) using default parameters (protocol GE1_1105_Oct12 and grid: 072363_D_F_20150612) to obtain background subtracted and spatially detrended processed signal intensities.
Raw expression data were imported and normalized using GeneSpring GX software (Agilent Technologies).

source_name: Bone marrow, short type 4

label_protocol: Cyanine3-labeled cRNA from each sample was prepared to mRNA amplification by using Low Input Quick Amp Labeling Kit (one-color) (Agilent Technologies) according to the manufacture's instruction.

extract_protocol: CD33+ cells of four short isoform APL samples and four long isoform APL samples were sorted directly into ISOGEN II (Nippongene). Total RNA was extracted according to the manufacturer's recommendations.

value: Bone marrow


title: short2

description: Gene expression of CD33+ short type APL Pt 2

source_name: Bone marrow, short type 2


title: short1

description: Gene expression of CD33+ short type APL Pt 1

source_name: Bone marrow, short type 1


title: A4 [WTCHG_823226_70125084]

description: adult, neurotypical


title: A4 [WTCHG_823226_70965072]

description: adult, neurotypical


title: A4 [WTCHG_823226_70075079]

description: adult, neurotypical


title: U937-EG 48h

city: Shanghai, China

first: Yifan

last: Zhang

address: Ruijin Hospital

institute: Shanghai Institute of Hematology

data_processing:
Clean sequenced reads were alignmented to hg38 by HISAT2 (2.0.5) with default parameters
Alignmented SAM files were handled using samtools(1.7)
Aligned reads were extracted by Htseq(0.9.1) with default parameters
FPKM were calculated by R script on its defination, differential genes were generated by R package Deseq2(1.22.2)
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

growth_protocol: U937 cells were maintained in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol: TRIzol Reagent (Invitrogen, 326401) was used to lysis U937 cells for acquiring total RNA

treatment_protocol: AML1-ETO or ETO2-GLIS2 was induced by treatment with 5ug/ml doxycycline (Sigma) for 0h, 12h and 48h.

value: monocytic cell line

value: EG over-expressed

value: doxycycline

tag: time


title: U937-EG 12h


title: Day7.360min_D4


title: long3

description: Gene expression of CD33+ long type APL Pt 3

source_name: Bone marrow, long type 3


title: GM23225_NPC_Pol2S2_Supt4-kd_rep1

city: Stanford

first: Stanley

middle: N.

last: Cohen

state: CA

address: 300 Pasteur Drive, Lane Bldg, Rm L-314

institute: Stanford University

library_source: genomic

data_processing:
Skewer version 0.2.1 was used to trim adaptor.
Reads after trimming adaptor were then aligned to the Human (hg19) genome using BWA version 0.7.10.
Accumulated reads for each gene (gene body, including both exon and intron) was calculated by FeatureCount version 1.4.6.
The fold change of accumulated read for each gene was further calculated by DEseq2 version 1.10.1.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: genomic DNA

source_name: Neural progenitor cells

growth_protocol: The NPC were differentiated from iPSC by 7 days of induction differentiation medium made with 15% KnockOut Serum Replacement (ThermoFisher Scientific), 1% Glutamax, 1% Non-Essential Amino Acids Solution, 1% GibcoTM 2-Mercaptoethanol, 10µM SB431542 and 500ng/ml Noggin in KnockOut DMEM (ThermoFisher Scientific). Medium was changed daily.

extract_protocol:
Lysates were clarified from sonicated nuclei and RNAAPII-S2-DNA complexes were isolated with antibody.
2x10e7 cells were collected and cross-linked in 1% formaldehyde for 10 min at room temperature, then quenched by addition of 125mM Glycine. Nuclear lysates were prepared by sonication using a Branson 250 Sonifier. Clarified lysates were treated overnight at 4 °C with 5 µg anti-pol II CTD repeat YSPTSPS (phosphor S2) (Abcam ab5095) antibody. Protein-DNA complexes were captured on Protein A/G agarose beads (EMD Millipore) and eluted in 1% SDS TE buffer at 65 °C. Following cross-link reversal and purification, ChIP DNA sequencing libraries were prepared according to Illumina DNA sample kit instructions (Illumina). Libraries were sequenced on an Illumina HiSeq 4000. More than 300 million reads were obtained from each library in order to assure accurate quantification of RNAPII-S2 occupancy.

treatment_protocol: Lentivirus carrying human Supt4h shRNA (clone ID: TRCN0000019645 from Dharmacon having the mature antisense sequence TTAAAGTTACTGACTCGCTGC) was introduced into the iPSC cell line GM23225 (Coriell Institute). Puromycin was used to select shRNA positive cells. Knocking down of Supt4h was confirmed by Realtime PCR for mRNA and by Western blotting for protein.

value: iPSC-derived neuronal progenitor cells

value: GM23225 (Coriell Institute)

tag: chip antibody

value: Anti-RNA polymerase II CTD repeat YSPTSPS (phospho S2) antibody (Abcam,ab5095)

value: Supt4h knockdown


title: Day7.120min_D4


title: Day7.360min_D1


title: A4 [WTCHG_823226_70065078]

description: adult, neurotypical

value: CTR M3 36S

value: keratinocytes iPSCs

value: exon2 -/-


title: GM23225_NPC_Pol2S2_Supt4-kd_rep2


title: long1

description: Gene expression of CD33+ long type APL Pt 1

source_name: Bone marrow, long type 1


title: long4

description: Gene expression of CD33+ long type APL Pt 4

source_name: Bone marrow, long type 4


title: Day7.120min_D1


title: Day7.120min_D3


title: Day7.120min_D2


title: Day7.60min_D4


title: long2

description: Gene expression of CD33+ long type APL Pt 2

source_name: Bone marrow, long type 2


title: GM23225_NPC_Pol2S2_unt_rep2

value: untreated


title: U937-AE 48h

value: AE over-expressed


title: U937-AE 0h


title: U937-EG 0h


title: U937-CTR 48h

value: WT


title: U937-CTR 12h


title: GM23225_NPC_Pol2S2_unt_rep1


title: Day7.60min_D3


title: iPS-derived Endothelial Cell Disomy (322-3) Dox Replicate 3

city: Worcester

middle: Eunmi

last: Moon

state: MA

address: 55 Lake Ave N

institute: University of Massachusetts Medical School

description:
EC_DE_Summary.tab.txt
EC_DIS322-3D_Rep3

data_processing:
For all samples, FastQC was used to evaluate quality of data.
Libraries were aligned to genome build GRch38 using HISAT2 (Kim et al., 2015, 2019)
Mapped reads were quantified using featureCounts (Liao et al., 2014).
Differential expression analysis was conducted by using the R package edgeR (McCarthy et al. 2012)
Genome_build: GRch38
Supplementary_files_format_and_content: Tab delimited files containg differentially expressed genes generated by edgeR within R (McCarthy et al., 2012)

growth_protocol:
Differentiation of iPS cells into endothelial cells were adapted from Lian et al. (2014) and Patsch et al. (2015). Cells were treated with 8 uM CHIR99021 (Tocris Bioscience) for on day 0 and day 1, and 2 uM CHIR99021 on day 2-4. Day 5, cells were collected for CD34+ were selected using the CD34 MicroBead Kit (Miltenyi Biotec). Purified CD34 cells were cultured on collagen coated plates with EGM-2 media (Lonza) supplemented with 25 ng/ml VEGF165 (PEPROTECH).
iPS cells were grown in feeder free conditions on vitronectin coated plates and cultured in Essential E8 medium (Invitrogen). Differentiation of iPS cells into endothelial cells were adapted from Lian et al. (2014) and Patsch et al. (2015). Cells were treated with 8 uM CHIR99021 (Tocris Bioscience) for on day 0 and day 1, and 2 uM CHIR99021 on day 2-4. Day 5, cells were collected for CD34+ were selected using the CD34 MicroBead Kit (Miltenyi Biotec). Purified CD34 cells were cultured on collagen coated plates with EGM-2 media (Lonza) supplemented with 25 ng/ml VEGF165 (PEPROTECH).

extract_protocol:
RNA samples were extracted using Trizol Reagent (ThermoFisher) adapted from the manufacturer’s instructions, using 100% ethanol in place of isopropanol. Precipitated RNA was resuspended in RNase- and DNase-free water and DNA digestion was performed using DNase I (Roche) with 2U/ul of RNasin Plus (Promega) for 1 hr at room temperature. RNeasy Mini Kit was used for RNA purification and DNase I removal following the RNA Cleanup protocol from the manufacturer’s instructions.
The NEBNext Ultra™ II Directional RNA Library Prep Kit for Illumina, NEBNext Poly(A) mRNA Magnetic Isolation Module, and NEBNext Multiplex Oligos for Illumina were used to prepare sequencing libraries following the manufacturer’s instructions (New England Biolabs, Inc). All libraries were prepared with 1 ug of starting RNA.

treatment_protocol: - or + doxycycline (500 ng/ml); 6 days for iPS cells and 14 days for iPS-derived endothelial cells

value: iPS cell line derived Endothelial Cells

tag: cell line type

value: Disomy 322-3


title: iPS-derived Endothelial Cell Disomy (322-3) Dox Replicate 2

description:
EC_DE_Summary.tab.txt
EC_DIS322-3D_Rep2


title: U937-AE 12h


title: iPS-derived Endothelial Cell Disomy (322-3) Dox Replicate 1

description:
EC_DE_Summary.tab.txt
EC_DIS322-3D_Rep1


title: iNeurons, CROPseq Enrichment

city: San Francisco

first: Martin

last: Kampmann

address: 675 Nelson Rising Lane, 3rd Floor

department: Institute for Neurodegenerative Diseases

institute: University of California San Francisco

description: CROP-seq PCR

data_processing: none provided by the submitter

source_name: Neurons

growth_protocol: Neurons:   Regular Neuronal Medium    Microglia:   For CROP-seq, inducible CRISPRi-iTF-iPSCs were infected with the pooled sgRNA library at <0.15 MOI and then selected for lentiviral integration. For both QuantSeq and CROP-seq, iTF-iPSCs were differentiated into iTF-microglia and cultured with the addition of TMP with the following conditions: iTF-iPSCs were grown in StemFlex until reaching at least 50% confluency and were grown for at least 24h without ROCK inhibitor. They were dissociated with Accutase and centrifuged and pelleted cells were resuspended in Day 0 differentiation medium containing the following: Essential 8™ Basal Medium (Gibco; Cat. No. A15169-01) as a base, 10nM ROCK inhibitor, and 2 mg/ml Doxycycline (Clontech; Cat. No. 631311). iTF-iPSCs were counted and seeded onto double coated plates (Poly-D-Lysine-precoated Bio plates (Corning, assorted Cat. No.) + Matrigel coating) with the following seeding densities: 10,000 cells/well for 96-well plate, 0.1 Mio/well for 12-well plate, 0.15 Mio/well for 6-well plate, 2 Mio/dish for 10-cm dish, and 8 Mio/dish for 15-cm dish. On day 2, media was replaced with Day 2 differentiation media containing Advanced DMEM/F12 Medium (Gibco; Cat. No. 12634-010) as a base medium containing the following: 1X Antibiotic-Antimycotic (Anti-Anti) (Gibco; Cat. No. 15240-062), 1X GlutaMAX™ (Gibco; Cat. No. 35050-061), 2 mg/ml doxycycline, 100 ng/ml Human IL34 (Peprotech; Cat. No. 200-34) and 10 ng/ml Human GM-CSF (Peprotech; Cat. No. 300-03). On day 4 and day 6, the medium was replaced with iTF-Microglia medium, containing Advanced DMEM/F12 as a base medium and the following: 1X Anti-Anti, 1X GlutaMAX, 2 mg/ml doxycycline, 100 ng/ml Human IL-34 and 10 ng/ml Human GM-CSF, 50 ng/ml Human M-CSF (Peprotech; Cat. No. 300-25) and 50 ng/ml Human TGFB1 (Peprotech; Cat. No. 100-21C).

extract_protocol:
Single cells were lysed in droplets using the 10X Chromium instrument.  Libraries were prepared according to the Chromium Single Cell 3' Reagent Kits User Guide (v3.1 Chemistry) from 10X Genomics.
10X

value: Neurons

tag: source

value: Human iPSC-derived


title: Day7.30min_D4

value: Plasmablast


title: iMicroglia, CROPseq Enrichment

description: CROP-seq PCR

source_name: Microglia

value: Microglia


title: Day7.60min_D2


title: iMicroglia, scRNAseq

description: CROP-seq 10X Genomics


title: iNeurons, scRNAseq

description: CROP-seq 10X Genomics


title: Day7.30min_D2


title: Day7.30min_D3


title: CH05 ATAC

city: New York

first: Neville

last: Dusaj

state: NY

institute: Weill Cornell Medicine

description: ATAC Fragments

library_source: genomic single cell

data_processing:
Pre-processing was performed using 10x Genomics Cell Ranger ARC (v1.0.1). Reads were de-multiplexed using the cellranger-arc mkfastq function. Single cell feature counts for each sample were then generated using the cellranger-arc count function. The gene expression information for these libraries exhibited exceedingly low UMI and genes per cell consistent with lower quality RNA in single-cell nuclei Multiome data; as such, we moved forward utilizing only the ATAC data for analysis. ATAC data was processed using the ArchR package (v1.0.1) using the atac_fragments.tsv.gz file generated by the cellranger-arc count function as input. Arrow files were created using a minimum TSS enrichment score of 5 and a minimum number of unique nuclear fragments of 1,000. Doublet scores were calculated using the addDoubletScores function with k = 10, knnMethod = “umap” and LSImethod = 1. Doublets were removed using the filterDoublets function with default parameters. Dimensionality reduction was performed through iterative semantic index (LSI) using the cell by genomic window (500 bp) matrix as input, using the addIterativeLSI function with the following parameters: iterations = 3, resolution = 0.2, sampleCells = 1,000, var.features = 25,000 and dimsToUse = 1:30. Cell clusters were identified using the addClusters function using the iterative latent semantic index (LSI) dimensions as input, with method = “Seurat”, resolution = 0.8. For visualization, UMAP dimensionality reduction was performed using the LSI dimensions as input, using the addUMAP function with: nNeighbors = 30, minDist = 0.5 and metric = “cosine”. Cell identities were assigned based on gene accessibility scores of known marker genes. Custom motif accessibility deviations were calculated as follows: position weight matrices in HOMER format (P < 0.001) were downloaded from the HOCOMOCO v11 mouse database. Motif occurrences were identified using the scanGenomeWide function of the HOMER package. To include only high confidence motif sites, we applied a minimum odds ratio score threshold of 6. We next created custom peakAnnotations using ArchR and performed ChromaVar analysis using the addDeviationsMatrix function with default parameters.
snATAC-seq data for CH05 was generated as described above using the Multiome platform (10x Genomics) and GoT performed as described above using the cDNA generated from the Multiome workflow. The gene expression information for these libraries exhibited very low UMI and genes per cell consistent with lower quality RNA in single-cell nuclei Multiome data; as such, we moved forward utilizing only the ATAC data for analysis. For the analysis, fragment files were generated by processing the fastq files using cell-ranger-ARC (v.1.0.0). Downstream analysis was performed using the ArchR (v1.0.1) pipeline. Based on the distribution of total fragments and TSS enrichment per cell, empty droplets were filtered out by requiring a minimum of 3,000 fragments per cell and a TSS enrichment score of 7.5. Potential doublets were detected using the addDoubletScores function, using KNN on the UMAP dimensionality reduction with k = 10. Cell barcodes with high enrichment for doublet scores were removed using the filterDoublets function with default parameters. Next, we performed dimensionality reduction through iterative latent semantic indexing (LSI) using the top 25,000 variable features. Cell clustering was performed using the addClusters function, with the following parameters: reduceDims = “IterativeLSI”; method = “Seurat”; resolution =1. For visualization, further dimensionality reduction was performed by applying UMAP to the iterative LSI space using the addUMAP function with the following parameters: nNeighbors = 30; minDist = 0.5; metric = “cosine”. Cell type identification was performed by manually inspecting the genes showing up-regulated gene accessibility scores (FDR < 0.01 and log2(fold change) > 1.25) for each of the defined clusters (Extended Data Fig. 13c). Motif occurrences were defined using the position weight matrices (PWMs) obtained from the Hocomoco (v.11.0) motif database or our custom PWMs for hypo-methylated and shuffled motifs using HOMER (v4.9), requiring a minimum enrichment score above 6. Transcription factor, hypo-methylated and shuffled motif accessibility was calculated using ChromVAR within the ArchR (v1.0.1) pipeline. Supervised pseudotime trajectories for either erythroid or lymphoid fates were defined within the ArchR (v1.0.1) pipeline applying the addTrajectory function.
Assembly: hg38
Supplementary files format and content: Processed 10X data is a fragments file of ATAC-seq fragments for each cell barcode.
Supplementary files format and content: Output matrices processed from amplicon data have two columns for cell barcode and assigned genotype

source_name: Bone marrow aspirate from patient

extract_protocol:
All animal procedures were completed in accordance with the Guidelines for the Care and Use of Laboratory Animals and were approved by the Institutional Animal Care and Use Committees at MSKCC. The Dnmt3a R878H mouse model has been described previously (Guryanova et al., 2016), and was crossed to the Tal1-creERT2 transgenic model to allow for inducible control of the R878H mutation within the hematopoietic system. To induce recombination of the conditional alleles, age and gender-matched 10-16 week old Tal1-creERT2 control mice and Dnmt3a R878H Tal1-creERT2 mice were treated with tamoxifen (4 mg/kg/day; Cayman Chemical, Ann Arbor, Michigan) for 2 doses, separated 2 days apart. The mice were sacrificed 4-8 weeks after tamoxifen-induction. Primary mouse bone marrow (BM) cells were isolated into cold phosphate-buffered saline (PBS), without Ca2+ and Mg2+, and supplemented with 2% bovine serum albumin (BSA) to generate single cell suspensions. Red blood cells (RBCs) were removed using ammonium chloride-potassium bicarbonate (ACK) lysis buffer, resuspended in PBS/2% BSA, and filtered through a 40μm cell strainer. Total nucleated cells were quantified by Vi-Cell XR cell counter (Beckman Coulter, Brea, CA) and used for downstream data production.  Cryopreserved patient samples approved by the Institutional Review Board of the University of Chicago were thawed and stained using standard procedures (10 min, 4°C) with the surface antibody CD34-PE-Vio770 (clone AC136, Miltenyi Biotec) and DAPI (Sigma-Aldrich). Cells were then sorted for DAPI-negative, CD34+ and CD34-negative cells using BD Influx.
Hematopoietic progenitors (Lin-1-, c-Kit+) were sorted from wildtype (n = 3 mice) or Dnmt3a R878H (n = 3 mice) via c-Kit enrichment as directed by the manufacturer (CD117 Microbeads, clone 3C1, Miltenyi, Auburn, CA; LS Columns (Cat. No. #130-042-401), Miltenyi) followed by FACS (Lin-1 BV421 (Cat. No. #133311), Biolegend, San Diego, CA; CD117 APC (clone 2B8, Invitrogen, Waltham, MA). Nuclei isolation was performed as suggested by the manufacturer (10x Genomics, Pleasanton, CA). Briefly, single cell suspensions were centrifuged at 300 rcf for 5 minutes and cell pellets were resuspended in 100 μl of lysis buffer (Tris-HCl pH 7.4, 10mM; NaCl 10mM; MgCl2 3mM; Tween-20 0.1%; Nonidet P40 substitute (Sigma-Aldrich, St. Louis, MO) 0.1%; Digitonin 0.01%; BSA 1%; DTT 1 mM; RNase inhibitor 1 U/µL (Sigma-Aldrich, St. Louis, MO)) and kept on ice for 3 minutes. Then, 1 ml of wash buffer (Tris-HCl pH 7.4, 10mM; NaCl 10mM; MgCl2 3mM; BSA 1%; Tween-20 0.1%; DTT 1 mM; Sigma Protector RNase inhibitor 1 U/µL) was added. The isolated nuclei were centrifuged for 5 min at 500 rcf, and pellets were resuspended in Diluted Nuclei Buffer (10x Genomics Nuclei Buffer 1X; DTT 1 mM; Sigma Protector RNase inhibitor 1 U/µL). Nuclei concentration was determined by hemocytometer and processed as indicated by the manufacturer (10x Genomics User Guide: Chromium Next GEM Single Cell Multiome ATAC + Gene Expression, CG000338). Single nucleus ATAC and Gene Expression (GEX) libraries were constructed in parallel and assessed for quality control metrics using Agilent Bioanalyzer 2100 and Qubit respectively. ATAC libraries were sequenced to a depth of 25,000 read pairs per nucleus (paired-end, dual indexing: Read 1N 50 cycles, i7 Index 8 cycles, i5 Index 24 cycles, Read 2N 49 cycles) and GEX libraries were sequenced to a depth of 20,000 read pairs per nucleus (paired-end, dual indexing: 28 cycles for Read 1, 10 cycles for i7 Index, 10 cycles for i5 Index, 90 cycles for Read 2).
Multiome Single-nucleus ATAC + RNA-seq (10X) with targeted amplification of a mutation of interest for the patient sample.

value: Bone marrow


title: CH05 Amplicon [genotype]


title: iPS-derived Endothelial Cell Disomy (322-3) No Dox Replicate 3

first: Jennifer

description:
EC_DE_Summary.tab.txt
EC_DIS322-3ND_Rep3

value: control


title: iPS-derived Endothelial Cell Disomy (322-3) No Dox Replicate 2

description:
EC_DE_Summary.tab.txt
EC_DIS322-3ND_Rep2


title: Day7.30min_D1


title: iPS-derived Endothelial Cell Trisomy (31627H) Dox Replicate 3

description:
EC_DE_Summary.tab.txt
EC_TRI31627HD_Rep3

value: Trisomy 31627H

value: doxycycline


title: iPS-derived Endothelial Cell Trisomy (31627H) Dox Replicate 2

description:
EC_DE_Summary.tab.txt
EC_TRI31627HD_Rep2


title: iPS-derived Endothelial Cell Trisomy (31627H) Dox Replicate 1

description:
EC_DE_Summary.tab.txt
EC_TRI31627HD_Rep1


title: Day7.0min_D4


title: Day7.0min_D3


title: Day7.0min_D2


title: short3

description: Gene expression of CD33+ short type APL Pt 3

source_name: Bone marrow, short type 3


title: Day7.60min_D1


title: Day7.0min_D1


title: U937-CTR 0h

value: monocytic cell line


title: iPS-derived Endothelial Cell Trisomy (31627H) No Dox Replicate 2

description:
EC_DE_Summary.tab.txt
EC_TRI31627HND_Rep2


title: iPS-derived Endothelial Cell Trisomy (31627H) No Dox Replicate 1

description:
EC_DE_Summary.tab.txt
EC_TRI31627HND_Rep1


title: Pseudomonas aeruginosa H103, Pf4 phage-treated, rep3

city: Evreux

first: Sylvie

last: Chevalier

address: 55 rue Saint Germain

country: France

institute: Normandie Université

description: Pf4 3

data_processing:
The RNA-seq data analyses started after the “base calling” step, performed during sequencing by the NCS 1.3.0.26 and RTA 2.1.3 Illumina software suite implemented on the NextSeq® Illumina sequencing machine. The format of data after this base calling is BCL (Base Call File). To get the number of raw reads per sample, the number of read passing filters (PF), the percentage of bases above Q30 (1 error out of 1,000 bases) among PF reads and the mean quality score, a demultiplexing step was assessed. This step which consisted in attributing each read to the corresponding sample using the index sequence was performed using the bcl2fastq 2.17.1.14 from Illumina, allowing no mismatch. The format of data after demultiplexing was Fastq. Quality reports for the Fastq files were generated with the tool FastQC v0.11.8 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Low-quality bases and contaminant adapters were trimmed using Trimmomatic v0.38, using a minimum read length threshold of 50 bases (Bolger et al., 2014; Liao et al., 2014).
The high-quality RNA-seq reads were mapped against the reference genome of P. aeruginosa PAO1 strain using Boowtie2 alignment tool v2.3.4.1 with default parameters.
Next, reads mapping on each annotated coding sequence of P. aeruginosa PAO1 genome were counted using featureCounts v1.6.4 (Liao et al., 2014) and default parameters were used, except for the orientation parameter stranded which was set to reverse.
To determine the impact of Pf4* phage treatment on P. aeruginosa H103 gene expression, we compared the transcriptome of untreated versus Pf4*-treated bacteria. Analysis of differentially expressed genes (DEG) was performed with the SARTools R package, including the DESeq2 package (Love et al., 2014; Varet et al., 2016). The analysis process included data normalization, graphical exploration of raw and normalized data, test for differential expression for each feature between the conditions and raw p-value adjustment. Genes were considered as significantly differentially expressed when the gene expression fold change (FC) was greater than or equal to 2 (DEG up-regulated) or was lower than or equal to -2 (DEG down-regulated) and the p-value (padj) adjusted by FDR (false discovery rate) is lower than 0.05 (Benjamini and Hochberg, 1995).
Assembly: GenBank assembly accession number GCA_000006765.1
Supplementary files format and content: Processed data file (excel sheet (.xlsx)) which presents genes considered as significantly differentially expressed, i.e. when the gene expression fold change (FC) was greater than or equal to 2 (DEG up-regulated) or was lower than or equal to -2 (DEG down-regulated) and the p-value (padj) adjusted by FDR (false discovery rate) is lower than 0.05.

organism: Pseudomonas aeruginosa

source_name: Bacteria

growth_protocol:
Liquid LB medium
Bacteria were cultivated in LB medium (50 mM NaCl), at 37 °C with shaking (180 r.p.m) until reaching an OD580nm = 2.8.

extract_protocol:
Total RNAs from Pf4* treated and untreated P. aeruginosa cultures were extracted using the hot acid-phenol method (Bouffartigues et al., 2012). Genomic DNA contamination was removed using rigorous treatment with RNA-free Turbo DNaseI kit (Invitrogen, Carlsbad, California, USA) following the manufacturer’s instructions.
rRNA depletion, cDNA library preparation and Illumina sequencing were performed by ViroScan3D (Lyon, France). RNA samples were quantified using QuantiFluor® RNA System (Promega, Madison, Wisconsin, USA) and qualified using Fragment analyzer system (Agilent, Les Ulis, France). All RNA sample profiles were validated with an RNA IQ score ≥8. Next, removal of 23S and 16S rRNAs was performed using Ribo-Zero rRNA Removal Kit for Gram-negative Bacteria (Illumina, San Diego, California, USA) according to the manufacturer’s instructions. At least 99% of the rRNAs was removed from total RNA, ensuring sufficient mRNA to be sequenced. After ribosomal depletion, libraries were generated using NextFlex® rapid directional RNAseq kit for Illumina® platforms (PerkinElmer, Waltham, Massachusetts, USA).

treatment_protocol: When needed, bacteria had been treated by Pf4 phages, at a final concentration of 1.5 x 109 phages/mL.

tag: strain

value: H103 (PAO1 derivative)

value: Bacteria

value: Pf4 phage treatment


title: Pseudomonas aeruginosa H103, Pf4 phage-treated, rep2

description: Pf4 2


title: Pseudomonas aeruginosa H103, Pf4 phage-treated, rep1

description: Pf4 1


title: iPS-derived Endothelial Cell Disomy (322-3) No Dox Replicate 1

description:
EC_DE_Summary.tab.txt
EC_DIS322-3ND_Rep1


title: iPS-derived Endothelial Cell Clone 7 Dox Replicate 3

description:
EC_DE_Summary.tab.txt
EC_TRANSC7D_Rep3

value: Clone 7


title: iPS-derived Endothelial Cell Clone 7 Dox Replicate 2

description:
EC_DE_Summary.tab.txt
EC_TRANSC7D_Rep2


title: Day7.360min_SDF1_D3

data_processing:
The fastq files were assessed for initial quality using FastQC v0.11.8, trimmed for adapter sequences using TrimGalore v0.6.0  and aligned to GRCh38.p12 (Gencode release 28) with STAR aligner (v2.6.0c) using twopassMode.
Transcript abundance was estimated using RSEM v1.3.0 and imported into R v3.5.1 using txImport v1.10.1 and then processed using DESeq2 v1.22.2, generating VST transformed data.
Assembly: GRCh38.p13/hg38 (Gencode release 35)
Supplementary files format and content: Tab separated sheets containing DESeq2 VST transformed data

growth_protocol: Total B-cells were isolated by negative selection with the Memory B-cell Isolation Kit (Miltenyi). Cells were maintained in Iscove’s Modified Dulbecco Medium (IMDM) supplemented with Glutamax and 10% heat-inactivated fetal bovine serum (HIFBS, Invitrogen); Lipid Mixture 1, chemically defined and MEM Amino Acids solution (both at 1x final concentration) were added from day 3 onwards. Day 0 to day 3 – B cells were cultured in 24 well plates at 2.5 X 10^5/ml with IL2 (20 U/ml), IL21 (50 ng/ml), F(ab’)2 goat anti-human IgM & IgG (2 µg/ml) on γ-irradiated CD40L expressing L-cells (6.25 X 10^4/well). Day 3 to day 6 – At day 3, cells were detached from the CD40L L-cell layer and reseeded at 1 X 10^5/ml in media supplemented with IL2 (20 U/ml) and IL21 (50 ng/ml). Gene expression data sets were generated from differentiating PBs (day 7). At day 6, PBs from 3 healthy donors were seeded at 1 X 10^6/ml in phenol red free IMDM supplemented with 0.5% HIFBS, IL6 (10 ng/ml), IL21 (10 ng/ml) and GSI (100nM) and incubated for 20 hours. A pre-treatment sample (0 minutes) and post treatment samples were removed at +60, and +360 minutes following treatments with Multimeric-APRIL (100ng/ml), sCD40L(100ng/ml), SDF1(10ng/ml) and IFNα (100U/ml).

tag: condition


title: Day7.360min_SDF1_D2


title: iPS-derived Endothelial Cell Clone 7 Dox Replicate 1

description:
EC_DE_Summary.tab.txt
EC_TRANSC7D_Rep1


title: Pseudomonas aeruginosa H103, WT, rep3

description: H103 3

value: No treatment


title: Day7.360min_SDF1_D1


title: Pseudomonas aeruginosa H103, WT, rep2

description: H103 2

value: WT


title: iPS-derived Endothelial Cell Clone 7 No Dox Replicate 3

description:
EC_DE_Summary.tab.txt
EC_TRANSC7ND_Rep3

value: iPS cell line derived Endothelial Cells


title: Day7.360min_sCD40L_D1


title: iPS-derived Endothelial Cell Trisomy (31627H) No Dox Replicate 3

description:
EC_DE_Summary.tab.txt
EC_TRI31627HND_Rep3


title: iPS-derived Endothelial Cell Clone 7 No Dox Replicate 2

description:
EC_DE_Summary.tab.txt
EC_TRANSC7ND_Rep2


title: Day7.360min_sCD40L_D2


title: Pseudomonas aeruginosa H103, WT, rep1

description: H103 1


title: Day7.360min_IFN_D1

value: IFN


title: Day7.360min_IFN_D2


title: Day7.360min_IFN_D3


title: Day7.360min_APRIL_D3

value: APRIL


title: Day7.360min_APRIL_D2


title: Day7.360min_APRIL_D1


title: Day7.60min_SDF1_D3


title: iPS-derived Endothelial Cell Clone 7 No Dox Replicate 1

description:
EC_DE_Summary.tab.txt
EC_TRANSC7ND_Rep1


title: iPS-derived Endothelial Cell Clone 5A Dox Replicate 3

description:
EC_DE_Summary.tab.txt
EC_TRANSC5AD_Rep3

value: Clone 5A


title: Day7.60min_SDF1_D2

value: Plasmablast


title: iPS-derived Endothelial Cell Clone 5A Dox Replicate 2

description:
EC_DE_Summary.tab.txt
EC_TRANSC5AD_Rep2


title: Day7.60min_sCD40L_D3


title: Day7.360min_sCD40L_D3


title: Day7.60min_SDF1_D1


title: Day7.60min_sCD40L_D2


title: iPS-derived Endothelial Cell Clone 5A Dox Replicate 1

description:
EC_DE_Summary.tab.txt
EC_TRANSC5AD_Rep1


title: iPS-derived Endothelial Cell Clone 5A No Dox Replicate 3

description:
EC_DE_Summary.tab.txt
EC_TRANSC5AND_Rep3


title: iPS-derived Endothelial Cell Clone 5A No Dox Replicate 1

description:
EC_DE_Summary.tab.txt
EC_TRANSC5AND_Rep1


title: Day7.60min_IFN_D2


title: Day7.60min_IFN_D1


title: Day7.60min_sCD40L_D1


title: Day7.60min_IFN_D3


title: iPS-derived Endothelial Cell Clone 5 Dox Replicate 3

description:
EC_DE_Summary.tab.txt
EC_TRANSC5D_Rep3

value: Clone 5


title: iPS-derived Endothelial Cell Clone 5 Dox Replicate 2

description:
EC_DE_Summary.tab.txt
EC_TRANSC5D_Rep2


title: Day7.60min_APRIL_D1


title: Day7.0min_None_D3


title: iPS-derived Endothelial Cell Clone 5 Dox Replicate 1

description:
EC_DE_Summary.tab.txt
EC_TRANSC5D_Rep1


title: SF12704v2_snRNA

first: Aaron

last: Diaz

department: Neurological Surgery

institute: University of California, San Francisco

description: Single Nuclei RNA-Seq

data_processing:
We utilized CellRanger (version 3.0.2) for data pre-processing and gene expression quantification, following the guidelines from the CellRanger website (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/advanced/references#premrna).
The CellRanger ATAC software (version 1.1.0) was used for read alignment, deduplication, and identifying transposase cut sites.
The presence/absence of somatic CNVs was assessed with CONICSmat. ELSA was used for cell type classification.
Assembly: hg38
Supplementary files format and content: SnRNA-seq: feature read count matrix (.txt)  files.   Includes cell barcodes, genes and count. SnATAC-seq: peak, matrix, barcode file.

source_name: Brain

extract_protocol:
Nuclei were extracted from frozen tissues following the “Frakenstein” protocol developed by Luciano Martelotto, Ph.D., Melbourne, Centre for Cancer Research, Victorian Comprehensive Cancer Centre, and available from 10X Genomics
For snRNA-seq(frozen tissues), ~15,000 nuclei were loaded per capture. Single-nucleus capture, reverse transcription, cell lysis, and library preparation were performed per manufacturer’s protocol. Sequencing was performed on an Illumina NovaSeq using a paired-end 100bp protocol.

tag: progression

value: Recurrent

tag: diagnosis

value: Brain tumor

tag: age

tag: gender

value: female

tag: pair#


title: Day7.0min_None_D1

tag: cell type


title: Day7.0min_None_D2


title: Day7.60min_APRIL_D2


title: SF9791_snRNA

description: Single Nuclei RNA-Seq

value: male


title: SF6118v2_snRNA

description: Single Nuclei RNA-Seq


title: SF12774_snRNA

description: Single Nuclei RNA-Seq


title: iPS-derived Endothelial Cell Clone 5 No Dox Replicate 3

description:
EC_DE_Summary.tab.txt
EC_TRANSC5ND_Rep3

value: control


title: iPS-derived Endothelial Cell Clone 5 No Dox Replicate 2

description:
EC_DE_Summary.tab.txt
EC_TRANSC5ND_Rep2


title: SF9715v2_snRNA

description: Single Nuclei RNA-Seq


title: SF12594_snRNA

description: Single Nuclei RNA-Seq