title: 218_Batch4_3_3296_S61_L004

value: Emavundleni

value: IVD

value: Nobs

value: Never married

value: Secondary school, some or complete

value: No


title: 92_20180727_8_sample2_IL13

status: Public on Sep 13 2023

type: SRA

city: Bunkyo-ku

first: Yoshitaka

last: Shirasaki

state: Tokyo

address: Hongo 7-3-1

department: Graduate School of Pharmaceutical Science

country: Japan

institute: The University of Tokyo

description: 3' mRNA library: read1 file contains transcript; read2 file contains cell barcord

library_source: transcriptomic single cell

data_processing:
After library demultiplexing (SMART-Seq DE3 Demultiplexer; Clontech) and adaptor trimming (by deleting 7 bases from the end), read 1 sequences were aligned to reference sequences (human: GRCh38.90) using TopHat2, and the read counts were calculated using HTSeq3.
Single-cell libraries stochastically lose information on low copy number transcripts in a quantity-dependent manner in the starting resource. Note should be taken of the correction for counts to avoid cell-to-cell bias.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: total RNA

organism: Mus musculus

source_name: Transition state (30min), index: IL13

extract_protocol:
We obtained pooled mesentery from 20 wildtype C57BL/6 mice. Lineage-negative cells were selected by negative selection using MicroBeads and AutoMACS (Miltenyi Biotec GmbH). Then, c-Kit+Sca-1+ cells were sorted as ILC2s using a FACSAria flow cytometer (BD Bioscience).
cDNA libraries were prepared using SMART-Seq v4 3’-DE Kits (Clontech) according to the manufacturer’s instructions, with some modifications. A total of 3,892 copies of ERCC spike-in RNA were added to each sample as a mixture of quantitative internal controls. The cDNA was purified using Agencourt AMPure XP magnetic beads (Beckman Coulter). Library quality check was performed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) and Agilent High Sensitivity DNA Kits (5067-4626). Degraded or low-yield samples were removed. Qubit High Sensitivity assays (Thermo Fisher Scientific) were performed to quantify the cDNA in each library, and 5 or 6 libraries with different indexed primers were evenly pooled. Pooled cDNA (400 pg) was tagmented using Nextera XT DNA Library Prep Kits (Illumina, San Diego, CA, USA), as described in the protocol. Library size and cDNA amount were quantified using an Agilent High Sensitivity DNA Kit and Qubit High Sensitivity assays, respectively.

tag: tissue

value: fat tissues

tag: cell type

tag: treatment

value: incubated with IL-2/IL-33


title: 105_20180727_9_sample4_IL13

source_name: Transition state (90min), index: IL13


title: AD patient, PBMC SNUBH-44-2

city: Seoul

first: Namphil

last: Kim

address: Gwanak-ro 1

department: Electrical and Computer Engineering

country: South Korea

institute: Seoul National University

description: AD patient, PBMC

library_source: transcriptomic

data_processing:
The raw NGS forward (R1) and reverse (R2) reads were merged, filtered based on Phred scores, and subclustered using UMI using paired-end read merger (PEAR), v0.9.10, and Clustal Omega, v1.2.4, with the default setting30,31. The sequence annotation process used the IMGT (International Immunogenetics Information System) constant gene database32 to obtain the isotype, and IgBLAST, v1.17.133 to obtain VJ genes, CDR1/2/3 sequences, and the number of mutations from the corresponding V genes as previously described16. To eliminate the possibility of contamination due to index swapping within Illumina flow cells between samples, reads with identical sequences including the UMI from different samples were excluded on the basis that such an event is highly unlikely without contamination34. The combined NGS throughput of each sample is listed in Extended table 2. Sequencing reads that have survived through the entire process is considered to be a productive BCR sequence.
Supplementary files format and content: sequence_id     duplicate_count frequency       sequence        sequence_aa     sequence_alignment      germline_alignment      v_call  j_call  c_call  junction        junction_aa      cdr1    cdr2    cdr3    cdr1_aa cdr2_aa cdr3_aa rev_comp        productive      v_cigar j_cigar v_alignment_length      v_alignment_mutation

organism: Homo sapiens

source_name: PBMC

extract_protocol:
All peripheral blood samples were collected by EDTA tubes (BD Vacutainer K2EDTA tubes, 367525) at least 15 ml in total per a patient29. Peripheral blood mononuclear cells (PBMCs) and plasma were separated by density-gradient centrifugation using Ficoll (Cytiva Ficoll-Paque Plus, 17-1440-02) solution. After the PBMC suspension was resuspended in CELLBANKER (Amsbio CELLBANKER 2, 11914), the collected PBMCs were immediately cryopreserved and stored in a Freezing container (Nalgene Mr. Frosty, C1562) for a week. Total RNA was isolated by TRIzol Reagent (Invitrogen TRIzol Reagents, 15596026) following the manufacturer’s instructions.
For the NGS library preparation of BCR heavy chain sequence, genes encoding the variable region of the heavy chain (VH) at the 5 prime forward part and the first constant region of the heavy chain (CH1) domain at the 3 prime reverse part were amplified by specific PCR primers as reported previously16. All primer sequences are listed in Extended Table 2. In short, one microgram of total RNA was used as the input template for library preparation. Next, reverse transcription was conducted as following the manufacturer’s instructions using SuperScript IV First-Strand Synthesis System (Invitrogen, 18091050) with CH1 gene-specific primers for five immunoglobulin heavy chain isotypes containing UMI (unique molecular identifiers) barcodes that consist of 12 random nucleotides, 14 base pair in total; NNNNTNNNNTNNNN, and partial Illumina adapters (No. 1-8). After first-strand cDNA synthesis, it was purified with SPRI beads (Beckman Coulter AMPure XP Reagents, A63882) at a 1:1.8 ratio and second-strand cDNA was synthesized using a KAPA Biosystems kit (Roche KAPA HiFi Hotstart PCR kit, KK2502) with VH gene-specific primers (No. 9-14; 95°C for 3 min, 98°C for 30 s, 60°C for 45 s, and 72°C for 6 min). Double-stranded cDNA was purified through SPRI beads at a 1:1 ratio. Following that, it was amplified using KAPA Biosystems kit and double primers containing Illumina adapters and index sequences (No. 15, 16; 95°C for 3 min, 25 cycles of 98°C for 30 s, 60°C for 30 s, 72°C for 1 min, and 72°C for 5 min). The PCR products were subjected to electrophoresis on a 1.5% agarose gel to separate through the length of DNA and purified using QIAquick gel extraction kit (QIAGEN, 28704) following the manufacturer’s protocols. The final NGS libraries were obtained using SPRI beads at a 1:1 ratio and quantified with a 4200 TapeStation System (Agilent Technologies, G2991BA) for QC.
Libraries with a single peak of appropriate length were subjected to NGS analysis using the Illumina Nocaseq6000 platform.

value: PBMC

tag: cell line


title: 219_Batch4_4_4736_S62_L005

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

country: USA

institute: Yerkes National Primate Research Center

data_processing:
The sequencing data was demultiplexed using Illumina bcl2fastq version 2.20.0.422 BCL to FastQ file converter.
The quality of raw reads was assessed with FastQC version 0.11.8
Reads were mapped to the GRCh38 human genome assembly [https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26/] using STAR version 2.5.2b with default alignment parameters.
Abundance estimation of raw read counts per transcript was done internally with STAR using the htseq-count algorithm
DESeq2 version 1.22.1 R package was used to produce Raw read counts.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab delimited text file containing Raw read counts for each sample (in columns) and each annotated transcript (in rows).

source_name: endocervical cells

growth_protocol: Cervical cytobrush samples collected at the baseline and the one month follow-up visit from 188 matched participants (n=376) were processed for RNA sequencing of cervical cells. The cervical cells were collected using a Digene cervical sampler (Digene Corporation, Gaithersburg, MD, USA). A cervical cytobrush was inserted into the endocervical os, rotated through 360 degrees and placed in a 15ml tube containing 3ml R10 media (10% heat-inactivated fetal calf serum (FCS) in RPMI supplemented with L-glutamine (50 ng/μl), anti-fungin (0.8 ng/μl), penicillin (50 U) and streptomycin (50 ng/μl)) and transported to the laboratory within 6 hours.

extract_protocol:
RNA was extracted from the endocervical cytobrush samples collected at the crossover visit using RNeasy Micro kit (Qiagen, CA) with DNase digest and QIAcube automation stations. The RNA was quantified, and the quality was assessed by Bioanalyzer analysis (Agilent Technologies, Santa Clara, CA)
Libraries were prepared using the Illumina (Illumina Inc. San Diego, CA, USA) TruSeq RNA Exome kit, as per manufacturer’s instructions, with 20 ng of total RNA as input. The libraries were quantified using Qubit dsDNA HS before normalization and pooling. The amplified libraries were assessed for their quality and sizing information by capillary electrophoresis on the Agilent 4200 TapeStation. The libraries were normalized, pooled and sequenced on the Illumina HiSeq3000 system employing a single-end 101 cycles run at average read depths of 23 million reads/sample.

treatment_protocol: Upon arrival of the cytobrush at the laboratory, the cytobrush was rotated against the side of the tube to dislodge the cells and the transport medium was used to flush the cytobrush bristles 30 times. The tubes were centrifuged at 1200 rpm for 10 mins to pellet cells. The supernatant was removed from the tube leaving about 50 μl and the pellet gently dislodged by vortexing. 350 μl RLT buffer (QIAGEN) with 1% beta-mercaptoethanol was added to sample. The samples were vortexed for one min to disrupt cells and immediately stored at -80℃.

tag: visit

tag: site

tag: rin

value: IVA

value: nonLD

value: TRUE

tag: bmi

tag: ngonorrhoeae

value: Negative

tag: chlamydiatrachomatis

tag: lactobacilli

value: Abs

tag: mobilincus

value: BV

tag: yeasts

tag: maritalstatus

value: Unchecked


title: 197_Batch3_54_JAA2P3LR-01_S40_L003

value: WRHI


title: 97_20180727_7_sample3_IL13

source_name: Transition state (60min), index: IL13


title: 89_20180725_10_sample6_IL13

source_name: Silent, index: IL13


title: AD patient, PBMC SNUBH-44-1

description: AD patient, PBMC


title: 88_20180725_9_sample6_IL13


title: AD patient, PBMC SNUBH-43-2

description: AD patient, PBMC


title: 196_Batch3_53_FAA2NW8R-01_S39_L003

value: baseline


title: 195_Batch3_52_BAA2NZ6W-01_S38_L003

value: IB

value: LD


title: AD patient, PBMC SNUBH-43-1

description: AD patient, PBMC


title: 86_20180725_7_sample6_IL13


title: AD patient, PBMC SNUBH-4-2

description: AD patient, PBMC


title: 193_Batch3_50_560240786601_S36_L003

value: KEMRI

value: IVB

value: Intermediate

value: Nobs

value: Married

value: Primary school, some or complete

value: Yes


title: 83_20180725_9_sample5_IL13

source_name: Activated, index: IL13

value: fat tissues

value: incubated with IL-2/IL-33


title: 84_20180725_10_sample5_IL13


title: 85_20180725_11_sample5_IL13


title: 194_Batch3_51_HAA2NLRN-01_S37_L003

value: IIIA

value: TRUE

value: Negative

value: Never married

value: Secondary school, some or complete

value: No


title: 82_20180725_8_sample5_IL13


title: AD patient, PBMC SNUBH-42-2

description: AD patient, PBMC

value: PBMC


title: 81_20180725_7_sample5_IL13


title: 181_Batch3_38_KAA2NTTR-01_S24_L002

value: WRHI

value: IVA

value: nonLD

value: Abs

value: BV

value: Unchecked


title: 80_20180725_11_sample4_IL13


title: 177_Batch3_34_7216_S20_L002

value: Emavundleni

value: LD

value: Obs


title: 79_20180725_10_sample4_IL13

value: fat tissues

value: incubated with IL-2/IL-33


title: AD patient, PBMC SNUBH-42-1

description: AD patient, PBMC


title: AD patient, PBMC SNUBH-4-1

description: AD patient, PBMC


title: 78_20180725_9_sample4_IL13


title: 77_20180725_8_sample4_IL13


title: 91_20180727_7_sample2_IL13


title: 90_20180725_11_sample6_IL13


title: 169_Batch3_26_560240976601_S12_L001

value: KEMRI

value: IIIA

value: TRUE

value: Nobs

value: Married


title: 76_20180725_7_sample4_IL13


title: 168_Batch3_25_560226156601_S11_L001

value: baseline

value: IVD

value: Negative

value: Secondary school, some or complete

value: No


title: 75_20180725_11_sample3_IL13


title: AD patient, PBMC SNUBH-41-2

description: AD patient, PBMC

value: PBMC


title: 73_20180725_9_sample3_IL13


title: 74_20180725_10_sample3_IL13


title: 87_20180725_8_sample6_IL13


title: 165_Batch3_22_8223_S8_L001

value: IB

value: Abs

value: Never married

value: Unchecked


title: AD patient, PBMC SNUBH-41-1

description: AD patient, PBMC


title: 71_20180725_7_sample3_IL13

value: fat tissues


title: 70_20180725_11_sample2_IL13

value: incubated with IL-2/IL-33


title: 135_Batch2_63_EAA2PGYP-01_S71_L005

value: WRHI

value: IVB

value: nonLD

value: Intermediate

value: Yes


title: 69_20180725_10_sample2_IL13


title: 68_20180725_9_sample2_IL13


title: 72_20180725_8_sample3_IL13


title: 148_Batch3_5_560238026601_S84_L006

value: baseline

value: KEMRI

value: IIIA

value: LD

value: TRUE

value: Nobs

value: Married

value: Primary school, some or complete


title: 114_Batch2_42_HAA2P4SS-01_S50_L004

value: Negative

value: Abs

value: Secondary school, some or complete


title: AD patient, PBMC SNUBH-40-1

description: AD patient, PBMC

value: PBMC


title: 65_20180725_11_sample1_IL13

source_name: Pre-stimulation, index: IL13

value: fat tissues


title: AD patient, PBMC SNUBH-39-1

description: AD patient, PBMC


title: 66_20180725_7_sample2_IL13

value: incubated with IL-2/IL-33


title: 64_20180725_10_sample1_IL13


title: AD patient, PBMC SNUBH-39-2

description: AD patient, PBMC


title: 67_20180725_8_sample2_IL13


title: AD patient, PBMC SNUBH-38-2

description: AD patient, PBMC


title: 63_20180725_9_sample1_IL13


title: 96_Batch2_24_560241286601_S32_L003

value: Post-secondary school

value: Unchecked


title: 62_20180725_8_sample1_IL13


title: AD patient, PBMC SNUBH-38-1

description: AD patient, PBMC


title: AD patient, PBMC SNUBH-40-2

description: AD patient, PBMC


title: 61_20180725_7_sample1_IL13


title: 95_Batch2_23_560236276601_S31_L003

value: Yes


title: 92_Batch2_20_8462_S28_L002

value: Emavundleni

value: IVD

value: nonLD

value: BV

value: Never married


title: AD patient, PBMC SNUBH-37-1

description: AD patient, PBMC


title: AD patient, PBMC SNUBH-36-2

description: AD patient, PBMC


title: 57_20180713_9_sample6_IL5

source_name: Silent, index: IL5


title: 60_20180713_12_sample6_IL5


title: AD patient, PBMC SNUBH-36-1

description: AD patient, PBMC


title: 55_20180713_7_sample6_IL5


title: 78_Batch2_6_10142_S15_L001

value: IIIA

value: LD

value: TRUE

value: Nobs

value: No


title: 91_Batch2_19_4304_S27_L002

value: baseline

value: IVA

value: Negative

value: Abs

value: Secondary school, some or complete


title: 53_20180713_11_sample5_IL5

source_name: Activated, index: IL5

value: fat tissues

value: incubated with IL-2/IL-33


title: AD patient, PBMC SNUBH-35-2

description: AD patient, PBMC

value: PBMC


title: 76_Batch2_4_560237786601_S13_L001

value: KEMRI

value: Yes

value: Unchecked


title: 113_Batch2_41_EAA2NXBC-01_S49_L004

value: WRHI

value: IVB

value: nonLD

value: Intermediate

value: Married


title: AD patient, PBMC SNUBH-35-1

description: AD patient, PBMC


title: 51_20180713_9_sample5_IL5


title: 72_Batch1_72_560237426601_S9_L001

value: TRUE

value: Nobs

value: Primary school, some or complete


title: 50_20180713_8_sample5_IL5


title: 52_20180713_10_sample5_IL5


title: AD patient, PBMC SNUBH-34-2

description: AD patient, PBMC


title: 49_20180713_7_sample5_IL5


title: 71_Batch1_71_560232716601_S8_L001

value: baseline

value: Negative

value: BV


title: 59_20180713_11_sample6_IL5

value: fat tissues


title: 48_20180713_12_sample4_IL5

source_name: Transition state (90min), index: IL5

value: incubated with IL-2/IL-33


title: AD patient, PBMC SNUBH-34-1

description: AD patient, PBMC

value: PBMC


title: 58_20180713_10_sample6_IL5


title: 46_20180713_10_sample4_IL5


title: AD patient, PBMC SNUBH-33-2

description: AD patient, PBMC


title: 56_Batch1_56_560243976601_S56_L008

value: KEMRI

value: Abs

value: Checked


title: 56_20180713_8_sample6_IL5


title: 54_20180713_12_sample5_IL5


title: 47_20180713_11_sample4_IL5


title: 45_20180713_9_sample4_IL5


title: 43_20180713_7_sample4_IL5


title: 34_Batch1_34_560238856601_S34_L007

value: IVD

value: Secondary school, some or complete

value: No

value: Unchecked


title: AD patient, PBMC SNUBH-32-2

description: AD patient, PBMC


title: AD patient, PBMC SNUBH-33-1

description: AD patient, PBMC


title: AD patient, PBMC SNUBH-32-1

description: AD patient, PBMC


title: 33_Batch1_33_560228976601_S33_L007

value: IVB

value: nonLD

value: Married


title: 40_20180713_10_sample3_IL5

source_name: Transition state (60min), index: IL5


title: 21_Batch1_21_560236266601_S21_L006

value: IIIA

value: LD

value: TRUE

value: Nobs

value: Primary school, some or complete

value: Yes


title: 41_20180713_11_sample3_IL5

value: fat tissues

value: incubated with IL-2/IL-33


title: AD patient, PBMC SNUBH-3-1

description: AD patient, PBMC

value: PBMC


title: 36_20180713_12_sample2_IL5

source_name: Transition state (30min), index: IL5


title: 38_20180713_8_sample3_IL5


title: AD patient, PBMC SNUBH-31-2

description: AD patient, PBMC


title: 42_20180713_12_sample3_IL5


title: 9_Batch1_9_560228636601_S9_L005

value: baseline

value: KEMRI

value: Positive

value: Negative

value: Abs

value: Obs

value: Never married


title: 55_Batch1_55_560236156601_S55_L008

value: IVD

value: nonLD

value: BV

value: Married

value: Checked


title: 35_20180713_11_sample2_IL5


title: 4_Batch1_4_EAA2P9PX-01_S4_L005

value: WRHI

value: IIIA

value: LD

value: TRUE

value: Nobs

value: Secondary school, some or complete

value: No

value: Unchecked


title: 44_20180713_8_sample4_IL5

value: fat tissues

value: incubated with IL-2/IL-33


title: AD patient, PBMC SNUBH-31-1

description: AD patient, PBMC

value: PBMC


title: 34_20180713_10_sample2_IL5


title: AD patient, PBMC SNUBH-30-1

description: AD patient, PBMC


title: 31_20180713_7_sample2_IL5


title: 30_20180708_11_sample6_IL5


title: 39_20180713_9_sample3_IL5


title: AD patient, PBMC SNUBH-29-2

description: AD patient, PBMC


title: 29_20180708_10_sample6_IL5


title: 362_Batch6_3_560229236601_S83_L006

value: baseline

value: KEMRI

value: IVB

value: FALSE

value: Negative

value: Abs

value: Intermediate

value: Yes


title: 386_Batch6_27_7296_S107_L007

value: Emavundleni

value: nonLD

value: LD

value: Married


title: 3_Batch1_3_AAA2P1LZ-01_S3_L005

value: WRHI

value: IIIA

value: TRUE

value: Nobs

value: Secondary school, some or complete

value: No


title: AD patient, PBMC SNUBH-29-1

description: AD patient, PBMC

value: PBMC


title: 28_20180708_9_sample6_IL5

value: fat tissues

value: incubated with IL-2/IL-33


title: 303_Batch5_16_JAA2P0JB-01_S24_L002

value: FALSE

value: Negative

value: Unchecked


title: 27_20180708_8_sample6_IL5


title: 26_20180708_7_sample6_IL5


title: 301_Batch5_14_JAA2NWWX-01_S22_L002

value: Abs

value: Never married

value: Yes


title: 24_20180708_10_sample5_IL5


title: AD patient, PBMC SNUBH-27-2

description: AD patient, PBMC


title: 23_20180708_9_sample5_IL5


title: 268_Batch4_53_BAA2P6JK-01_S111_L008

value: baseline

value: LD

value: Intermediate


title: 33_20180713_9_sample2_IL5


title: 22_20180708_8_sample5_IL5


title: 226_Batch4_11_BAA2P2RP-01_S69_L005

value: WRHI

value: IVB

value: nonLD

value: Married


title: 20_20180708_11_sample4_IL5


title: AD patient, PBMC SNUBH-27-1

description: AD patient, PBMC


title: 19_20180708_10_sample4_IL5


title: 192_Batch3_49_560236576601_S35_L003

value: KEMRI

value: Nobs

value: Primary school, some or complete


title: 32_20180713_8_sample2_IL5

value: fat tissues

value: incubated with IL-2/IL-33


title: 18_20180708_9_sample4_IL5


title: AD patient, PBMC SNUBH-26-1

description: AD patient, PBMC

value: PBMC


title: AD patient, PBMC SNUBH-26-2

description: AD patient, PBMC


title: 17_20180708_8_sample4_IL5


title: 180_Batch3_37_BAA2NNN7-01_S23_L002

value: IIIA

value: FALSE

value: Negative

value: Secondary school, some or complete

value: Unchecked


title: 176_Batch3_33_5632_S19_L002

value: baseline

value: Emavundleni

value: LD

value: Abs

value: Never married

value: No


title: 13_20180708_9_sample3_IL5


title: 15_20180708_11_sample3_IL5


title: AD patient, PBMC SNUBH-25-1

description: AD patient, PBMC


title: 25_20180708_11_sample5_IL5


title: AD patient, PBMC SNUBH-25-2

description: AD patient, PBMC


title: 164_Batch3_21_7328_S7_L001

value: IVD

value: nonLD


title: 21_20180708_7_sample5_IL5


title: AD patient, PBMC SNUBH-24-2

description: AD patient, PBMC


title: 149_Batch3_6_560241786601_S85_L006

value: KEMRI

value: Nobs

value: Married

value: Primary school, some or complete

value: Yes


title: 11_20180708_7_sample3_IL5

value: fat tissues

value: incubated with IL-2/IL-33


title: AD patient, PBMC SNUBH-24-1

description: AD patient, PBMC

value: PBMC


title: 10_20180708_11_sample2_IL5


title: 12_20180708_8_sample3_IL5


title: 9_20180708_10_sample2_IL5


title: 8_20180708_9_sample2_IL5


title: 134_Batch2_62_AAA2P7W3-01_S70_L005

value: WRHI

value: IVB

value: FALSE

value: Negative

value: Secondary school, some or complete

value: Unchecked


title: 77_Batch2_5_7152_S14_L001

value: baseline

value: Emavundleni

value: LD

value: Abs

value: Never married

value: No


title: 7_20180708_8_sample2_IL5


title: 6_20180708_7_sample2_IL5


title: 5_20180708_11_sample1_IL5

source_name: Pre-stimulation, index: IL5


title: AD patient, PBMC SNUBH-23-2

description: AD patient, PBMC


title: 75_Batch2_3_560233066601_S12_L001

value: KEMRI

value: IIIA

value: nonLD

value: Nobs


title: 16_20180708_7_sample4_IL5

value: fat tissues

value: incubated with IL-2/IL-33


title: AD patient, PBMC SNUBH-2-2

description: AD patient, PBMC

value: PBMC


title: 22_Batch1_22_560241196601_S22_L006

value: FALSE

value: BV

value: Married

value: Primary school, some or complete

value: Yes


title: 2_20180708_8_sample1_IL5


title: 4_20180708_10_sample1_IL5


title: 1_20180708_7_sample1_IL5


title: 3_20180708_9_sample1_IL5


title: AD patient, PBMC SNUBH-22-2

description: AD patient, PBMC


title: 346_Batch5_59_3952_S67_L005

value: baseline

value: Emavundleni

value: IB

value: Negative

value: Secondary school, some or complete

value: Unchecked


title: 10_Batch1_10_560240666601_S10_L005

value: KEMRI

value: Positive

value: Abs

value: Obs

value: Never married


title: AD patient, PBMC SNUBH-2-1

description: AD patient, PBMC

value: PBMC


title: AD patient, PBMC SNUBH-22-1

description: AD patient, PBMC


title: 241_Batch4_26_EAA2NRGL-01_S84_L006

value: WRHI

value: IVB

value: nonLD

value: Nobs

value: Post-secondary school


title: AD patient, PBMC SNUBH-23-1

description: AD patient, PBMC


title: CM3: colorectal tumor tissues with metastasis 3

type: RNA

city: Guangzhou

first: wang

middle: yi

last: qing

country: China

institute: South Medical University

description: LncRNA experssion in colorectal tumor tissues with metastasis

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 2.2ul containing 25X Fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55ul of 2x GEx Hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to Hybridization oven rotator for Agilent Microarray Hybridization Chambers (Agilent p/n G2530-60029) for 17 hours at 65Â°C . After hybridization, microarrays were washed 5 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (Agilent p/n G2565BA) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: The human colorectal tumor tissues are obtained from  Department of pathology , Nanfang Hospital (Guangzhou, China).

extract_protocol: RNA was prepared using RNasey Mini Kit(Qiagen p/n 74104) following the manufacturer's recommendations.  The protocol includes lysis of cells, and an on-column DNase digestion.  RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: Tissues are keep in liquid nitrogen.

tag: gender

value: male


title: 163_Batch3_20_GAA2PKNW-01_S6_L001

value: No


title: 398_Batch6_39_6224_S119_L008

value: Emavundleni

value: IVA

value: TRUE

value: BV


title: AD patient, PBMC SNUBH-21-2

description: AD patient, PBMC


title: AD patient, PBMC SNUBH-20-2

description: AD patient, PBMC


title: AD patient, PBMC SNUBH-21-1

description: AD patient, PBMC


title: 397_Batch6_38_4512_S118_L008

value: baseline

value: Negative

value: Secondary school, some or complete

value: Unchecked


title: AD patient, PBMC SNUBH-20-1

description: AD patient, PBMC


title: CM2: colorectal tumor tissues with metastasis 2


title: CM1: colorectal tumor tissues with metastasis 1


title: 37_20180713_7_sample3_IL5

value: fat tissues

value: incubated with IL-2/IL-33


title: AD patient, PBMC SNUBH-28-1

description: AD patient, PBMC

value: PBMC


title: 378_Batch6_19_560237766601_S99_L007

value: KEMRI

value: Positive

value: Abs

value: Married

value: Primary school, some or complete

value: Yes


title: C2: colorectal tumor tissues without metastasis 2

description: LncRNA experssion in colorectal tumor tissues without metastasis

value: male


title: AD patient, PBMC SNUBH-18-2

description: AD patient, PBMC


title: Microvascular endothelium, 16 Gy, 7d, rep4

city: Boston

first: Amanda

last: Jiang

state: MA

address: 201 Brookline Avenue

institute: Wyss Institute

data_processing:
These sequence reads were trimmed using Trimmomatic v.0.36 to eliminate adapter sequences and nucleotides with poor quality.
These trimmed reads were mapped onto the Homo sapiens GRCh38 reference genome using STAR aligner v.2.5.2b.
Unique gene hit counts were computed using Counts from the Subread package v.1.5.2.
Differential expression analysis was performed
Supplementary files format and content: tab-delimited text files includes raw counts for each sample

source_name: Lung

growth_protocol: Human Alveolus chips were seeded with lung epithelial cells on the apical side of the membrane and endothelial cells on the basal side of the membrane. The apical and basal channels were perfused with Alveolar epithelial growth medium and endothelial growth medium , respectively at a flow rate of 45 uL/h. On day 5, the apical medium is supplemented with 1 uM dexamethasone to enhance barrier formation. Following this, on day 7, medium is removed from the apical channel to establish an air-liquid interface. Chips continued to be perfused with EGM2-MV in the basal channel.  On day 9, the perfusing medium was changed to EGM2-MV with 0.5% FBS. On day 11,  5% mechanical strain was applied, at 0.25 Hz frequency to mimic breathing. The mechanical strain is applied for 4 days before the chips are exposed to radiation.

extract_protocol:
RNA isolation is performed using the RNeasy Plus Micro Kit (Qiagen 74034),
RNA-seq package including polyA selection
and sequencing using an Illumina HiSeq for 150 bp pair-ended reads.

treatment_protocol: PBMCs were perfused into the bottom endothelial channel. Following PBMC perfusion, alveolus chips were exposed to gamma radiation using a Cesium source (Cs-137). The chips were exposed to 16 Gy radiation. The control samples were left in the biosafety cabinet to mimic sham irradiation and were not exposed to radiation.

value: Lung

value: Human lung microvascular endothelial cells

value: Lung endothelium

value: 16 Gy radiation


title: Microvascular endothelium, 16 Gy, 7d, rep2


title: Microvascular endothelium, Ctrl 0 Gy, 7d, rep4

value: Control 0 Gy


title: Microvascular endothelium, 16 Gy, 7d, rep3


title: Microvascular endothelium, 16 Gy, 7d, rep1


title: 377_Batch6_18_560232076601_S98_L007

value: baseline

value: IVA

value: nonLD

value: TRUE

value: Negative

value: BV

value: Nobs


title: Microvascular endothelium, Ctrl 0 Gy, 7d, rep3


title: N3: paracancer normal intestinal mucosal tissues of colorectal tumor 3

description: LncRNA experssion in paracancer normal intestinal mucosal tissues of colorectal tumor


title: N2: paracancer normal intestinal mucosal tissues of colorectal tumor 2


title: N1: paracancer normal intestinal mucosal tissues of colorectal tumor 1


title: 370_Batch6_11_4272_S91_L006

value: Emavundleni

value: IIIA

value: LD

value: Abs

value: Never married

value: Secondary school, some or complete

value: No

value: Unchecked


title: 369_Batch6_10_2752_S90_L006


title: Microvascular endothelium, Ctrl 0 Gy, 7d, rep1

value: Lung

value: Human primary alveolar epithelial cells

value: Lung endothelium


title: C1: colorectal tumor tissues without metastasis 1

value: male


title: Alveolar epithelium, 16 Gy, 7d, rep4

value: Lung epithelium

value: 16 Gy radiation


title: AD patient, PBMC SNUBH-18-1

description: AD patient, PBMC

value: PBMC


title: AD patient, PBMC SNUBH-17-2

description: AD patient, PBMC


title: 14_20180708_10_sample3_IL5

value: fat tissues

value: incubated with IL-2/IL-33


title: Microvascular endothelium, Ctrl 0 Gy, 7d, rep2

value: Human lung microvascular endothelial cells

value: Control 0 Gy


title: AD patient, PBMC SNUBH-19-1

description: AD patient, PBMC


title: C3: colorectal tumor tissues without metastasis 3


title: Alveolar epithelium, 16 Gy, 7d, rep2


title: 367_Batch6_8_560241256601_S88_L006

value: KEMRI

value: IVD

value: nonLD

value: TRUE

value: Negative

value: BV

value: Nobs

value: Married

value: Primary school, some or complete

value: Yes


title: 366_Batch6_7_560236186601_S87_L006

value: baseline

value: IVB

value: Abs

value: Intermediate

value: Unchecked


title: Alveolar epithelium, 16 Gy, 7d, rep1

value: Lung

value: Human primary alveolar epithelial cells

value: Lung epithelium

value: 16 Gy radiation


title: WT Ly49Hpos NK cells, d2 MCMV, biol rep 4

city: New York

first: Hyunu

state: NY

address: 417 E 68th St

department: Immunology

institute: Memorial Sloan Kettering Cancer Center

data_processing:
RNA-seq reads were trimmed for quality and adaptors using Trimmomatic (v.0.38) and aligned to the mm10 genome assembly using salmon (v.0.13.1).
Assembly: mm10
Supplementary files format and content: text file is tab delinited raw counts (1 count per pair of reads) calculated using the summarizeOverlaps function from the GenomicAlignments R package (v10.10.1)

extract_protocol:
Total RNA was extracted from sorted NK cells using PicoPure RNA Isolation Kit (Thermo Fisher Scientific). ). After RiboGreen quantification and quality control by Agilent BioAnalyzer, 2 ng total RNA with RNA integrity numbers ranging from 8.4 to 10 underwent amplification using the SMART-Seq v4 Ultra Low Input RNA Kit (Clonetech catalog # 63488), with 12 cycles of amplification.
Subsequently, 10 ng of amplified cDNA was used to prepare libraries with the KAPA Hyper Prep Kit (Kapa Biosystems KK8504) using 8 cycles of PCR. Samples were barcoded and run on a HiSeq 4000 in a PE50 run, using the HiSeq 3000/4000 SBS Kit (Illumina).  An average of 36 million paired reads were generated per sample and the percent of mRNA bases per sample ranged from 60% to 71%.

tag: genotype

value: WT

tag: infection

tag: replicate


title: AD patient, PBMC SNUBH-16-2

description: AD patient, PBMC

tag: tissue

value: PBMC

tag: cell type


title: 359_Batch5_72_BAA2P2QX-01_S80_L006

value: WRHI

value: nonLD

value: TRUE

value: Negative

value: Never married

value: Secondary school, some or complete


title: WT Ly49Hpos NK cells, d2 MCMV, biol rep 2


title: 358_Batch5_71_DAA2NVRR-01_S79_L006

value: baseline

value: Nobs

value: Yes


title: AD patient, PBMC SNUBH-15-2

description: AD patient, PBMC

tag: cell line


title: AD patient, PBMC SNUBH-16-1

description: AD patient, PBMC


title: WT Ly49Hpos NK cells, d0 MCMV, biol rep 2


title: Alveolar epithelium, Ctrl 0 Gy, 7d, rep3

tag: treatment

value: Control 0 Gy


title: Alveolar epithelium, Ctrl 0 Gy, 7d, rep4


title: 353_Batch5_66_560249786601_S74_L005

tag: visit

tag: site

value: KEMRI

value: IVA

value: Abs

value: BV

value: Primary school, some or complete

value: Unchecked


title: WT Ly49Hpos NK cells, d2 MCMV, biol rep 5

value: WT


title: Alveolar epithelium, 16 Gy, 7d, rep3

value: Lung

value: Human primary alveolar epithelial cells

value: Lung epithelium

value: 16 Gy radiation


title: 352_Batch5_65_560237796601_S73_L005

tag: rin

value: nonLD

value: TRUE

tag: bmi

value: Negative

value: Never married


title: Alveolar epithelium, Ctrl 0 Gy, 7d, rep2


title: WT Ly49Hpos NK cells, d0 MCMV, biol rep 1


title: AD patient, PBMC SNUBH-15-1

description: AD patient, PBMC

value: PBMC


title: 351_Batch5_64_560238226601_S72_L005

value: IVB

tag: ngonorrhoeae

tag: chlamydiatrachomatis

value: Nobs

value: Yes


title: AD patient, PBMC SNUBH-14-1

description: AD patient, PBMC


title: Alveolar epithelium, Ctrl 0 Gy, 7d rep1

value: Control 0 Gy


title: Bhlhe40 KO Ly49Hpos NK cells, d2 MCMV, biol rep 4


title: 347_Batch5_60_5792_S68_L005

value: Emavundleni

value: IB

value: LD

tag: lactobacilli

value: Abs

tag: mobilincus

value: Secondary school, some or complete

value: No


title: AD patient, PBMC SNUBH-14-2

description: AD patient, PBMC


title: WT Ly49Hpos NK cells, d2 MCMV, biol rep 3

value: WT


title: AD patient, PBMC SNUBH-13-2

description: AD patient, PBMC


title: Microvascular endothelium, 16 Gy, 6h, rep4

value: Lung

value: Human lung microvascular endothelial cells

value: Lung endothelium

value: 16 Gy radiation


title: Bhlhe40 KO Ly49Hpos NK cells, d2 MCMV, biol rep 3


title: Microvascular endothelium, 16 Gy, 6h, rep3


title: 344_Batch5_57_5072_S65_L005

value: baseline

value: IVA

value: nonLD

value: TRUE

value: Negative

value: BV

tag: yeasts

tag: maritalstatus

value: Never married

value: Unchecked


title: Bhlhe40 KO Ly49Hpos NK cells, d0 MCMV, biol rep 2

tag: genotype


title: AD patient, PBMC SNUBH-1-2

description: AD patient, PBMC

value: PBMC


title: AD patient, PBMC SNUBH-13-1

description: AD patient, PBMC


title: Microvascular endothelium, 16 Gy, 6h, rep2


title: 335_Batch5_48_4464_S56_L004

value: Emavundleni

value: Abs

value: Nobs


title: AD patient, PBMC SNUBH-12-2

description: AD patient, PBMC


title: Microvascular endothelium, 16 Gy, 6h, rep1


title: Bhlhe40 KO Ly49Hpos NK cells, d2 MCMV, biol rep 5

tag: infection


title: 334_Batch5_47_2960_S55_L004

value: Secondary school, some or complete

value: No


title: Bhlhe40 KO Ly49Hpos NK cells, d0 MCMV, biol rep 1

tag: replicate


title: Microvascular endothelium, Ctrl 0 Gy, 6h, rep4

tag: tissue

value: Lung

value: Human lung microvascular endothelial cells

value: Control 0 Gy


title: AD patient, PBMC SNUBH-12-1

description: AD patient, PBMC

tag: cell type


title: Microvascular endothelium, Ctrl 0 Gy, 6h, rep3

tag: cell line

value: Lung endothelium


title: 321_Batch5_34_8558_S42_L003

value: IVD

value: Yes


title: 345_Batch5_58_8766_S66_L005

value: nonLD

value: TRUE


title: AD patient, PBMC SNUBH-1-1

description: AD patient, PBMC


title: AGO2_MS_24H_KA

city: Aarhus N

first: Morten

middle: T

last: Veno

state: DK

address: Aabogade 15

country: Denmark

institute: Omiics ApS

description: Small RNA sequencing of microRNA bound to circulating plasma

data_processing:
Chimera software was used to trim adapters, size-select miRNA reads and to align identified reads to the reference genome of interest.
Reads are aligned to miRBase using BLASTn.
Downstream analyses to identify differentially expressed miRNA were performed using edgeR and Limma packages from Bioconductor.
Graphics were produced using the glimma package.
Based on the fact that that the mice are genetically identical, a square root value (BCV) of 0.1 was set to allow an estimated p value based on dispersion values.
Assembly: miRBase V21
Supplementary files format and content: Tab delimited txt file with miRNA expression levels in raw read count. Samples as columns, miRNAs as rows

source_name: plasma

extract_protocol:
Ago2 immuporeciptate with antibody C34C6; Cell Signalling Technology and trizol extraction of bound RNA.
Illumina TruSeq Small RNA Library Prep Kit (Illumina, UK) with reagent volumes halved to account for lower concentrations of miRNA to prevent excessive formation of adapter dimers.

value: plasma

tag: strain

tag: time point

tag: treatment

value: KA


title: AGO2_MS_2WK_KA


title: AD patient, PBMC SNUBH-11-2

description: AD patient, PBMC


title: AGO2_MS_24H_PBS

value: PBS


title: 320_Batch5_33_6880_S41_L003

tag: visit

value: baseline

tag: site

tag: rin

value: IVA

value: Negative

value: BV

value: Never married

value: Unchecked


title: Microvascular endothelium, Ctrl 0 Gy, 6h, rep2

value: Lung


title: Microvascular endothelium, Ctrl 0 Gy, 6h, rep1

value: Human primary alveolar epithelial cells


title: Alveolar epithelium, 16 Gy, 6h, rep4

value: Lung epithelium

value: 16 Gy radiation


title: 317_Batch5_30_5552_S38_L003

value: Emavundleni

value: IVB

tag: bmi

tag: ngonorrhoeae

tag: chlamydiatrachomatis

value: Positive

value: Abs

value: Nobs

value: Primary school, some or complete


title: Bhlhe40 KO Ly49Hpos NK cells, d2 MCMV, biol rep 2


title: AD patient, PBMC SNUBH-11-1

description: AD patient, PBMC

value: PBMC


title: 316_Batch5_29_3760_S37_L003

value: baseline

value: IVD

value: nonLD

value: TRUE

tag: lactobacilli

tag: mobilincus

tag: yeasts

value: Yes


title: AD patient, PBMC SNUBH-10-2

description: AD patient, PBMC


title: Alveolar epithelium, 16 Gy, 6h, rep3


title: Alveolar epithelium, 16 Gy, 6h, rep2


title: 299_Batch5_12_7872_S20_L002

value: IIIA

value: LD

value: Negative

tag: maritalstatus

value: Never married

value: Secondary school, some or complete

value: Unchecked


title: AGO2_MS_8H_PBS

value: plasma

value: PBS


title: AD patient, PBMC SNUBH-10-1

description: AD patient, PBMC


title: AGO2_MS_4H_KA

value: KA


title: 298_Batch5_11_3744_S19_L002

value: Emavundleni

value: Abs

value: Obs


title: Alveolar epithelium, 16 Gy, 6h, rep1

value: Lung

value: Human primary alveolar epithelial cells

value: Lung epithelium

value: 16 Gy radiation


title: ob4

city: Changzhou

first: Shuai

last: Chen

state: Jiangsu

address: 68 Gehu Rd, Wujin District

institute: The Affiliated Changzhou NO.2 People’s Hospital of Nanjing Medical University

data_processing:
Raw reads generated during high-throughput sequencing were fastq format sequences. In  order to get high-quality reads that could be used for later analysis, raw reads needed to be further  quality filtered. Trimmomatic software was first used for adpter removing, And then low-quality  bases and N-bases or low-quality reads were filtered out. Finally, we got high-quality clean reads. Using hisat2 to align clean reads to the reference genome of the experimental specie, the  sample should be assessed by genomic and gene alignment.
Supplementary files format and content: processed  data.xls

source_name: visceral adipose tissue

extract_protocol:
Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) following the  manufacturer’s protocol.
RNA integrity was evaluated using the Agilent 2100 Bioanalyzer (Agilent  Technologies, Santa Clara, CA, USA). The samples with RNA Integrity Number (RIN) ≥ 7 were  subjected to the subsequent analysis. The libraries were constructed using TruSeq Stranded Total

value: visceral adipose tissue

tag: phenotype

value: obese


title: AGO2_MS_4H_PBS

tag: tissue


title: ob3


title: Alveolar epithelium, Ctrl 0 Gy, 6h, rep4

tag: cell type

value: Control 0 Gy


title: 290_Batch5_3_560232036601_S11_L001

value: baseline

value: KEMRI

value: IIIA

value: LD

value: TRUE

value: Negative

value: Nobs

value: Primary school, some or complete

value: Yes


title: Alveolar epithelium, Ctrl 0 Gy, 6h, rep2

tag: cell line


title: AGO2_MS_8H_KA

value: plasma

tag: strain

value: KA


title: 280_Batch4_65_560236716601_S1_L001

value: Abs

value: Married

value: No schooling

value: Unchecked


title: ob2

value: visceral adipose tissue

value: obese


title: Old_Extratumoral tissue_Naive

city: Chicago

first: April

last: Bell

state: IL

address: 2053 N Mozart St Apt 3F

institute: Northwestern University

data_processing:
Data was analyzed by HISAT2
Assembly: mm10
Supplementary files format and content: FPKM

source_name: Brain

extract_protocol:
Total RNA was isolated with Trizol reagent and a PureLink RNA Mini Kit (Ambion 12183025).
Messenger RNA was purified from total RNA using poly-Toligo-attached magneticbeads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the directional library, it was ready after end repair, A-tailing, adapter ligation, sizeselection, USER enzyme digestion, amplification, andpurification.
The clustering of the index-coded samples was performed according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform and paired-end reads were generated.

value: Brain

tag: age

value: Old

tag: group

value: Naive


title: ob1


title: 275_Batch4_60_560237546601_S118_L008

tag: visit

value: KEMRI

value: IIIA

value: LD

value: Intermediate

value: Never married

value: Secondary school, some or complete

value: Checked


title: Old_Extratumoral tissue_Tumor bearing

value: Tumor bearing

tag: treatment


title: Alveolar epithelium, Ctrl 0 Gy, 6h, rep3

value: Lung

value: Human primary alveolar epithelial cells

value: Lung epithelium

value: Control 0 Gy


title: Alveolar epithelium, Ctrl 0 Gy, 6h, rep1


title: 274_Batch4_59_560233996601_S117_L008

value: baseline

tag: site

tag: rin

value: TRUE

value: Negative

value: Abs

value: Nobs

value: Yes


title: ln4

value: visceral adipose tissue

value: lean


title: Young_Extratumoral tissue_Tumor bearing

value: Brain

value: Young


title: ln3


title: Young_Extratumoral tissue_Naive

value: Naive


title: HEk293 GTPBP8 knock out cells clone1

city: STOCKHOLM

first: Miriam

last: Cipullo

address: Solnavägen 9

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

library_source: other

data_processing:
The BCL files were transfered to the FASTAQ by bcl2fastq
The common 3′ adapter sequence (TGGAATTCTCGGGTGCCAAGG) was trimmed off from the adaptor reads by using Cutadapt (filter settings: max-n 0.2 -m 32 -M 40).
The trimmed reads were aligned to the 30 823 mitochondrial genome by using the Bowtie 2 local alignment.
The P-site of the mapped reads was identified by Plastid.The offset of the P-site from the 5′ ends of reads was calibrated using the mtCOX1 stop codon peak. Periodicity was checked across all ORFs and exact P-site locations were adjusted (32: 15; 33: 15; 34:16; 35:16; 36:16; 37: 16; 38:16; 39: 18; 40:16; 41:16; 42: 16)
Codon count vectors for all transcripts were generated. Ratios of ribosome counts of GTPBP8KO1 vs. control cells were calculated for each transcript.
Assembly: Homo_sapiens.GRCh38
Library strategy: Ribosome profiling

molecule: other

source_name: Human Embryonic Kidney

growth_protocol: HEK293 wild type and GTPBP8 knockout cells were grown to 80 % confluency on 15-cm dishes.

extract_protocol:
RNA was isolated from cells using TRIZOL reagent (Thermo Fisher) according to manufacturer’s instructions with the following minor changes: RNA solution was incubated with isopropanol for 30 min, and the pellet was washed with absolute ethanol. RNA was solubilized at 4 °C in water containing 40 units of RNase block (Agilent Technologies).
Isolated RNA was heated at 80 °C for 3 min, put on ice for 1 min, mixed with Gel Loading Buffer II (Thermo Fisher) and loaded onto a 15 % Novex TBE-Urea gel (Thermo Fisher). The gel was run in 1x TBE buffer at 100 V for ~2 h. After completion of the run the gel was stained with 1x SYBR Gold Nucleic Acid Gel Stain (Thermo Fisher) in 1x TBE. Nucleic acids were visualized and bands referring from 30 to 40 nt were excised. RNA was extracted from gel slices in 600 µl RNA extraction buffer (300 mM NaOAc pH 5.5, 1 mM EDTA, 0.25 % SDS) rotating at 4 °C ON. The next day, RNA was precipitated by adding 1.8 ml ice-cold EtOH together with 4 µl GlycoBlue Coprecipitant (Thermo Fisher) and subsequent storage at -80 °C ON. Precipitated RNA was pelleted by centrifugation (5,000 xg, 10 min, 4 °C). Pellet was once washed with 1 ml EtOH, dried for ~5 min and resuspended in 15 µl 10 mM Tris pH 7.5 supplemented with 1 µl RNase inhibitor (SUPERase-In, Thermo Fisher). Samples were heated at 80 °C for 2 min before placing on ice. Next, 3’ phosphates were removed by T4 PNK treatment (1 µl T4 PNK (NEB) added) in 1x T4 PNK buffer (NEB) at 37 °C for 2 h. Reaction was stopped by heat inactivation (65 °C, 10 min). RNA was pelleted by addition of 70 µl water, 2 µl GlycoBlue Coprecipitant (Thermo Fisher), 10 µl 1 M NaOAc and 300 µl EtOH and subsequent storage at -80 °C. RNA was washed and dried as described earlier and finally resuspended in 7 µl 10 mM Tris pH 7.5 supplemented with 1 µl RNase inhibitor. RNA libraries were generated using TrueSeq Small RNA Library Prep Kit (Illumina) according to manufacturer’s protocol with some modifications. Preparation was started by adding 1.2 µl adenylated RA3 to dephosphorylated RNA and incubating the mixture at 80 °C for 2 min. Afterwards, ligation was performed by addition of 2 µl of T4 RNA Ligase 2 (truncated K227Q), 2 µl T4 RNA Ligase 2 buffer and 6 µl PEG8000 (all components from NEB) and incubation at 14 °C ON. RNA was precipitated as described earlier, 20 µl 3 M NaOAc and 600 µl EtOH) and resuspended in 4 µl 10 mM Tris pH 7.5. Ligation products were then purified on a 15 % Novex TBE-Urea gel (Thermo Fisher), extracted, and precipitated as described earlier. Next, RNA was resuspended in 13 µl 10 mM Tris pH 7.5 supplemented with 1 µl RNase inhibitor. Then, 2 mM ATP, 2 µl 10x T4 PNK buffer and 2 µl T4 PNK (NEB) were added, and the reaction mixture was incubated for 2 h at 37 °C, followed by heat inactivation (65 °C, 10 min). RNA was precipitated and resuspended in 13 µl 10 mM Tris pH 7.5 supplemented with 1 µl RNase inhibitor. Thereafter, RNA footprints were ligated with 5’ RNA adaptor (RA5, Illumina) by adding 1.2 µl RA5, 2 µl 10x T4 buffer and 2 µl T4 RNA ligase 38 (Promega) and incubating at 14 °C ON. RNA was precipitated and resuspended in 3 µl 10 mM Tris pH 7.5. Reverse transcription and PCR amplification of library Reverse transcription was performed using RNA RT primers from TrueSeq Small RNA Library Prep Kit (Illumina) and SuperScript III First-Strand Synthesis System (Thermo Fisher) according to manufacturer’s protocol. Afterwards, 2 µl of RT products were PCR amplified using Phusion High-Fidelity PCR master mix (NEB) and DNA primers from TrueSeq Small RNA Library Prep Kit (Illumina). The PCR products were purified using QIAquick PCR Purification Kit (Qiagen), precipitated as usual and resolved on a 10 % Novex non-denaturing TBE gel (Thermo Fisher) using 1x TBE running buffer. PCR products were excised and extracted using DNA extraction buffer (300 mM NaCl, 10 mM Tris pH 8, 1 mM EDTA). Subsequently, PCR products were precipitated and pelleted.
Libraries were resuspended in 11 µl 10 mM Tris pH 785 7.5 and 3 ng were used for sequencing respectively on the Illumina NextSeq 500.

treatment_protocol: Medium was discarded and plates were shortly submerged in liquid nitrogen to snap freeze cells. 2x lysis buffer (100 mM Tris pH 7.5, 200 mM NaCl, 40 mM MgCl2, 2 mM DTT, 200 µg/ml chloramphenicol, 200 µg/ml cycloheximide, 2 % Triton X-100, 2x Complete EDTA-free 725 protease inhibitor cocktail (Roche), 4000 U/ml TURBO DNase I (Thermo Fisher)) was added dropwise on the plates and lysates were collected using cell scrapers. Lysis was completed by triturating samples 10 x with a 20-G needle and cell debris were removed by centrifugation (13,000 xg, 20 min, 4 °C). 200 µl of supernatant were subjected to RNase treatment for 30 min at RT (450 U, Ambion RNase I, Thermo Fisher). RNase treatment was stopped by the addition of 10 µl RNase inhibitor (1 U/µl, SUPERase-In, Thermo Fisher), which was followed by a short centrifugation step to remove insoluble material (5,000 xg, 5 min). Supernatants were loaded on 10-30 % sucrose gradients (50 mM Tris pH 7.4, 100 mM NaCl, 20 mM MgCl2, 1 mM DTT, 100 µg/ml chloramphenicol, 100 µg/ml cycloheximide, 1x Complete EDTA-free protease inhibitor cocktail (Roche), 40 U/ml RNase inhibitor (SUPERase-In, Thermo Fisher) in 11 x 34 mm tubes (Beckman Coulter) and run at 39.000 rpm for 2 h 15 min in a TLS-55 rotor (Beckman Coulter). Afterwards, 100 µl fractions were collected, and 10 µl of each were used for western blot analysis. The remaining volumes of fractions 11-16, representing monosome containing fractions, were combined, and further processed for mitoribosome profiling.

value: Human Embryonic Kidney

value: Flp-In T-REx 293

tag: genotype

value: GTPBP8 -/-


title: Mouse oligodendrocyte precursor cells isolated from postnatal mouse forebrains

city: Bronx

first: Kosaku

last: Shinoda

address: 1301 Morris Park Ave

institute: Albert Einstein College of Medicine

data_processing:
Cell Ranger Version 3.0.2
Assembly: mm10 (mouse) and GRCh38 (human)
Supplementary files format and content: Loupe Browser File (extention .cloupe)

source_name: Brain (forebrain)

extract_protocol:
Donated human brain tissues obtained with consent was dissociated, immunopanned with PDGFRa antibody,  collected with trypsinization, and frozen in freezing medium until RNA extraction. Postnatal mice were anesthetized with hypothermia, brains removed, forebrain dissected, dissociated with papain, immunopanned with PDGFRa antibody,  collected with trypsinization, and frozen in freezing medium until RNA extraction.
10X Genomics Chromium 3' gene expression RNA-seq

value: Brain (forebrain)

value: oligodendrocyte precursor cells

value: Postnatal day 4 to 6

value: wildtype, mixed background


title: HEK293 wild type cells

value: wildtype


title: 291_Batch5_4_560236046601_S12_L001

source_name: endocervical cells

value: KEMRI

value: IIIA

value: LD

value: TRUE

tag: bmi

tag: ngonorrhoeae

value: Negative

tag: chlamydiatrachomatis

value: Never married

value: Primary school, some or complete

value: Unchecked


title: Pot1afl/fl BM cells rep4

city: Fukuoka

first: Yuichiro

last: Semba

address: 3-1-1 Maidashi

institute: Kyushu University

data_processing:
The sequencing reads were aligned to the reference mouse genome by STAR embeddfd in the Drop-seq software available from McCarroll Lab (Macosko et al., 2015).
The expression matrix of read counts for each gene and cell was prepared using the said software.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix tables with raw gene counts.

source_name: Whole bone marrow cells

extract_protocol:
After pre-run setup, the pump of the cells, then the beads, and finally the oil were started. After assessment of droplet quality and bead droplets, the beads were in the whiter layer on top. Through the breakage treatment, the white beads were gathered and washed with 5X RT buffer. cDNA strands were generated on the RNA hybridized to the bead primer with reverse transcription mix. After exonuclease Ⅰ treatment by incubating at 37°C for 45 minutes with rotation, PCR program was exceeded by 95°C 3 minutes—4 cycles of 98°C 20 seconds, 65°C 45 seconds, 72°C 3 minutes—9 cycles of 98°C 20 seconds, 67°C 20 seconds, 72°C 3 minutes—72°C 5 minutes; 4°C hold. The purified cDNA by AMPure XP beads was measured by Bioanalyzer.
Pooled libraries were sequenced on the NextSeq 500 system using a 75-cycle kit. The sequencing reads were aligned to the reference mouse genome (mm10) and an expression matrix of read counts for each gene and cell was prepared using the Drop-seq software available from McCarroll Lab.

value: 2-3 weeks old


title: 247_Batch4_32_560239036601_S90_L006

value: IVA

value: nonLD

tag: lactobacilli

value: Abs

tag: mobilincus

value: BV

tag: yeasts

value: Nobs

value: No


title: ln1

tag: tissue

value: visceral adipose tissue

tag: phenotype

value: lean


title: 246_Batch4_31_560235216601_S89_L006

value: baseline

value: KEMRI

tag: maritalstatus


title: Pot1afl/fl BM cells rep3

tag: strain


title: Differentiation Ctrl

city: Utrecht

first: Daisong

last: Wang

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

data_processing:
Paired-end reads from illumina sequencing were aligned to the human transcriptome with BWA (Li and Durbin, 2009). Read 1 was used for assigning reads to correct cells and libraries, while read 2 was mapped to gene models. Reads that mapped equally well to multiple locations were discarded. Read counts were first corrected for UMI barcode by removing duplicate reads that had identical combinations of library, cellular, and molecular barcodes and were mapped to the same gene. Transcript counts were then adjusted to the expected number of molecules based on counts, 256 possible UMI’s and poissonian counting statistics.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files

source_name: Intestine

extract_protocol:
Cells were lysed by 5 min at 65 ℃, after which RT and second strand mixes were dispersed with the Nanodrop II liquid handling platform (GC biotech). Aqueous phase was separated from the oil phase after pooling all cells in one library, followed by IVT transcription.
The CEL-Seq2 protocol was used for library prep. Primers consisted of a 24 bp polyT stretch, a 4bp random molecular barcode (UMI), a cell-specific 8bp barcode, the 50 Illumina TruSeq small RNA kit adaptor and a T7 promoter. mRNA of each cell was then reverse transcribed, converted to double-stranded cDNA, pooled and in vitro transcribed for linear following the CEL-Seq 2 protocol (Hashimshony et al., 2016). Illumina sequencing libraries were then prepared with the TruSeq small RNA primers (Illumina) and sequenced paired-end at 75 bp read length the Illumina NextSeq

value: Intestine

tag: cell line

value: orgnaoid

tag: cell type

value: wild-type

value: NO


title: Differentiation with IFN-gamma

value: organoid

value: IFN-gamma


title: 240_Batch4_25_JAA2NLXY-01_S83_L006

tag: visit

value: WRHI

value: IIIA

value: LD

value: TRUE

value: Negative

value: Positive

value: Never married

value: Post-secondary school

value: Unchecked


title: shLuc, 8h, asparaginase

city: Hannover

first: Laura

last: Hinze

state: Niedersachsen

address: Carl-Neuberg-Straße 1

country: Germany

institute: Hannover Medical School

data_processing:
Initial quality control of transcriptomics data was performed using FastQC version 0.11.9
“filter by tile” function of BBMap was used to discard low-quality reads
trimming with trimmomatic version 0.39 using specifications: ILLUMINACLIP:TruSeq3-PE.fa:2:30:10:2:True HEADCROP:14 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Orphaned reads were merged to their respective paired fastq files using the cat command of Ubuntu 22.04.1 LTS
Preprocessed reads were mapped using kallisto version 0.46.1 with a transcriptome index created using homo sapiens Ensembl v108 GRCh38.p13
Transcripts of genes with an associated HGNC accession were categorized as protein-coding or non-protein-coding using Ensembl gene biotype information. Transcripts with labels "IG_C_gene", "IG_D_gene", "IG_V_gene", "IG_J_gene", "protein_coding", "TR_D_gene", "TR_J_gene", "TR_V_gene" were considered as protein coding.
Counts with a count < 10 across all analyzed samples were discarded for transcripts.
The remaining transcripts were normalized to obtain transcript per million (TPM) values.
TPMs of transcripts associated with the same HGNC accession were added up to calculate gene level expression. On the gene level, a zTPM cut-off was used to exclude lowly expressed genes and their transcripts (T. Hart, H. K. Komori, S. LaMere, K. Podshivalova, and D. R. Salomon, "Finding the active genes in deep RNA-seq gene expression studies," (in eng), BMC genomics, vol. 14, p. 778, Nov 11 2013, doi: 10.1186/1471-2164-14-778.).
Assembly: homo sapiens Ensembl v108 GRCh38.p13
Supplementary files format and content: table in tab-separated values formating including kallisto estcount, as well as TPM and log2FC for the samples

source_name: Jurkat

growth_protocol: Cells were maintained in RPMI 1640 (Thermo Fisher Scientific) with 10% fetal bovine serum (FBS, Sigma-Aldrich, Saint Louis, MO) and 1% penicillin/streptomycin (Thermo Fisher Scientific) at 37°C, 5% CO2.

extract_protocol:
Total RNA was isolated at indicated time points using the RNeasy kit (Qiagen) according to the manufacturer’s protocols.
Library preparation was performed by eurofins genomics

treatment_protocol: Cells were treated with vehicle or 100 U/L asparaginase at indicated timepoints before harvesting.

value: Jurkat

value: T-ALL cells

value: shLuc

tag: timepoint

tag: treatment

value: aps


title: Pot1afl/fl BM cells rep2

tag: age

value: 2-3 weeks old


title: shLuc, 8h, vehicle

tag: genotype

value: veh


title: A375 Day21 rep2

first: Megan

middle: D

last: Schertzer

state: New York

address: 101 Avenue of the Americas, 4th Floor, Knowles lab

institute: New York Genome Center

description:
lentivirus
R15-Fwd_06

library_source: genomic

data_processing:
library strategy: high-throughput essentiality screen
Reads were demultiplexed based on forward primer barcode using Cutadapt v3.5 (Martin 2011). We included the 8bp barcode plus 8bp of the U6 sequence (“TCTTGTGG”) to ensure the proper position of the barcode match within the read. We allowed for 1 mismatch within the 16bp sequence (-e 1 -O 16, –action=none).
Reads were trimmed at the 5' and 3' end using Cutadapt to isolate the 23bp gRNA sequence.
Bowtie v1.1.2 (Langmead et al. 2009) index was built from the screen library fasta file and reads were subsequently aligned to the library index with strict parameters of -v 0 that do not allow for mismatches and -m 1 that only allow for a single alignment (--norc --best --strata).
Raw count matrix of gRNA read counts per sample was generated from sam alignment files using an in-house R script.
Technical replicates, re-sequencing of the same library for greater read depth, were combined for each sample and all future analyses were performed on this pool. Then, we added 1 to all values to prevent division by 0 for entirely depleted gRNAs. We divided counts for each guide by its geometric mean (across conditions) before normalizing by the median of ratios (Love, Huber, and Anders 2014) corresponding to the non-targeting gRNAs. We visualized normalized counts and removed gRNAs that had low or high detection in the Day 0 sample (cutoffs are 0.01 and 0.99 quartiles of normalized gRNA count distribution). Finally, we calculated log2 fold changes (LFCs) by dividing normalized counts across each time point by the corresponding replicate at Day 0 and taking their log2.
Assembly: hg38 using GENCODE v41 basic annoation gtf
Supplementary files format and content: Table gives the LFC values relative to Day 0 for each biological replicate.

molecule: genomic DNA

growth_protocol: A375 cells were acquired from American Type Culture Collection (ATCC Cat #CRL-1619). A375 cells were maintained at 37°C with 5% CO2 in DMEM media (ThermoFisher Cat #11965118) supplemented with 10% serum (Serum Plus II, Sigma-Aldrich, Cat #14009C).

extract_protocol:
To extract gDNA, screen cells were lysed as in (Sidi Chen et al. 2015) with 12 ml of NK lysis buffer for 100 million cells (50 mM Tris, 50 mM ethylenediaminetetraacetic acid, 1% SDS and pH 8). Once cells were resuspended, 60 µl of 20 mg/ml Proteinase K (Qiagen) was added and the sample was incubated at 55 °C overnight. The next day, 60 µl of 20 mg/ml RNase A (Qiagen) was added and mixed, and samples were incubated at 37 °C for 30 min. Then, 4 ml of prechilled 7.5 M ammonium acetate was added, and samples were vortexed and spun at 4,000g for 10 min. The supernatant was placed in a new tube, mixed well with 12 ml isopropanol and spun at 4,000g for 10 min. DNA pellets were washed with 12 ml of 70% ethanol, spun and dried, and pellets were resuspended with 0.2× TE buffer (Sigma-Aldrich). In addition, we also generated linearized plasmid library input and diluted it down to mimic similar copy number conditions as the gDNA samples.
To amplify the gRNA cassette from gDNA and add indexing for Illumina sequencing, we used a two-step PCR protocol, PCR1 and PCR2, respectively. For the PCR1 reaction, we used 960 µg gDNA for each sample. We performed 96× 100 µl PCR1 reactions per sample (10 µl 10× Taq buffer, 0.02 U/µl Taq-B enzyme (Enzymatics, P7250L), 0.2 mM dNTPs, 0.2 µM forward and reverse primers and 100 ng gDNA per µl). Thermocycler conditions were 94 °C/30 s, 20× (94 °C/10 s, 55 °C/30 s, 68 °C/45 s) and 68 °C/3 min. For each sample, all PCR1 products were pooled and mixed. For the PCR2 reaction, we performed 2 reactions per sample (20 µl 5× NEB Q5 buffer, 0.01 U/µl Q5 enzyme, 20 µl PCR1 product, 0.2 mM dNTPs and 0.4 µM forward and reverse PCR2 primers in 100 µl). Thermocycling conditions for PCR2 were 98 °C/30 s, 7× (98 °C/10 s, 63 °C/30 s and 72 °C/45 s) and 72 °C/5 min. For each sample, PCR2 products were pooled, followed by normalization (gel-based band densitometry quantification), before combining equal amounts of uniquely barcoded samples.    The pooled product was then purified using SPRI beads. First, we performed a 0.6× vol/vol SPRI to remove gDNA carryover, followed by the addition of a 0.3× vol/vol SPRI (0.6 + 0.3 = 0.9× final) to the supernatant to purify the ~260 bp PCR product. The final amplicons were sequenced on Illumina NextSeq 500-II HighOutput 1 × 150 v2.5 (Cat #20024907).

treatment_protocol: 1ug/ml doxycycline

tag: replicate

value: 1ug/ml doxycycline


title: A375 Day14 rep2

description:
lentivirus
R15-Fwd_05


title: Pot1afl/fl BM cells rep1


title: A375 Day7 rep2

description:
lentivirus
R15-Fwd_04


title: 232_Batch4_17_560234966601_S75_L005

value: baseline

tag: site

value: KEMRI

tag: rin

tag: bmi

tag: ngonorrhoeae

value: Abs

value: Nobs

value: Married

value: Primary school, some or complete

value: Yes


title: Pot1awt/wt BM cells rep5


title: shLuc, 56h, asparaginase


title: 259_Batch4_44_7408_S102_L007

value: Emavundleni

value: IVD

value: nonLD

value: TRUE

value: Negative

tag: chlamydiatrachomatis

tag: lactobacilli

tag: mobilincus

value: BV

tag: yeasts

value: Never married

value: Secondary school, some or complete


title: shLuc, 56h, vehicle

value: Jurkat

value: T-ALL cells

value: shLuc

value: veh


title: 230_Batch4_15_JAA2NXSP-01_S73_L005

value: baseline

value: WRHI

value: IVB

value: Positive

value: Abs

value: Intermediate

tag: maritalstatus

value: Unchecked


title: ln2

tag: tissue

value: visceral adipose tissue

tag: phenotype

value: lean


title: Pot1awt/wt BM cells rep3

tag: strain

value: 2-3 weeks old


title: 207_Batch3_64_5760_S50_L004

tag: visit

value: Emavundleni

value: IVD

value: nonLD

value: TRUE

value: Negative

value: Nobs

value: No


title: A375 Day0 rep2

description:
lentivirus
R15-Fwd_03

tag: cell line

tag: timepoint

tag: treatment


title: A375 Day21 rep1

description:
lentivirus
R14-Fwd_06

tag: genotype

tag: replicate

value: 1ug/ml doxycycline


title: 206_Batch3_63_3856_S49_L004

value: baseline

tag: site

tag: rin

value: Never married

value: Secondary school, some or complete


title: 233_Batch4_18_560238756601_S76_L005

value: KEMRI

tag: bmi

tag: ngonorrhoeae

value: Abs

value: BV

value: Married

value: Primary school, some or complete

value: Yes


title: Pot1awt/wt BM cells rep2

tag: age

value: 2-3 weeks old


title: shLuc, 32h, asparaginase

value: Jurkat

tag: cell type

value: T-ALL cells

value: shLuc

value: aps


title: A375 Day14 rep1

description:
lentivirus
R14-Fwd_05


title: shLuc, 16h, vehicle

value: veh


title: Pot1aΔ/Δ MSPCs in vivo rep3

description:
counts.txt
KO3

data_processing:
The reads were mapped against the mouse reference genome by HISAT2 (v. 2.0.4).
The expression matrix of read counts for each gene and cell was prepared using the said software.
The expression levels of all genes were quantified by using the software featureCounts (v. 1.6.3).
Genome_build: mm10
Supplementary_files_format_and_content: Matrix tables with raw gene counts.

source_name: Bone marrow

growth_protocol: In vitro, bone marrow cells flushed out from mouse femurs and tibiae were cultured on 6-well-plate for 1 week in MesenCult expansion kit media (STEMCELL technologies). Adherent cells were collected on day7, CD51+/PDGFRɑ+ cells were sorted and further cultured on 24-well-plates for 3 days. Cre Recombinase Gesicles (CLN) were applied at 10 μL/well and exposed for 12 hours. After 48 hours culture, tdTomato fluorescently colored cells were re-sorted. The sorted cells were cultured for about 4 weeks and used for gene analyses.

extract_protocol:
mRNA was isolated from sorted tdTomato+ MSPCs with NucleoSpin® RNA XS (Takara Bio USA, Inc.) and cDNA was synthesized using SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing (Takara Bio USA, Inc.). The full-length cDNA was processed with the Nextera XT DNA Library Preparation Kits (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: MSPCs

value: 2 weeks old

value: NG2-cre / loxp-tdTomato / POT1afl/fl mice


title: Pot1awt/wt BM cells rep4


title: shLuc, 16h, asparaginase


title: shLuc, 0h


title: 205_Batch3_62_EAA2P41F-01_S48_L004

value: WRHI

value: IVD

value: nonLD

value: TRUE

value: Negative

tag: chlamydiatrachomatis

tag: lactobacilli

tag: mobilincus

tag: yeasts

value: Nobs

value: Never married

value: No

value: Unchecked


title: Pot1awt/wt BM cells rep1

tag: strain

value: 2-3 weeks old


title: Pot1aΔ/Δ MSPCs in vivo rep2

description:
counts.txt
KO2


title: A375 Day0 rep1

description:
lentivirus
R14-Fwd_03


title: 204_Batch3_61_CAA2NW81-01_S47_L004

tag: visit

value: baseline

value: Abs

value: BV

tag: maritalstatus

value: Secondary school, some or complete


title: Pot1aΔ/Δ MSPCs in vivo rep1

description:
counts.txt
KO1

value: MSPCs


title: 188_Batch3_45_560237236601_S31_L002

value: KEMRI

value: IIIA

value: LD

value: Married

value: Primary school, some or complete

value: Yes


title: A375 Day7 rep1

description:
lentivirus
R14-Fwd_04

tag: cell line

tag: timepoint

value: 1ug/ml doxycycline


title: 189_Batch3_46_560241376601_S32_L003

value: IVD

value: nonLD

value: TRUE

value: Negative

value: Nobs


title: shGSK3a, 8h, asparaginase

value: Jurkat

value: T-ALL cells

tag: genotype

tag: treatment

value: aps


title: shGSK3a, 8h, vehicle

value: veh


title: shGSK3a, 56h, vehicle


title: shLuc, 32h, vehicle

value: shLuc


title: Pot1awt/Δ MSPCs in vivo rep3

description:
counts.txt
HT3

value: MSPCs

value: 2 weeks old

value: NG2-cre / loxp-tdTomato / POT1afl/fl mice


title: HEK293 WT RNA

description:
23b_hek293-wt
ribo-depleted

data_processing:
RNA-seq reads were aligned to hg38 genome using STAR v2.7.1 and ‘--twopassMode Basic’ and ‘--outSAMstrandField intronMotif’ parameters (Dobin et al. 2013).
Samtools v1.9 was used to filter for reads with a mapping quality greater than 20, sorted, and indexed (H. Li et al. 2009).
HEK293, hESC, and A375 junction counts (provided in Isoviz and used for non-sequence features in Figure 2) were generated using Regtools extract v0.5.2 (Cotto et al. 2023) with ‘-a 8 -m 50 -M 500000 -s 0’ parameters.
Assembly: hg38
Supplementary files format and content: Text file regtools junction count output for each cell line.

growth_protocol: A375 cells were acquired from American Type Culture Collection (ATCC Cat #CRL-1619). A375 cells were maintained at 37°C with 5% CO2 in DMEM media (ThermoFisher Cat #11965118) supplemented with 10% serum (Serum Plus II, Sigma-Aldrich, Cat #14009C). HEK293 cells were acquired from ATCC (Cat #CRL-1573). HEK293 cells were maintained at 37°C with 5% CO2 in DMEM media (ThermoFisher Cat #11965118) supplemented with 10% serum (Serum Plus II, Sigma-Aldrich, Cat #14009C). HUES66 human embryonic stem cells (hESCs) were obtained from Harvard University. Cells were maintained at 37°C with 5% CO2 in StemFlex media (ThermoFisher Cat #A3349401) and grown on Geltrex-coated plates (ThermoFisher Cat #A1413302). For passaging, Accutase (ThermoFisher Cat #A1110501) was used to dissociate cells and 10 µM ROCK inhibitor Y-27632 dihydrochloride (Tocris Cat #1254) was added to the media for plating.

extract_protocol:
Total RNA was extracted using TRIzol (Invitrogen #15596018) according to the manufacturer's protocol.  To isolate RNA from cytosolic and nuclear fractions, cells were washed twice with 1mL cold PBS and scraped in 1mL PBS + 1mM PMSF + 1:100 protease inhibitor cocktail (PIC, Sigma P8340). 200uL was removed at this step and added to 1mL Trizol (total RNA). The remaining cells were centrifuged at 1500xrcf. for 5 min, and resuspended in 250uL low salt solution (10mM KCl, 1.5mM MgCl2, 20mM Tris-HCl pH 7.5) supplemented with 1mM PMSF, 1mM DTT, and 1x PIC. Triton X-100 was added to a final concentration of 0.1% and cells were rotated for 10 min at 4C, then centrifuged for 5 min at 1500xrcf. 200uL of supernatant was removed and added to 1mL Trizol (cytosolic fraction). The remaining supernatant was discarded and the nuclear pellet was washed by rotating for 2min at 4C in low salt solution without Triton X-100 and centrifuged at 1300rpm for 10 min. Nuclear pellet was resuspended in 1mL Trizol (nuclear fraction). Isolation of RNA from Trizol was performed according to the manufacturer protocol.
Per RNA sample, we combined 1 µg of total RNA + 2 µl 1:100 ERCC RNA Spike-in Mix #1 (Invitrogen #4456740). Libraries were prepared using the Kapa RNA HyperPrep Kit with RiboErase (Roche #08098131702), pooled, and sequenced using the Nextseq 500/550 High Output Kit with 150 cycles (Illumina #20024907).


title: A375 cytoplasmic RNA

description:
22a_a375_cyt
ribo-depleted

molecule: cytoplasmic RNA


title: Pot1awt/Δ MSPCs in vivo rep2

description:
counts.txt
HT2


title: 185_Batch3_42_6240_S28_L002

tag: site

value: Emavundleni

value: IVA

value: Positive

value: Abs

value: BV

value: Never married

value: Secondary school, some or complete

value: Unchecked


title: 162_Batch3_19_EAA2P1L2-01_S5_L001

value: baseline

value: WRHI

tag: rin

value: IIIA

value: LD

value: TRUE

value: Negative

value: Nobs

value: No


title: 159_Batch3_16_5312_S2_L001

value: IVD

value: nonLD

tag: bmi


title: shGSK3a, 56h, asparaginase

value: Jurkat

value: T-ALL cells

value: aps


title: A375 nuclear RNA

description:
22a_a375_nuc
ribo-depleted

molecule: nuclear RNA


title: Pot1awt/Δ MSPCs in vivo rep1

description:
counts.txt
HT1

value: MSPCs

value: 2 weeks old

value: NG2-cre / loxp-tdTomato / POT1afl/fl mice


title: Pot1aΔ/Δ MSPCs in vitro week4 rep3

description:
w1w4_counts.txt
w4KO3

value: 4-6 months old

value: Pot1aflox/flox / flox-stop-flox tdTomato mice


title: shGSK3a, 32h, vehicle

value: veh


title: HUES66 WT RNA

description:
21c_hESC_RB2_empty
ribo-depleted


title: CD8 CD33 CAR T cells from Young patient Donor 3, Day 14

city: PAMPLONA

first: Juan R

last: Rodriguez-Madoz

address: AV PIO XII 53

country: Spain

institute: CIMA

description:
YHD3_CD33_41BB_CD8_14d_S12
CD8_Filtered_Rawcounts.txt

data_processing:
Samples were aligned to the Human genome (GRCh38) with STAR (v2.6.1). Gene expression was quantified with quant3p (github.com/ctlab/quant3p).
Downstream analyses were performed in R (v3.6.2). Data transformation, normalization, and differential gene expression analysis were performed with DESeq2. Genes were considered adjusted p value (p-adj)<0.05 and absolute log transformed fold-change (|log2FC|)>1, unless otherwise indicated. vst expression values were used for data visualization and unsupervised analysis.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes filtered raw counts (filtered to have counts >0 at least in one sample) for all the CAR T cells samples divided in CD4 or CD8 cells

growth_protocol: CAR T Cell generation: Peripheral Blood Mononuclear Cells (PBMCs) were isolated with Ficoll-Paque and CD4+ and CD8+ T cells were selected using CD4 and CD8 MicroBeads (Miltenyi Biotec) in the AutoMACS Pro Separator (Miltenyi Biotec). Isolated T cells were activated with 10 µl/ml T cell TransAct (Miltenyi Biotec) for 48h and infected with the CAR lentiviral vector at MOI 2 with 10 µl/ml of LentiBoost (Sirion Biotech). CAR-T cells were expanded in RPMI 1640 culture medium supplemented with 3% human serum (Sigma), 1% penicillin/streptomycin and 625 IU/ml of human IL-7 and 85 IU/ml of human IL-15 (Miltenyi Biotec). CAR-T cells were counted, and the concentration was adjusted to 1×106 cells/ml every two days.

extract_protocol:
RNA-seq was performed following MARS-seq protocol adapted for bulk RNA-seq with minor modifications. Briefly, 7000 to 10000 cells were sorted in 100µl of Lysis/Binding Buffer (Ambion), vortexed and stored at -80ºC until further processing. Poly-A RNA was reverse-transcribed using poly-dT oligos carrying a 7 nt-index. Pooled samples were subjected to linear amplification by IVT. Resulting aRNA was fragmented and dephosphorylated.
RNA-seq libraries quantification was done with Qubit 3.0 Fluorometer (Life Technologies) and size profiles were examined using Agilent’s 4200 TapeStation System. Libraries were sequenced in an Illumina NextSeq500 at a sequence depth of 10 million reads per sample.

tag: group

value: Young patient

tag: time

value: Day 14


title: shGSK3a, 32h, asparaginase

tag: cell type


title: shGSK3a, 16h, vehicle


title: CD8 CD33 CAR T cells from Young patient Donor 3, Day 0

description:
YHD3_CD33_41BB_CD8_0d_S10
CD8_Filtered_Rawcounts.txt

value: Day 0


title: Pot1aΔ/Δ MSPCs in vitro week4 rep1

description:
w1w4_counts.txt
w4KO1

tag: age


title: Pot1awt/wt MSPCs in vitro week4 rep2

description:
w1w4_counts.txt
w4WT2

value: Pot1awild/wild / flox-stop-flox tdTomato mice


title: 156_Batch3_13_HAA2P162-01_S92_L006

value: baseline

value: WRHI

value: IB

value: LD

value: TRUE

tag: ngonorrhoeae

value: Negative

tag: chlamydiatrachomatis

tag: lactobacilli

value: Abs

value: Nobs

value: Never married

value: Secondary school, some or complete

value: Unchecked


title: CD4 CD33 CAR T cells from Young patient Donor 3, Day 14

description:
YHD3_CD33_41BB_CD4_14d_S11
CD4_Filtered_Rawcounts.txt


title: 136_Batch2_64_AAA2P0JX-01_S72_L005

value: Positive

tag: mobilincus

tag: yeasts

value: Post-secondary school


title: BioR3_3

city: Shanghai, China

first: Liming

last: Ouyang

state: Shanghai

address: East China University of Science and Technology, 130 Meilong Road, Xuhui District, Shanghai, China

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
paired-end clean reads were aligned to the Homo Sapiens(GRCh38/hg38) usinghisat2 (v2.0.5)
featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample.

growth_protocol: Human umbilical cord mesenchymal stem cells are cultured in serum-free medium in an incubator containing 5% carbon dioxide, 37 °C

extract_protocol:
Then total RNA of cells was extracted by Trizol reagent method . Total amounts and integrity of RNA were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA) .
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® or NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® following manufacture's protocols.

treatment_protocol: P6 generation human umbilical cord mesenchymal stem cells were harvested for microcarrier bioreactor culture

tag: tissue

value: umbilical cord

value: WT

value: No serum culture


title: Pot1aΔ/Δ MSPCs in vitro week4 rep2

description:
w1w4_counts.txt
w4KO2

value: MSPCs

tag: strain

value: 4-6 months old

value: Pot1aflox/flox / flox-stop-flox tdTomato mice


title: shGSK3a, 16h, asparaginase

tag: cell line

value: Jurkat

value: T-ALL cells

tag: timepoint

value: aps


title: Pot1awt/wt MSPCs in vitro week4 rep3

description:
w1w4_counts.txt
w4WT3

tag: genotype

value: Pot1awild/wild / flox-stop-flox tdTomato mice


title: CD4 CD33 CAR T cells from Young patient Donor 3, Day 0

description:
YHD3_CD33_41BB_CD4_0d_S9
CD4_Filtered_Rawcounts.txt

value: Young patient

value: Day 0


title: CD8 CD33 CAR T cells from Young patient Donor 2, Day 14

description:
YHD2_CD33_41BB_CD8_14d_S8
CD8_Filtered_Rawcounts.txt

value: Day 14


title: shGSK3a, 0h

tag: treatment


title: Pot1awt/wt MSPCs in vitro week4 rep1

description:
w1w4_counts.txt
w4WT1


title: A375 WT RNA

description:
22a_a375_total
ribo-depleted


title: 158_Batch3_15_3264_S1_L001

data_processing:
The sequencing data was demultiplexed using Illumina bcl2fastq version 2.20.0.422 BCL to FastQ file converter.
The quality of raw reads was assessed with FastQC version 0.11.8
Reads were mapped to the GRCh38 human genome assembly [https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26/] using STAR version 2.5.2b with default alignment parameters.
Abundance estimation of raw read counts per transcript was done internally with STAR using the htseq-count algorithm
DESeq2 version 1.22.1 R package was used to produce Raw read counts.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab delimited text file containing Raw read counts for each sample (in columns) and each annotated transcript (in rows).

extract_protocol:
RNA was extracted from the endocervical cytobrush samples collected at the crossover visit using RNeasy Micro kit (Qiagen, CA) with DNase digest and QIAcube automation stations. The RNA was quantified, and the quality was assessed by Bioanalyzer analysis (Agilent Technologies, Santa Clara, CA)
Libraries were prepared using the Illumina (Illumina Inc. San Diego, CA, USA) TruSeq RNA Exome kit, as per manufacturer’s instructions, with 20 ng of total RNA as input. The libraries were quantified using Qubit dsDNA HS before normalization and pooling. The amplified libraries were assessed for their quality and sizing information by capillary electrophoresis on the Agilent 4200 TapeStation. The libraries were normalized, pooled and sequenced on the Illumina HiSeq3000 system employing a single-end 101 cycles run at average read depths of 23 million reads/sample.

tag: visit

value: baseline

tag: site

value: Emavundleni

tag: rin

value: IVD

value: nonLD

value: TRUE

value: Negative

value: Abs

value: BV

value: Nobs

tag: maritalstatus

value: Never married

value: Secondary school, some or complete

value: No


title: 131_Batch2_59_CAA2P4DM-01_S67_L005

value: WRHI

value: IVB

tag: bmi

value: Intermediate

value: Obs

value: Married

value: Yes

value: Unchecked


title: AD patient, PBMC SNUBH-17-1

description: AD patient, PBMC

data_processing:
The raw NGS forward (R1) and reverse (R2) reads were merged, filtered based on Phred scores, and subclustered using UMI using paired-end read merger (PEAR), v0.9.10, and Clustal Omega, v1.2.4, with the default setting30,31. The sequence annotation process used the IMGT (International Immunogenetics Information System) constant gene database32 to obtain the isotype, and IgBLAST, v1.17.133 to obtain VJ genes, CDR1/2/3 sequences, and the number of mutations from the corresponding V genes as previously described16. To eliminate the possibility of contamination due to index swapping within Illumina flow cells between samples, reads with identical sequences including the UMI from different samples were excluded on the basis that such an event is highly unlikely without contamination34. The combined NGS throughput of each sample is listed in Extended table 2. Sequencing reads that have survived through the entire process is considered to be a productive BCR sequence.
Supplementary files format and content: sequence_id     duplicate_count frequency       sequence        sequence_aa     sequence_alignment      germline_alignment      v_call  j_call  c_call  junction        junction_aa      cdr1    cdr2    cdr3    cdr1_aa cdr2_aa cdr3_aa rev_comp        productive      v_cigar j_cigar v_alignment_length      v_alignment_mutation

source_name: PBMC

extract_protocol:
All peripheral blood samples were collected by EDTA tubes (BD Vacutainer K2EDTA tubes, 367525) at least 15 ml in total per a patient29. Peripheral blood mononuclear cells (PBMCs) and plasma were separated by density-gradient centrifugation using Ficoll (Cytiva Ficoll-Paque Plus, 17-1440-02) solution. After the PBMC suspension was resuspended in CELLBANKER (Amsbio CELLBANKER 2, 11914), the collected PBMCs were immediately cryopreserved and stored in a Freezing container (Nalgene Mr. Frosty, C1562) for a week. Total RNA was isolated by TRIzol Reagent (Invitrogen TRIzol Reagents, 15596026) following the manufacturer’s instructions.
For the NGS library preparation of BCR heavy chain sequence, genes encoding the variable region of the heavy chain (VH) at the 5 prime forward part and the first constant region of the heavy chain (CH1) domain at the 3 prime reverse part were amplified by specific PCR primers as reported previously16. All primer sequences are listed in Extended Table 2. In short, one microgram of total RNA was used as the input template for library preparation. Next, reverse transcription was conducted as following the manufacturer’s instructions using SuperScript IV First-Strand Synthesis System (Invitrogen, 18091050) with CH1 gene-specific primers for five immunoglobulin heavy chain isotypes containing UMI (unique molecular identifiers) barcodes that consist of 12 random nucleotides, 14 base pair in total; NNNNTNNNNTNNNN, and partial Illumina adapters (No. 1-8). After first-strand cDNA synthesis, it was purified with SPRI beads (Beckman Coulter AMPure XP Reagents, A63882) at a 1:1.8 ratio and second-strand cDNA was synthesized using a KAPA Biosystems kit (Roche KAPA HiFi Hotstart PCR kit, KK2502) with VH gene-specific primers (No. 9-14; 95°C for 3 min, 98°C for 30 s, 60°C for 45 s, and 72°C for 6 min). Double-stranded cDNA was purified through SPRI beads at a 1:1 ratio. Following that, it was amplified using KAPA Biosystems kit and double primers containing Illumina adapters and index sequences (No. 15, 16; 95°C for 3 min, 25 cycles of 98°C for 30 s, 60°C for 30 s, 72°C for 1 min, and 72°C for 5 min). The PCR products were subjected to electrophoresis on a 1.5% agarose gel to separate through the length of DNA and purified using QIAquick gel extraction kit (QIAGEN, 28704) following the manufacturer’s protocols. The final NGS libraries were obtained using SPRI beads at a 1:1 ratio and quantified with a 4200 TapeStation System (Agilent Technologies, G2991BA) for QC.
Libraries with a single peak of appropriate length were subjected to NGS analysis using the Illumina Nocaseq6000 platform.

value: PBMC

tag: cell type


title: BioR3_2

institute: East China University of Science and Technology

value: umbilical cord

value: Human umbilical cord mesenchymal stem cells

value: WT

value: No serum culture

tag: group


title: CD8 CD33 CAR T cells from Young patient Donor 2, Day 0

description:
YHD2_CD33_41BB_CD8_0d_S6
CD8_Filtered_Rawcounts.txt

value: Young patient

tag: time

value: Day 0


title: Pot1aΔ/Δ MSPCs in vitro week1 rep3

description:
w1w4_counts.txt
w1KO3

value: MSPCs

tag: age

value: 4-6 months old

value: Pot1aflox/flox / flox-stop-flox tdTomato mice


title: BioR3_1


title: 157_Batch3_14_FAA2P5TT-01_S93_L006

value: WRHI

value: IIIA

value: LD

value: TRUE

tag: ngonorrhoeae

value: Negative

tag: chlamydiatrachomatis

tag: lactobacilli

value: Abs

tag: mobilincus

value: Nobs

value: Never married

value: Secondary school, some or complete

value: No


title: Pot1aΔ/Δ MSPCs in vitro week1 rep2

description:
w1w4_counts.txt
w1KO2

tag: strain


title: CD4 CD33 CAR T cells from Young patient Donor 2, Day 14

description:
YHD2_CD33_41BB_CD4_14d_S7
CD4_Filtered_Rawcounts.txt

value: Day 14


title: 137_Batch2_65_AAA2PG15-01_S73_L005

value: Positive

tag: yeasts

value: Post-secondary school

value: Unchecked


title: 129_Batch2_57_560238536601_S65_L005

value: KEMRI

value: IVD

value: nonLD

value: BV

value: Married

value: Primary school, some or complete

value: Yes


title: BioR1_1

tag: tissue

value: umbilical cord

value: Human umbilical cord mesenchymal stem cells

tag: genotype

value: WT

value: No serum culture


title: Pot1awt/wt MSPCs in vitro week1 rep3

description:
w1w4_counts.txt
w1WT3

value: MSPCs

value: 4-6 months old

value: Pot1awild/wild / flox-stop-flox tdTomato mice


title: Pot1aΔ/Δ MSPCs in vitro week1 rep1

description:
w1w4_counts.txt
w1KO1

value: Pot1aflox/flox / flox-stop-flox tdTomato mice


title: P12_3

tag: treatment


title: 108_Batch2_36_560240076601_S44_L003

tag: visit

tag: site

value: TRUE

value: Negative

value: Abs

value: Nobs

value: Secondary school, some or complete


title: Pot1awt/wt MSPCs in vitro week1 rep1

description:
w1w4_counts.txt
w1WT1


title: BioR1_3


title: CD4 CD33 CAR T cells from Young patient Donor 2, Day 0

description:
YHD2_CD33_41BB_CD4_0d_S5
CD4_Filtered_Rawcounts.txt

value: Young patient

value: Day 0


title: 128_Batch2_56_560233986601_S64_L005

value: baseline

value: KEMRI

tag: rin

value: IVD

value: nonLD

value: BV

tag: maritalstatus

value: Married

value: Primary school, some or complete

value: Unchecked


title: CD8 CD33 CAR T cells from Young patient Donor 1, Day 0

description:
YHD1_CD33_41BB_CD8_0d_S2
CD8_Filtered_Rawcounts.txt

tag: cell type


title: BioR1_2

value: umbilical cord

value: Human umbilical cord mesenchymal stem cells

value: WT

value: No serum culture

tag: group


title: P12_2


title: 99_Batch2_27_4128_S35_L003

value: Emavundleni

value: TRUE

tag: bmi

value: Negative

value: Intermediate

value: Never married


title: P12_1


title: CD8 CD33 CAR T cells from Senior patient Donor 3, Day 14

description:
SHD3_CD33_41BB_CD8_14d_S34
CD8_Filtered_Rawcounts.txt

value: Senior patient

tag: time

value: Day 14


title: 100_Batch2_28_5744_S36_L003

value: IVA

tag: ngonorrhoeae

value: Abs

value: Nobs

value: Secondary school, some or complete


title: CD4 CD33 CAR T cells from Young patient Donor 1, Day 0

description:
YHD1_CD33_41BB_CD4_0d_S1
CD4_Filtered_Rawcounts.txt

value: Young patient

value: Day 0


title: CD8 CD33 CAR T cells from Senior patient Donor 3, Day 0

description:
SHD3_CD33_41BB_CD8_0d_S30
CD8_Filtered_Rawcounts.txt


title: Passage 7 Pkd2KO cells with DOX, replicate 2

city: Baltimore

first: Hyun Jun

last: Jung

state: MD

address: 720 Rutland Ave, Ross Research Building 1165B

department: Medicine (Nephrology)

institute: Johns Hopkins University School of Medicine

data_processing:
Four technical repliates of each experimental group were prepared for further downstream data processing.
Counts and abundance of transcripts were generated by quantifying sequence reads on transcripts from Gencode GRCm38.p6 using Star (2.6.0c) with a qaunt mode.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: mouse inner medullary collecting duct cell line

growth_protocol: The Pkd2 knockout cells were grown on the permeable filter membrane for 10 days in the RenaLife Epithelial Basal Medium (LM-0010, LIFELINE CELL TECHNOLOGY) supplemented with a RenaLife LifeFactors Kit (LS-1048, LIFELINE CELL TECHNOLOGY) and 5% FBS.

extract_protocol:
Cells were lyzed in Trizol. Total RNA was extracted using Direct-zol RNA Miniprep kit (ZYMO RESEARCH).
To enrich mRNA, 1-3 ug of total RNA was applied to oligo dT-based mRNA isolation using NEBNext® Poly(A) mRNA Magnetic Isolation Module (E7490, NEW ENGLAND BioLabs Inc.) as a manufacturer’s instruction. mRNA (20-30 ng) was sequentially used for the further sequencing library preparation using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7760, NEW ENGLAND BioLabs Inc.) and NEBNext® Multiplex Oligos (E7335; E7500, NEW ENGLAND BioLabs Inc.). cDNA libraries were sequenced on Illumina HiSeq 4000 platform. Sequence reads (2 × 75 bp, paired-end) were aligned on Ensembl genome GRCm38p6 using STAR (2.6.0c).

treatment_protocol: Cells (passage 4 and passage 7) were grown on the permeable filters of a transwell system (6-well) for 10 days and treated with or without doxycycline (2 ug/mL) for 6 days. Media were daily changed.

value: kidney

tag: dox treatment

value: with DOX

value: Pkd2KO induced by DOX

tag: passage


title: 89_Batch2_17_560245136601_S25_L002

value: baseline

value: KEMRI

value: IIIA

value: LD

tag: chlamydiatrachomatis

tag: lactobacilli

tag: mobilincus

value: Obs

value: Yes

value: Checked


title: P9_3

tag: tissue

value: umbilical cord

value: Human umbilical cord mesenchymal stem cells

value: WT

value: No serum culture


title: Passage 7 Pkd2KO cells with DOX, replicate 3

tag: genotype

value: mouse inner medullary collecting duct cell line


title: 90_Batch2_18_560252226601_S26_L002

value: TRUE

value: Negative

value: Abs

tag: yeasts

value: Nobs

value: Never married

value: Secondary school, some or complete


title: 130_Batch2_58_EAA2NWVQ-01_S66_L005

tag: visit

value: baseline

value: WRHI

value: Intermediate

value: Married

value: Unchecked


title: CD8 CD33 CAR T cells from Young patient Donor 1, Day 14

description:
YHD1_CD33_41BB_CD8_14d_S4
CD8_Filtered_Rawcounts.txt

value: Young patient

value: Day 14


title: CD4 CD33 CAR T cells from Senior patient Donor 3, Day 14

description:
SHD3_CD33_41BB_CD4_14d_S33
CD4_Filtered_Rawcounts.txt

value: Senior patient


title: Passage 7 Pkd2KO cells with DOX, replicate 4

value: kidney

value: with DOX

value: Pkd2KO induced by DOX


title: CD4 CD33 CAR T cells from Young patient Donor 1, Day 14

description:
YHD1_CD33_41BB_CD4_14d_S3
CD4_Filtered_Rawcounts.txt


title: Pot1awt/wt MSPCs in vitro week1 rep2

description:
w1w4_counts.txt
w1WT2

value: MSPCs

tag: strain

tag: age

value: 4-6 months old

value: Pot1awild/wild / flox-stop-flox tdTomato mice


title: 107_Batch2_35_560231156601_S43_L003

tag: site

value: KEMRI

tag: rin

value: IVD

value: nonLD

value: TRUE

value: Negative

value: Abs

value: BV

value: Nobs

tag: maritalstatus

value: Yes


title: CD8 CD33 CAR T cells from Senior patient Donor 2, Day 14

description:
SHD2_CD33_41BB_CD8_14d_S26
CD8_Filtered_Rawcounts.txt

tag: cell type

tag: group

value: Day 14


title: P6_3

value: umbilical cord

value: Human umbilical cord mesenchymal stem cells

value: WT

tag: treatment

value: No serum culture


title: 85_Batch2_13_4400_S21_L002

value: baseline

value: Emavundleni

tag: bmi

tag: ngonorrhoeae

value: Never married

value: Secondary school, some or complete

value: Unchecked


title: P9_1


title: 86_Batch2_14_7904_S22_L002

value: IVB

value: nonLD

tag: chlamydiatrachomatis


title: Passage 7 Pkd2KO cells without DOX, replicate 4

value: kidney

tag: dox treatment

value: without DOX

value: wild type

value: mouse inner medullary collecting duct cell line

tag: passage


title: Passage 7 Pkd2KO cells with DOX, replicate 1

tag: tissue

value: with DOX

value: Pkd2KO induced by DOX


title: Passage 7 Pkd2KO cells without DOX, replicate 3

tag: genotype


title: CD8 CD33 CAR T cells from Senior patient Donor 2, Day 0

description:
SHD2_CD33_41BB_CD8_0d_S22
CD8_Filtered_Rawcounts.txt

value: Senior patient

tag: time

value: Day 0


title: P6_2

value: umbilical cord

value: Human umbilical cord mesenchymal stem cells

value: WT


title: 80_Batch2_8_FAA2NVDJ-01_S17_L002

tag: visit

value: WRHI

value: IVA

value: TRUE

value: Negative

tag: lactobacilli

value: Abs

tag: mobilincus

value: BV

tag: yeasts

value: Nobs

value: Married

value: Yes


title: P6_1

value: No serum culture


title: P3_3


title: 74_Batch2_2_8830_S11_L001

tag: site

value: Emavundleni

tag: rin

value: IB

value: LD

value: Positive

value: Never married

value: Secondary school, some or complete

value: Unchecked


title: 79_Batch2_7_BAA2NNXT-01_S16_L002

value: baseline

value: WRHI

value: nonLD

tag: maritalstatus


title: Passage 7 Pkd2KO cells without DOX, replicate 1

value: kidney

value: without DOX

value: wild type

tag: cell type

value: mouse inner medullary collecting duct cell line


title: Passage 4 Pkd2KO cells with DOX, replicate 4

value: with DOX

value: Pkd2KO induced by DOX


title: Passage 4 Pkd2KO cells with DOX, replicate 3


title: 73_Batch2_1_5232_S10_L001

value: IIIA

value: TRUE

value: Negative

value: Abs

value: Nobs


title: P3_2

value: umbilical cord

value: Human umbilical cord mesenchymal stem cells

value: WT

tag: treatment

value: No serum culture

tag: group


title: CD8 CD33 CAR T cells from Senior patient Donor 1, Day 14

description:
SHD1_CD33_41BB_CD8_14d_S18
CD8_Filtered_Rawcounts.txt

value: Senior patient

value: Day 14


title: CD4 CD33 CAR T cells from Senior patient Donor 2, Day 0

description:
SHD2_CD33_41BB_CD4_0d_S21
CD4_Filtered_Rawcounts.txt

value: Day 0


title: 68_Batch1_68_BAA2P237-01_S5_L001

value: WRHI

value: IB

value: LD

tag: bmi

tag: ngonorrhoeae

value: Obs

value: Never married

value: Secondary school, some or complete

value: No

value: Unchecked


title: CD8 CD33 CAR T cells from Senior patient Donor 1, Day 0

description:
SHD1_CD33_41BB_CD8_0d_S14
CD8_Filtered_Rawcounts.txt


title: P3_1


title: P9_2


title: Passage 4 Pkd2KO cells with DOX, replicate 2

value: kidney

tag: dox treatment

value: with DOX

value: Pkd2KO induced by DOX

value: mouse inner medullary collecting duct cell line


title: CD4 CD33 CAR T cells from Senior patient Donor 3, Day 0

description:
SHD3_CD33_41BB_CD4_0d_S29
CD4_Filtered_Rawcounts.txt


title: 67_Batch1_67_KAA2NT6L-01_S4_L001

value: baseline

value: TRUE

value: Negative

tag: chlamydiatrachomatis

value: Abs

value: Nobs


title: CD4 CD33 CAR T cells from Senior patient Donor 1, Day 0

description:
SHD1_CD33_41BB_CD4_0d_S13
CD4_Filtered_Rawcounts.txt

value: Senior patient

value: Day 0


title: CD4 CD33 CAR T cells from Senior patient Donor 2, Day 14

description:
SHD2_CD33_41BB_CD4_14d_S25
CD4_Filtered_Rawcounts.txt

value: Day 14


title: CD4 CD33 CAR T cells from Senior patient Donor 1, Day 14

description:
SHD1_CD33_41BB_CD4_14d_S17
CD4_Filtered_Rawcounts.txt


title: 62_Batch1_62_FAA2PKBQ-01_S62_L008

value: WRHI

value: IVB

value: nonLD

value: Obs

value: Married

value: Primary school, some or complete


title: u2os_wt_3

city: St Louis

first: Sridhar

last: Nonavinkere Srivatsan

address: 660 S Eucild Ave

institute: WashU School Of Medicine

description:
paired-end
group_u2os_ko_Differential_Expression_sanitized.tsv

data_processing:
Basecalls and de-multiplexing 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 Ensembl GRCh38.76 or Ensembl GRCm38.76 assembly for human or mouse samples, respectively, with STAR version 2.7.9a
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 2.0.3
Isoform expression of known Ensembl transcripts were quantified with Salmon version 1.5.2
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.
Assembly: Ensembl GRCh38.76 or Ensembl GRCm38.76 assembly for human or mouse samples, respectively
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Bone; Osteocarcoma

growth_protocol: Human cell lines (HeLa-S, and U2OS; both originally from ATCC) were cultured in Dulbecco’s modified eagle medium (Invitrogen), supplemented with 10% fetal bovine serum (Sigma), 100 U/ml of penicillin-streptomycin (GIBCO) at 37°C and 5% CO2.

extract_protocol:
RNA was purified from cell lines using the Qiagen miRNeasy mini kit to accomodate small RNA isolation (#217004). For RNA isolation from mouse cortex, cerebral cortex was dissected in ice-cold PBS from 5 female Ttdn1-/- and 5 WT littermates at 8 weeks of age, then flash frozen. RNA was purified from cortex using the Qiagen miRNeasy mini kit.
Samples for small RNA-sequencing were prepped with TruSeq Small RNA library preparations kits; otherwise all other samples were prepared according to library kit manufacturer’s protocol, indexed, pooled, and sequenced on an Illumina NovaSeq 6000 2x150bp with the Genome Technology Access Center at Washington University in St. Louis, typically yielding 200 million paired-end reads per sample.

treatment_protocol: Where indicated, cells were treated with 250 nM pladienolide-B for 24h.

tag: cell line

tag: tissue

value: Bone; Osteocarcoma

value: WT


title: u2os_wt_2

tag: genotype


title: CD8 CD33 CAR T cells from AML patient Donor 9b, Day 14

description:
AML9b_CD33_41BB_CD8_14d_S50
CD8_Filtered_Rawcounts.txt

value: AML patient

tag: time